HEADER VIRAL PROTEIN/IMMUNE SYSTEM 05-DEC-24 9KVD TITLE CRYO-EM STRUCTURE OF SARS-COV-2 PROTOTYPE SPIKE PROTEIN IN COMPLEX TITLE 2 WITH TRIPLE-NAB 3G5, 4H5 AND 4C11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THE HEAVY CHAIN OF 4C11; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: THE LIGHT CHAIN OF 4C11; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: THE HEAVY CHAIN OF 4H5; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: THE LIGHT CHAIN OF 4H5; COMPND 15 CHAIN: F; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: SPIKE PROTEIN S1; COMPND 19 CHAIN: C; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: THE HEAVY CHAIN OF 3G5; COMPND 23 CHAIN: E; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 7; COMPND 26 MOLECULE: THE LIGHT CHAIN OF 3G5; COMPND 27 CHAIN: G; COMPND 28 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 3 ORGANISM_TAXID: 9544; SOURCE 4 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 8 ORGANISM_TAXID: 9544; SOURCE 9 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 13 ORGANISM_TAXID: 9544; SOURCE 14 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 16 MOL_ID: 4; SOURCE 17 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 18 ORGANISM_TAXID: 9544; SOURCE 19 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 21 MOL_ID: 5; SOURCE 22 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 23 2; SOURCE 24 ORGANISM_TAXID: 2697049; SOURCE 25 GENE: S, 2; SOURCE 26 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 28 MOL_ID: 6; SOURCE 29 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 30 ORGANISM_TAXID: 9544; SOURCE 31 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 32 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 33 MOL_ID: 7; SOURCE 34 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 35 ORGANISM_TAXID: 9544; SOURCE 36 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 37 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS SARS-COV-2, NEUTRALIZING ANTIBODY, CRYO-EM, VIRAL PROTEIN/IMMUNE KEYWDS 2 SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.SUN,Y.JIANG,S.WANG,Z.ZHENG,S.LI,Q.ZHENG REVDAT 1 20-AUG-25 9KVD 0 JRNL AUTH H.SUN,Y.JIANG,S.WANG,Z.ZHENG,S.LI,Q.ZHENG JRNL TITL CRYO-EM STRUCTURE OF SARS-COV-2 PROTOTYPE SPIKE PROTEIN IN JRNL TITL 2 COMPLEX WITH TRIPLE-NAB 3G5, 4H5 AND 4C11 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.440 REMARK 3 NUMBER OF PARTICLES : 63542 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9KVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 05-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300054327. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SARS-COV-2 PROTOYPE SPIKE REMARK 245 PROTEIN IN COMPLEX WITH TRIPLE- REMARK 245 NAB 3G5, 4C11 AND 4H5; SARS-COV- REMARK 245 2 PROTOTYPE SPIKE PROTEIN; THE REMARK 245 FRAGMENTS OF TRIPLE-NAB 3G5, REMARK 245 4C11 AND 4H5 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEPTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, F, C, E, G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 1 REMARK 465 SER A 123 REMARK 465 GLN D 1 REMARK 465 SER D 121 REMARK 465 GLN F 137 REMARK 465 LYS F 138 REMARK 465 LEU F 231 REMARK 465 CYS C 391 REMARK 465 PHE C 392 REMARK 465 GLN E 1 REMARK 465 SER E 25 REMARK 465 GLY E 26 REMARK 465 THR E 87 REMARK 465 ALA E 88 REMARK 465 THR G 148 REMARK 465 LEU G 149 REMARK 465 LEU G 150 REMARK 465 HIS G 151 REMARK 465 SER G 152 REMARK 465 GLY G 153 REMARK 465 SER G 154 REMARK 465 ALA G 155 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 3 CG CD OE1 NE2 REMARK 470 ASP A 10 CG OD1 OD2 REMARK 470 LEU A 11 CG CD1 CD2 REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 ARG A 31 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 LEU A 48 CG CD1 CD2 REMARK 470 GLU A 53 CG CD OE1 OE2 REMARK 470 LYS A 65 CG CD CE NZ REMARK 470 ASP A 73 CG OD1 OD2 REMARK 470 ASN A 74 CG OD1 ND2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 ARG A 87 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 89 CG CD OE1 OE2 REMARK 470 THR A 91 OG1 CG2 REMARK 470 ASP A 99 CG OD1 OD2 REMARK 470 ASP A 102 CG OD1 OD2 REMARK 470 THR A 106 OG1 CG2 REMARK 470 LEU A 118 CG CD1 CD2 REMARK 470 THR A 120 OG1 CG2 REMARK 470 VAL A 121 CG1 CG2 REMARK 470 GLN B 126 CG CD OE1 NE2 REMARK 470 SER B 132 OG REMARK 470 SER B 133 OG REMARK 470 LEU B 134 CG CD1 CD2 REMARK 470 SER B 137 OG REMARK 470 ASP B 140 CG OD1 OD2 REMARK 470 ARG B 141 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 142 CG1 CG2 REMARK 470 ILE B 144 CG1 CG2 CD1 REMARK 470 THR B 145 OG1 CG2 REMARK 470 ARG B 147 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 150 CG CD OE1 NE2 REMARK 470 ILE B 152 CG1 CG2 CD1 REMARK 470 THR B 153 OG1 CG2 REMARK 470 LYS B 165 CG CD CE NZ REMARK 470 ARG B 176 CG CD NE CZ NH1 NH2 REMARK 470 SER B 183 OG REMARK 470 ARG B 184 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 193 CG CD OE1 OE2 REMARK 470 THR B 195 OG1 CG2 REMARK 470 THR B 197 OG1 CG2 REMARK 470 ILE B 198 CG1 CG2 CD1 REMARK 470 SER B 200 OG REMARK 470 GLN B 202 CG CD OE1 NE2 REMARK 470 GLU B 204 CG CD OE1 OE2 REMARK 470 PHE B 206 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 226 CG CD CE NZ REMARK 470 GLU B 228 CG CD OE1 OE2 REMARK 470 LEU B 229 CG CD1 CD2 REMARK 470 LYS B 230 CG CD CE NZ REMARK 470 GLN D 3 CG CD OE1 NE2 REMARK 470 LEU D 4 CG CD1 CD2 REMARK 470 LEU D 11 CG CD1 CD2 REMARK 470 VAL D 12 CG1 CG2 REMARK 470 LYS D 13 CG CD CE NZ REMARK 470 SER D 15 OG REMARK 470 GLU D 16 CG CD OE1 OE2 REMARK 470 THR D 17 OG1 CG2 REMARK 470 SER D 19 OG REMARK 470 THR D 21 OG1 CG2 REMARK 470 LYS D 44 CG CD CE NZ REMARK 470 GLU D 47 CG CD OE1 OE2 REMARK 470 SER D 56 OG REMARK 470 THR D 59 OG1 CG2 REMARK 470 SER D 72 OG REMARK 470 LYS D 73 CG CD CE NZ REMARK 470 ASP D 74 CG OD1 OD2 REMARK 470 LYS D 77 CG CD CE NZ REMARK 470 ARG D 85 CG CD NE CZ NH1 NH2 REMARK 470 SER D 86 OG REMARK 470 VAL D 87 CG1 CG2 REMARK 470 ASP D 91 CG OD1 OD2 REMARK 470 ILE D 94 CG1 CG2 CD1 REMARK 470 GLN D 113 CG CD OE1 NE2 REMARK 470 VAL D 119 CG1 CG2 REMARK 470 SER D 120 OG REMARK 470 GLN F 122 CG CD OE1 NE2 REMARK 470 VAL F 124 CG1 CG2 REMARK 470 VAL F 139 CG1 CG2 REMARK 470 GLU F 151 CG CD OE1 OE2 REMARK 470 LEU F 161 CG CD1 CD2 REMARK 470 THR F 164 OG1 CG2 REMARK 470 LYS F 167 CG CD CE NZ REMARK 470 SER F 181 OG REMARK 470 ASP F 182 CG OD1 OD2 REMARK 470 THR F 198 OG1 CG2 REMARK 470 LEU F 200 CG CD1 CD2 REMARK 470 GLN F 201 CG CD OE1 NE2 REMARK 470 THR F 202 OG1 CG2 REMARK 470 GLU F 203 CG CD OE1 OE2 REMARK 470 ASP F 204 CG OD1 OD2 REMARK 470 GLU F 205 CG CD OE1 OE2 REMARK 470 ARG F 227 CG CD NE CZ NH1 NH2 REMARK 470 THR F 229 OG1 CG2 REMARK 470 VAL F 230 CG1 CG2 REMARK 470 ASN C 334 CG OD1 ND2 REMARK 470 GLU C 340 CG CD OE1 OE2 REMARK 470 ASN C 360 CG OD1 ND2 REMARK 470 ASP C 364 CG OD1 OD2 REMARK 470 LEU C 368 CG CD1 CD2 REMARK 470 TYR C 369 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN C 370 CG OD1 ND2 REMARK 470 SER C 375 OG REMARK 470 LYS C 378 CG CD CE NZ REMARK 470 CYS C 379 SG REMARK 470 LYS C 386 CG CD CE NZ REMARK 470 LEU C 387 CG CD1 CD2 REMARK 470 ASP C 389 CG OD1 OD2 REMARK 470 LEU C 390 CG CD1 CD2 REMARK 470 ASP C 405 CG OD1 OD2 REMARK 470 GLU C 406 CG CD OE1 OE2 REMARK 470 THR C 415 OG1 CG2 REMARK 470 LYS C 417 CG CD CE NZ REMARK 470 ASP C 420 CG OD1 OD2 REMARK 470 LYS C 424 CG CD CE NZ REMARK 470 ASP C 428 CG OD1 OD2 REMARK 470 CYS C 432 SG REMARK 470 VAL C 433 CG1 CG2 REMARK 470 ASN C 440 CG OD1 ND2 REMARK 470 LYS C 444 CG CD CE NZ REMARK 470 LEU C 455 CG CD1 CD2 REMARK 470 LYS C 458 CG CD CE NZ REMARK 470 SER C 459 OG REMARK 470 ASN C 460 CG OD1 ND2 REMARK 470 LYS C 462 CG CD CE NZ REMARK 470 GLU C 465 CG CD OE1 OE2 REMARK 470 ASP C 467 CG OD1 OD2 REMARK 470 GLN C 474 CG CD OE1 NE2 REMARK 470 GLU C 516 CG CD OE1 OE2 REMARK 470 LEU C 517 CG CD1 CD2 REMARK 470 LEU C 518 CG CD1 CD2 REMARK 470 HIS C 519 CG ND1 CD2 CE1 NE2 REMARK 470 GLN E 3 CG CD OE1 NE2 REMARK 470 GLN E 5 CG CD OE1 NE2 REMARK 470 GLU E 6 CG CD OE1 OE2 REMARK 470 LEU E 11 CG CD1 CD2 REMARK 470 LYS E 13 CG CD CE NZ REMARK 470 GLU E 16 CG CD OE1 OE2 REMARK 470 LEU E 18 CG CD1 CD2 REMARK 470 LYS E 43 CG CD CE NZ REMARK 470 GLU E 46 CG CD OE1 OE2 REMARK 470 GLU E 50 CG CD OE1 OE2 REMARK 470 LEU E 64 CG CD1 CD2 REMARK 470 LYS E 65 CG CD CE NZ REMARK 470 ARG E 67 CG CD NE CZ NH1 NH2 REMARK 470 THR E 69 OG1 CG2 REMARK 470 LYS E 72 CG CD CE NZ REMARK 470 ASP E 73 CG OD1 OD2 REMARK 470 SER E 75 OG REMARK 470 LYS E 76 CG CD CE NZ REMARK 470 GLN E 78 CG CD OE1 NE2 REMARK 470 ILE E 82 CG1 CG2 CD1 REMARK 470 SER E 85 OG REMARK 470 ASP E 90 CG OD1 OD2 REMARK 470 ASP E 107 CG OD1 OD2 REMARK 470 LEU E 115 CG CD1 CD2 REMARK 470 THR E 117 OG1 CG2 REMARK 470 SER E 119 OG REMARK 470 SER E 120 OG REMARK 470 ASP G 121 CG OD1 OD2 REMARK 470 VAL G 123 CG1 CG2 REMARK 470 THR G 125 OG1 CG2 REMARK 470 ILE G 127 CG1 CG2 CD1 REMARK 470 LEU G 129 CG CD1 CD2 REMARK 470 GLU G 137 CG CD OE1 OE2 REMARK 470 ARG G 144 CG CD NE CZ NH1 NH2 REMARK 470 GLN G 147 CG CD OE1 NE2 REMARK 470 HIS G 156 CG ND1 CD2 CE1 NE2 REMARK 470 VAL G 177 CG1 CG2 REMARK 470 ASP G 186 CG OD1 OD2 REMARK 470 SER G 191 OG REMARK 470 SER G 193 OG REMARK 470 THR G 195 OG1 CG2 REMARK 470 ASP G 196 CG OD1 OD2 REMARK 470 LEU G 199 CG CD1 CD2 REMARK 470 LYS G 200 CG CD CE NZ REMARK 470 ILE G 201 CG1 CG2 CD1 REMARK 470 ARG G 203 CG CD NE CZ NH1 NH2 REMARK 470 GLU G 207 CG CD OE1 OE2 REMARK 470 ASP G 208 CG OD1 OD2 REMARK 470 PHE G 220 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS G 229 CG CD CE NZ REMARK 470 GLU G 231 CG CD OE1 OE2 REMARK 470 LYS G 233 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 7 -168.55 -161.08 REMARK 500 ASP A 90 50.70 -93.73 REMARK 500 ASP A 111 -71.59 -84.02 REMARK 500 LEU B 156 126.87 -38.08 REMARK 500 LEU B 170 -61.77 -99.98 REMARK 500 SER B 174 -6.52 66.00 REMARK 500 GLU B 204 32.69 -98.73 REMARK 500 TYR B 214 26.80 -141.85 REMARK 500 ASN D 67 15.86 -143.90 REMARK 500 TYR D 110 61.80 60.04 REMARK 500 GLU F 151 -2.00 76.06 REMARK 500 TYR F 153 -169.35 -126.63 REMARK 500 ASN F 173 -21.47 72.71 REMARK 500 ASN F 174 -0.16 -151.92 REMARK 500 ARG C 355 111.49 -160.76 REMARK 500 THR C 385 -10.06 71.41 REMARK 500 ASN C 422 -50.35 -123.01 REMARK 500 SER C 477 -54.61 -124.17 REMARK 500 TYR C 505 78.98 -119.46 REMARK 500 SER E 15 21.82 -140.02 REMARK 500 ARG E 67 42.39 -142.59 REMARK 500 PHE E 79 119.94 -165.06 REMARK 500 THR E 91 65.97 61.53 REMARK 500 ARG E 104 57.02 -95.73 REMARK 500 ASP E 108 68.29 60.37 REMARK 500 MET G 176 -168.20 -125.24 REMARK 500 ALA G 181 -166.92 -79.75 REMARK 500 GLU G 207 -14.02 -143.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62589 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SARS-COV-2 PROTOTYPE SPIKE PROTEIN IN COMPLEX REMARK 900 WITH TRIPLE-NAB 3G5, 4H5 AND 4C11 DBREF 9KVD A 1 123 PDB 9KVD 9KVD 1 123 DBREF 9KVD B 124 230 PDB 9KVD 9KVD 124 230 DBREF 9KVD D 1 121 PDB 9KVD 9KVD 1 121 DBREF 9KVD F 122 231 PDB 9KVD 9KVD 122 231 DBREF 9KVD C 334 527 UNP P0DTC2 SPIKE_SARS2 334 527 DBREF 9KVD E 1 120 PDB 9KVD 9KVD 1 120 DBREF 9KVD G 121 233 PDB 9KVD 9KVD 121 233 SEQRES 1 A 123 GLU VAL GLN LEU VAL GLU SER GLY GLY ASP LEU VAL LYS SEQRES 2 A 123 PRO GLY GLY SER LEU ARG LEU SER CYS VAL ALA SER GLY SEQRES 3 A 123 PHE THR PHE SER ARG HIS GLU MET HIS TRP VAL ARG GLN SEQRES 4 A 123 ALA PRO GLY GLU GLY LEU GLU TRP LEU SER VAL ILE SER SEQRES 5 A 123 GLU THR GLY GLY THR THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 123 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 A 123 VAL PHE LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 A 123 ALA VAL TYR PHE CYS VAL ARG ASP GLY GLY ASP PRO ALA SEQRES 9 A 123 GLY THR VAL ARG PHE PHE ASP TYR TRP GLY GLN GLY VAL SEQRES 10 A 123 LEU VAL THR VAL SER SER SEQRES 1 B 107 ASP ILE GLN MET SER GLN SER PRO SER SER LEU SER ALA SEQRES 2 B 107 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 B 107 GLN GLY ILE THR SER PHE LEU ASN TRP TYR GLN LYS LYS SEQRES 4 B 107 PRO GLY LYS ALA PRO THR LEU LEU ILE TYR SER SER ASN SEQRES 5 B 107 ARG LEU ALA SER ALA VAL PRO SER ARG PHE SER GLY SER SEQRES 6 B 107 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 B 107 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 B 107 ILE SER PHE PRO LEU THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 B 107 GLU LEU LYS SEQRES 1 D 121 GLN VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 D 121 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 D 121 GLY SER ILE SER SER GLY TYR GLY TRP ASN TRP ILE ARG SEQRES 4 D 121 GLN PRO PRO GLY LYS GLY LEU GLU TRP VAL GLY TYR ILE SEQRES 5 D 121 TYR GLY SER SER GLY SER THR ASN TYR ASN PRO SER LEU SEQRES 6 D 121 LYS ASN ARG VAL THR ILE SER LYS ASP ALA SER LYS ASN SEQRES 7 D 121 GLN PHE SER LEU LYS VAL ARG SER VAL THR ALA THR ASP SEQRES 8 D 121 THR ALA ILE TYR TYR CYS ALA ARG ASP THR TYR PRO SER SEQRES 9 D 121 ALA TRP SER TRP GLY TYR TRP GLY GLN GLY VAL LEU VAL SEQRES 10 D 121 THR VAL SER SER SEQRES 1 F 110 GLN SER VAL LEU THR GLN PRO PRO SER VAL SER GLY ALA SEQRES 2 F 110 PRO GLY GLN LYS VAL THR ILE SER CYS THR GLY SER SER SEQRES 3 F 110 SER ASN ILE GLU VAL TYR ASP VAL HIS TRP TYR GLN GLN SEQRES 4 F 110 LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR ASP ASN SEQRES 5 F 110 ASN GLN ARG PRO SER GLY ILE SER ASP ARG PHE SER GLY SEQRES 6 F 110 SER LYS SER GLY THR SER ALA SER LEU ALA ILE THR GLY SEQRES 7 F 110 LEU GLN THR GLU ASP GLU ALA ASP TYR TYR CYS GLN SER SEQRES 8 F 110 TYR ASP THR SER LEU ASN ALA TYR ILE PHE GLY ALA GLY SEQRES 9 F 110 THR ARG LEU THR VAL LEU SEQRES 1 C 194 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 C 194 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 C 194 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 C 194 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 C 194 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 C 194 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 C 194 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 C 194 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 C 194 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 C 194 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 C 194 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 C 194 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 C 194 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 C 194 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 C 194 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 1 E 120 GLN VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 E 120 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 E 120 VAL SER ILE SER SER PHE LEU TRP ASN TRP ILE ARG GLN SEQRES 4 E 120 PRO PRO GLY LYS GLY LEU GLU TRP ILE GLY GLU ILE ASN SEQRES 5 E 120 GLY ASN SER GLY SER THR TYR TYR ASN PRO SER LEU LYS SEQRES 6 E 120 SER ARG VAL THR ILE SER LYS ASP ALA SER LYS SER GLN SEQRES 7 E 120 PHE SER LEU ILE LEU GLY SER VAL THR ALA ALA ASP THR SEQRES 8 E 120 ALA VAL TYR TYR CYS ALA THR ARG ASP SER GLY PRO ARG SEQRES 9 E 120 GLY VAL ASP ASP TYR TRP GLY GLN GLY VAL LEU VAL THR SEQRES 10 E 120 VAL SER SER SEQRES 1 G 113 ASP ILE VAL MET THR GLN ILE PRO LEU SER LEU PRO VAL SEQRES 2 G 113 THR PRO GLY GLU PRO ALA SER ILE SER CYS ARG SER SER SEQRES 3 G 113 GLN THR LEU LEU HIS SER GLY SER ALA HIS THR SER LEU SEQRES 4 G 113 ASP TRP TYR LEU GLN LYS PRO GLY GLN SER PRO GLN LEU SEQRES 5 G 113 LEU ILE TYR MET VAL SER ASN ARG ALA SER GLY VAL PRO SEQRES 6 G 113 ASP ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 G 113 LEU LYS ILE SER ARG VAL GLU ALA GLU ASP VAL GLY VAL SEQRES 8 G 113 TYR TYR CYS MET GLN SER VAL ASP PHE PRO TYR SER PHE SEQRES 9 G 113 GLY GLN GLY THR LYS VAL GLU ILE LYS HET NAG C 601 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 8 NAG C8 H15 N O6 HELIX 1 AA1 THR A 28 HIS A 32 5 5 HELIX 2 AA2 PRO C 337 PHE C 342 1 6 HELIX 3 AA3 VAL C 367 ALA C 372 1 6 HELIX 4 AA4 ARG C 403 ILE C 410 5 8 HELIX 5 AA5 SER C 438 SER C 443 1 6 SHEET 1 AA1 4 GLN A 3 VAL A 5 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 SER A 78 MET A 83 -1 O VAL A 79 N CYS A 22 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N SER A 71 O PHE A 80 SHEET 1 AA2 5 LEU A 11 VAL A 12 0 SHEET 2 AA2 5 VAL A 117 VAL A 121 1 O THR A 120 N VAL A 12 SHEET 3 AA2 5 ALA A 92 GLY A 100 -1 N TYR A 94 O VAL A 117 SHEET 4 AA2 5 MET A 34 GLN A 39 -1 N HIS A 35 O VAL A 97 SHEET 5 AA2 5 LEU A 45 TRP A 47 -1 O GLU A 46 N ARG A 38 SHEET 1 AA3 4 LEU A 11 VAL A 12 0 SHEET 2 AA3 4 VAL A 117 VAL A 121 1 O THR A 120 N VAL A 12 SHEET 3 AA3 4 ALA A 92 GLY A 100 -1 N TYR A 94 O VAL A 117 SHEET 4 AA3 4 PHE A 109 PHE A 110 -1 O PHE A 109 N GLY A 100 SHEET 1 AA4 4 SER B 128 SER B 130 0 SHEET 2 AA4 4 VAL B 142 ARG B 147 -1 O ARG B 147 N SER B 128 SHEET 3 AA4 4 GLU B 193 ILE B 198 -1 O LEU B 196 N ILE B 144 SHEET 4 AA4 4 PHE B 185 SER B 190 -1 N SER B 186 O THR B 197 SHEET 1 AA5 6 SER B 133 ALA B 136 0 SHEET 2 AA5 6 THR B 225 LEU B 229 1 O LYS B 226 N LEU B 134 SHEET 3 AA5 6 THR B 208 GLN B 213 -1 N TYR B 209 O THR B 225 SHEET 4 AA5 6 ASN B 157 LYS B 161 -1 N LYS B 161 O THR B 208 SHEET 5 AA5 6 THR B 168 TYR B 172 -1 O THR B 168 N GLN B 160 SHEET 6 AA5 6 ARG B 176 LEU B 177 -1 O ARG B 176 N TYR B 172 SHEET 1 AA6 4 SER B 133 ALA B 136 0 SHEET 2 AA6 4 THR B 225 LEU B 229 1 O LYS B 226 N LEU B 134 SHEET 3 AA6 4 THR B 208 GLN B 213 -1 N TYR B 209 O THR B 225 SHEET 4 AA6 4 THR B 220 PHE B 221 -1 O THR B 220 N GLN B 213 SHEET 1 AA7 4 GLN D 3 GLN D 5 0 SHEET 2 AA7 4 CYS D 22 SER D 25 -1 O ALA D 23 N GLN D 5 SHEET 3 AA7 4 GLN D 79 PHE D 80 -1 O PHE D 80 N CYS D 22 SHEET 4 AA7 4 LYS D 73 ASP D 74 -1 N ASP D 74 O GLN D 79 SHEET 1 AA8 5 LEU D 11 VAL D 12 0 SHEET 2 AA8 5 VAL D 115 VAL D 119 1 O THR D 118 N VAL D 12 SHEET 3 AA8 5 ALA D 93 ASP D 100 -1 N ALA D 93 O VAL D 117 SHEET 4 AA8 5 GLY D 34 GLN D 40 -1 N GLN D 40 O ILE D 94 SHEET 5 AA8 5 GLU D 47 TYR D 53 -1 O ILE D 52 N TRP D 35 SHEET 1 AA9 4 LEU D 11 VAL D 12 0 SHEET 2 AA9 4 VAL D 115 VAL D 119 1 O THR D 118 N VAL D 12 SHEET 3 AA9 4 ALA D 93 ASP D 100 -1 N ALA D 93 O VAL D 117 SHEET 4 AA9 4 TRP D 108 GLY D 109 -1 O GLY D 109 N ARG D 99 SHEET 1 AB1 5 VAL F 131 SER F 132 0 SHEET 2 AB1 5 THR F 226 THR F 229 1 O ARG F 227 N VAL F 131 SHEET 3 AB1 5 ASP F 207 TYR F 213 -1 N TYR F 208 O THR F 226 SHEET 4 AB1 5 HIS F 156 GLN F 160 -1 N GLN F 160 O ASP F 207 SHEET 5 AB1 5 PRO F 166 ILE F 170 -1 O LYS F 167 N GLN F 159 SHEET 1 AB2 4 VAL F 131 SER F 132 0 SHEET 2 AB2 4 THR F 226 THR F 229 1 O ARG F 227 N VAL F 131 SHEET 3 AB2 4 ASP F 207 TYR F 213 -1 N TYR F 208 O THR F 226 SHEET 4 AB2 4 TYR F 220 PHE F 222 -1 O ILE F 221 N SER F 212 SHEET 1 AB3 3 THR F 140 THR F 144 0 SHEET 2 AB3 3 SER F 192 ILE F 197 -1 O LEU F 195 N ILE F 141 SHEET 3 AB3 3 PHE F 184 GLY F 186 -1 N SER F 185 O ALA F 196 SHEET 1 AB4 5 ASN C 354 ARG C 355 0 SHEET 2 AB4 5 ASN C 394 ILE C 402 -1 O SER C 399 N ASN C 354 SHEET 3 AB4 5 TYR C 508 GLU C 516 -1 O TYR C 508 N ILE C 402 SHEET 4 AB4 5 GLY C 431 ASN C 437 -1 N CYS C 432 O LEU C 513 SHEET 5 AB4 5 THR C 376 TYR C 380 -1 N TYR C 380 O GLY C 431 SHEET 1 AB5 2 CYS C 361 VAL C 362 0 SHEET 2 AB5 2 VAL C 524 CYS C 525 1 O CYS C 525 N CYS C 361 SHEET 1 AB6 2 LEU C 452 ARG C 454 0 SHEET 2 AB6 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AB7 2 TYR C 473 GLN C 474 0 SHEET 2 AB7 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SHEET 1 AB8 4 GLN E 5 SER E 7 0 SHEET 2 AB8 4 LEU E 18 ALA E 23 -1 O THR E 21 N SER E 7 SHEET 3 AB8 4 PHE E 79 LEU E 83 -1 O LEU E 83 N LEU E 18 SHEET 4 AB8 4 VAL E 68 LYS E 72 -1 N THR E 69 O ILE E 82 SHEET 1 AB9 5 THR E 58 TYR E 60 0 SHEET 2 AB9 5 GLU E 46 ILE E 51 -1 N GLU E 50 O TYR E 59 SHEET 3 AB9 5 TRP E 34 GLN E 39 -1 N ARG E 38 O GLU E 46 SHEET 4 AB9 5 ALA E 92 ALA E 97 -1 O TYR E 95 N ILE E 37 SHEET 5 AB9 5 VAL E 114 VAL E 116 -1 O VAL E 116 N ALA E 92 SHEET 1 AC1 4 MET G 124 THR G 125 0 SHEET 2 AC1 4 ILE G 141 SER G 145 -1 O ARG G 144 N THR G 125 SHEET 3 AC1 4 PHE G 197 LEU G 199 -1 O LEU G 199 N ILE G 141 SHEET 4 AC1 4 GLY G 190 SER G 191 -1 N SER G 191 O THR G 198 SHEET 1 AC2 2 SER G 130 VAL G 133 0 SHEET 2 AC2 2 LYS G 229 ILE G 232 1 O GLU G 231 N VAL G 133 SHEET 1 AC3 2 TRP G 161 LEU G 163 0 SHEET 2 AC3 2 GLN G 171 ILE G 174 -1 O LEU G 173 N TRP G 161 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.02 SSBOND 2 CYS B 146 CYS B 211 1555 1555 2.04 SSBOND 3 CYS D 22 CYS D 97 1555 1555 2.03 SSBOND 4 CYS F 143 CYS F 210 1555 1555 2.03 SSBOND 5 CYS C 336 CYS C 361 1555 1555 2.03 SSBOND 6 CYS C 480 CYS C 488 1555 1555 2.04 SSBOND 7 CYS E 22 CYS E 96 1555 1555 2.03 SSBOND 8 CYS G 143 CYS G 214 1555 1555 2.04 LINK ND2 ASN C 343 C1 NAG C 601 1555 1555 1.43 CISPEP 1 SER B 130 PRO B 131 0 -1.79 CISPEP 2 PHE B 217 PRO B 218 0 -5.46 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000