HEADER VIRAL PROTEIN/IMMUNE SYSTEM 05-DEC-24 9KVJ TITLE CRYO-EM STRUCTURE OF SARS-COV-2 BA.5 SPIKE PROTEIN IN COMPLEX WITH NAB TITLE 2 1C4 (LOCAL REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF NAB 1C4; COMPND 3 CHAIN: C; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: LIGHT CHAIN OF NAB 1C4; COMPND 6 CHAIN: D; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: SPIKE PROTEIN S1; COMPND 9 CHAIN: G; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 6 ORGANISM_TAXID: 10090; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 9 2; SOURCE 10 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 11 ORGANISM_TAXID: 2697049; SOURCE 12 STRAIN: BA.5, OMICRON; SOURCE 13 GENE: S, 2; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606 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.LI,Q.ZHENG REVDAT 1 10-DEC-25 9KVJ 0 JRNL AUTH H.SUN,Y.JIANG,S.LI,Q.ZHENG JRNL TITL CRYO-EM STRUCTURE OF SARS-COV-2 BA.5 SPIKE PROTEIN IN JRNL TITL 2 COMPLEX WITH NAB 1C4 (LOCAL REFINEMENT) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.82 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) : 3.820 REMARK 3 NUMBER OF PARTICLES : 148009 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 9KVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 10-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300049863. 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 : CRYO-EM STRUCTURE OF SARS-COV-2 REMARK 245 BA.5 SPIKE PROTEIN IN COMPLEX REMARK 245 WITH NAB 1C4; SARS-COV-2 SPIKE REMARK 245 PROTEIN OF BA.5 VARIANT; THE REMARK 245 FRAGMENT OF NAB 1C4 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) : 2200.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, G, A 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 LEU G 518 REMARK 465 HIS G 519 REMARK 465 LYS G 527 REMARK 465 LYS G 528 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG1 THR D 14 OD2 ASP D 17 2.15 REMARK 500 O SER D 7 OG SER D 22 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 LEU C 11 116.12 -160.78 REMARK 500 PHE C 64 53.99 -94.11 REMARK 500 ARG C 67 -3.85 68.03 REMARK 500 ASP C 90 36.07 -96.93 REMARK 500 LEU D 47 -61.82 -94.39 REMARK 500 ALA D 51 -8.83 71.96 REMARK 500 SER D 91 10.33 -141.27 REMARK 500 PRO G 337 77.19 -66.24 REMARK 500 ASN G 343 41.08 -91.83 REMARK 500 PRO G 373 9.17 -56.70 REMARK 500 ASN G 422 -54.49 -120.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62596 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SARS-COV-2 BA.5 SPIKE PROTEIN IN COMPLEX WITH REMARK 900 NAB 1C4 (LOCAL REFINEMENT) DBREF 9KVJ C 1 119 PDB 9KVJ 9KVJ 1 119 DBREF 9KVJ D 1 107 PDB 9KVJ 9KVJ 1 107 DBREF 9KVJ G 333 528 UNP P0DTC2 SPIKE_SARS2 333 528 SEQADV 9KVJ ASP G 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 9KVJ PHE G 371 UNP P0DTC2 SER 371 VARIANT SEQADV 9KVJ PRO G 373 UNP P0DTC2 SER 373 VARIANT SEQADV 9KVJ PHE G 375 UNP P0DTC2 SER 375 VARIANT SEQADV 9KVJ ALA G 376 UNP P0DTC2 THR 376 VARIANT SEQADV 9KVJ ASN G 405 UNP P0DTC2 ASP 405 VARIANT SEQADV 9KVJ SER G 408 UNP P0DTC2 ARG 408 VARIANT SEQADV 9KVJ ASN G 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 9KVJ LYS G 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 9KVJ ARG G 452 UNP P0DTC2 LEU 452 VARIANT SEQADV 9KVJ ASN G 477 UNP P0DTC2 SER 477 VARIANT SEQADV 9KVJ LYS G 478 UNP P0DTC2 THR 478 VARIANT SEQADV 9KVJ ALA G 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 9KVJ VAL G 486 UNP P0DTC2 PHE 486 VARIANT SEQADV 9KVJ ARG G 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 9KVJ TYR G 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 9KVJ HIS G 505 UNP P0DTC2 TYR 505 VARIANT SEQADV 9KVJ LYS G 527 UNP P0DTC2 PRO 527 CONFLICT SEQRES 1 C 119 GLN ILE GLN LEU VAL GLN SER GLY PRO GLU LEU LYS LYS SEQRES 2 C 119 PRO GLY GLU THR VAL LYS ILE SER CYS LYS ALA SER GLY SEQRES 3 C 119 TYR THR PHE THR ASP TYR GLY LEU ASN TRP VAL LYS GLN SEQRES 4 C 119 ALA PRO GLY LYS GLY LEU LYS TRP MET GLY TRP ILE ASN SEQRES 5 C 119 THR TYR SER GLY GLU PRO THR TYR ASN ASP GLU PHE ARG SEQRES 6 C 119 GLY ARG PHE ALA PHE SER LEU GLU THR SER THR ILE THR SEQRES 7 C 119 ALA TYR LEU LYS ILE ASN ASN LEU LYS ASN GLU ASP THR SEQRES 8 C 119 ALA THR TYR PHE CYS ALA ARG GLY GLY ASN TRP ASP TRP SEQRES 9 C 119 TYR PHE ASP VAL TRP GLY ALA GLY THR THR VAL THR VAL SEQRES 10 C 119 SER SER SEQRES 1 D 107 ASP ILE VAL LEU THR GLN SER PRO ALA THR LEU SER VAL SEQRES 2 D 107 THR PRO GLY ASP ASN VAL SER LEU SER CYS ARG ALA SER SEQRES 3 D 107 GLN ILE ILE SER ASN ASN LEU HIS TRP TYR GLN GLN LYS SEQRES 4 D 107 SER HIS GLU SER PRO ARG LEU LEU ILE LYS TYR ALA SER SEQRES 5 D 107 GLN SER ILE SER GLY ILE PRO SER ARG PHE SER GLY SER SEQRES 6 D 107 GLY SER GLY THR ASP PHE THR LEU SER ILE ASN SER VAL SEQRES 7 D 107 GLU THR GLU ASP PHE GLY MET TYR PHE CYS GLN GLN SER SEQRES 8 D 107 ASN THR TRP PRO LEU THR CYS GLY SER GLY THR LYS LEU SEQRES 9 D 107 GLU LEU ASN SEQRES 1 G 196 THR ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA THR SEQRES 2 G 196 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 G 196 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN PHE SEQRES 4 G 196 ALA PRO PHE PHE ALA PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 G 196 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 G 196 ASP SER PHE VAL ILE ARG GLY ASN GLU VAL SER GLN ILE SEQRES 7 G 196 ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR SEQRES 8 G 196 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 G 196 ASN SER ASN LYS LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 G 196 ASN TYR ARG TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 G 196 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 G 196 GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY VAL ASN CYS SEQRES 13 G 196 TYR PHE PRO LEU GLN SER TYR GLY PHE ARG PRO THR TYR SEQRES 14 G 196 GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 G 196 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY LYS SEQRES 16 G 196 LYS HET NAG A 1 14 HET NAG A 2 14 HET BMA A 3 11 HET FUC A 4 10 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 FORMUL 4 FUC C6 H12 O5 HELIX 1 AA1 THR C 28 TYR C 32 5 5 HELIX 2 AA2 GLU D 79 PHE D 83 5 5 HELIX 3 AA3 PHE G 338 ASN G 343 1 6 HELIX 4 AA4 TYR G 365 PHE G 371 1 7 HELIX 5 AA5 SER G 383 ASN G 388 5 6 HELIX 6 AA6 GLY G 404 ILE G 410 5 7 HELIX 7 AA7 ASN G 417 ASN G 422 1 6 SHEET 1 AA1 4 GLN C 3 GLN C 6 0 SHEET 2 AA1 4 VAL C 18 SER C 25 -1 O LYS C 23 N VAL C 5 SHEET 3 AA1 4 THR C 78 ILE C 83 -1 O LEU C 81 N ILE C 20 SHEET 4 AA1 4 PHE C 68 ALA C 69 -1 N ALA C 69 O LYS C 82 SHEET 1 AA2 4 GLN C 3 GLN C 6 0 SHEET 2 AA2 4 VAL C 18 SER C 25 -1 O LYS C 23 N VAL C 5 SHEET 3 AA2 4 THR C 78 ILE C 83 -1 O LEU C 81 N ILE C 20 SHEET 4 AA2 4 LEU C 72 GLU C 73 -1 N GLU C 73 O THR C 78 SHEET 1 AA3 5 GLU C 10 LYS C 12 0 SHEET 2 AA3 5 THR C 113 VAL C 117 1 O THR C 114 N GLU C 10 SHEET 3 AA3 5 ALA C 92 TYR C 94 -1 N TYR C 94 O THR C 113 SHEET 4 AA3 5 VAL C 37 GLN C 39 -1 N GLN C 39 O THR C 93 SHEET 5 AA3 5 LEU C 45 TRP C 47 -1 O LYS C 46 N LYS C 38 SHEET 1 AA4 2 ARG C 98 GLY C 99 0 SHEET 2 AA4 2 PHE C 106 VAL C 108 -1 O VAL C 108 N ARG C 98 SHEET 1 AA5 4 THR D 5 SER D 7 0 SHEET 2 AA5 4 VAL D 19 ARG D 24 -1 O SER D 22 N SER D 7 SHEET 3 AA5 4 THR D 72 ILE D 75 -1 O LEU D 73 N LEU D 21 SHEET 4 AA5 4 PHE D 62 SER D 65 -1 N SER D 65 O THR D 72 SHEET 1 AA6 6 SER D 12 VAL D 13 0 SHEET 2 AA6 6 THR D 102 LEU D 106 1 O GLU D 105 N VAL D 13 SHEET 3 AA6 6 GLY D 84 GLN D 90 -1 N TYR D 86 O THR D 102 SHEET 4 AA6 6 LEU D 33 GLN D 38 -1 N TYR D 36 O PHE D 87 SHEET 5 AA6 6 ARG D 45 LYS D 49 -1 O ARG D 45 N GLN D 37 SHEET 6 AA6 6 GLN D 53 SER D 54 -1 O GLN D 53 N LYS D 49 SHEET 1 AA7 5 ASN G 354 ILE G 358 0 SHEET 2 AA7 5 VAL G 395 ILE G 402 -1 O VAL G 395 N ILE G 358 SHEET 3 AA7 5 TYR G 508 SER G 514 -1 O TYR G 508 N ILE G 402 SHEET 4 AA7 5 CYS G 432 ALA G 435 -1 N CYS G 432 O LEU G 513 SHEET 5 AA7 5 LYS G 378 CYS G 379 -1 N LYS G 378 O VAL G 433 SHEET 1 AA8 2 ARG G 452 ARG G 454 0 SHEET 2 AA8 2 LEU G 492 SER G 494 -1 O GLN G 493 N TYR G 453 SSBOND 1 CYS C 22 CYS C 96 1555 1555 2.03 SSBOND 2 CYS D 23 CYS D 88 1555 1555 2.04 SSBOND 3 CYS G 336 CYS G 361 1555 1555 2.03 SSBOND 4 CYS G 379 CYS G 432 1555 1555 2.03 SSBOND 5 CYS G 480 CYS G 488 1555 1555 2.04 LINK ND2 ASN G 343 C1 NAG A 1 1555 1555 1.46 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.44 LINK O6 NAG A 1 C1 FUC A 4 1555 1555 1.43 LINK O4 NAG A 2 C1 BMA A 3 1555 1555 1.44 CISPEP 1 SER D 7 PRO D 8 0 -2.08 CISPEP 2 TRP D 94 PRO D 95 0 -1.69 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