HEADER VIRAL PROTEIN 21-AUG-23 8KHD TITLE THE INTERFACE STRUCTURE OF OMICRON RBD BINDING TO 5817 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF 5817; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF 5817; COMPND 7 CHAIN: J; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: RBD; COMPND 13 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 13 2; SOURCE 14 ORGANISM_TAXID: 2697049; SOURCE 15 GENE: S, 2; SOURCE 16 EXPRESSION_SYSTEM: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 2697049 KEYWDS SARS-COV-2, OMICRON, RBD, FAB, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.CAO,X.WANG REVDAT 1 17-APR-24 8KHD 0 JRNL AUTH Y.WANG,Z.ZHANG,M.YANG,X.XIONG,Q.YAN,L.CAO,P.WEI,Y.ZHANG, JRNL AUTH 2 L.ZHANG,K.LV,J.CHEN,X.LIU,X.ZHAO,J.XIAO,S.ZHANG,A.ZHU,M.GAN, JRNL AUTH 3 J.ZHANG,R.CAI,J.ZHUO,Y.ZHANG,H.RAO,B.QU,Y.ZHANG,L.CHEN, JRNL AUTH 4 J.DAI,L.CHENG,Q.HU,Y.CHEN,H.LV,R.T.Y.SO,M.PEIRIS,J.ZHAO, JRNL AUTH 5 X.LIU,C.K.P.MOK,X.WANG,J.ZHAO JRNL TITL IDENTIFICATION OF A BROAD SARBECOVIRUS NEUTRALIZING ANTIBODY JRNL TITL 2 TARGETING A CONSERVED EPITOPE ON THE RECEPTOR-BINDING JRNL TITL 3 DOMAIN. JRNL REF CELL REP V. 43 13653 2024 JRNL REFN ESSN 2211-1247 JRNL PMID 38175758 JRNL DOI 10.1016/J.CELREP.2023.113653 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 5129 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 8KHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300038717. 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 : THE INTERFACE STRUCTURE OF REMARK 245 OMICRON RBD BINDING TO 5817 FAB 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 : 7.50 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 4500.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, J, C 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 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 LYS H 13 CG CD CE NZ REMARK 470 LYS H 67 CG CD CE NZ REMARK 470 LYS H 78 CG CD CE NZ REMARK 470 GLN H 84 CG CD OE1 NE2 REMARK 470 LYS H 89 CG CD CE NZ REMARK 470 PHE C 497 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG C 498 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS C 379 CA - CB - SG ANGL. DEV. = 8.8 DEGREES 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 SER H 52 -173.18 57.16 REMARK 500 THR H 60 109.72 -59.99 REMARK 500 ASP H 103 -57.62 -121.93 REMARK 500 MET H 108 -3.02 59.04 REMARK 500 PHE H 114 65.36 60.44 REMARK 500 VAL J 46 -56.98 -123.55 REMARK 500 ILE J 98 -43.32 46.42 REMARK 500 PHE J 99 -172.94 57.77 REMARK 500 ASN C 334 58.61 -94.47 REMARK 500 ILE C 418 -49.33 65.99 REMARK 500 ASP C 428 33.22 -99.21 REMARK 500 LYS C 478 150.61 72.75 REMARK 500 HIS C 519 -1.01 -141.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37241 RELATED DB: EMDB REMARK 900 THE INTERFACE STRUCTURE OF OMICRON RBD BINDING TO 5817 FAB DBREF 8KHD H 1 125 PDB 8KHD 8KHD 1 125 DBREF 8KHD J 3 110 PDB 8KHD 8KHD 3 110 DBREF 8KHD C 330 530 UNP P0DTC2 SPIKE_SARS2 330 530 SEQADV 8KHD ASP C 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8KHD LEU C 371 UNP P0DTC2 SER 371 VARIANT SEQADV 8KHD PRO C 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8KHD PHE C 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8KHD ASN C 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8KHD LYS C 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8KHD SER C 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 8KHD ASN C 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8KHD LYS C 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8KHD ALA C 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8KHD ARG C 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 8KHD SER C 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 8KHD ARG C 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8KHD TYR C 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8KHD HIS C 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 H 125 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL LYS SEQRES 2 H 125 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 125 PHE SER PHE SER ASP ALA TRP MET SER TRP VAL ARG GLN SEQRES 4 H 125 ALA PRO GLY LYS GLY LEU GLU TRP VAL GLY ARG VAL SER SEQRES 5 H 125 SER GLU ILE GLY GLY GLY THR THR ASP TYR ALA ALA PRO SEQRES 6 H 125 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASP SER LYS SEQRES 7 H 125 ASN THR LEU PHE LEU GLN MET SER SER LEU LYS THR GLU SEQRES 8 H 125 ASP THR ALA VAL TYR TYR CYS THR THR GLY VAL ASP ILE SEQRES 9 H 125 VAL VAL MET MET TYR ALA ASP ASP ALA PHE ASP ILE TRP SEQRES 10 H 125 GLY GLN GLY THR MET VAL THR VAL SEQRES 1 J 108 GLU LEU THR GLN ASP PRO ALA VAL SER VAL ALA LEU GLY SEQRES 2 J 108 GLN THR VAL ARG ILE THR CYS GLN GLY ASP SER LEU ARG SEQRES 3 J 108 SER TYR TYR ALA SER TRP TYR GLN GLN LYS PRO GLY GLN SEQRES 4 J 108 ALA PRO VAL LEU VAL ILE TYR GLY LYS ASN ASN ARG PRO SEQRES 5 J 108 SER GLY ILE PRO ASP ARG PHE SER GLY SER SER SER GLY SEQRES 6 J 108 ASN THR ALA SER LEU THR ILE THR GLY PRO GLN ALA GLU SEQRES 7 J 108 ASP GLU ALA ASP TYR TYR CYS THR SER ARG ASP SER SER SEQRES 8 J 108 GLY ASN HIS VAL ILE PHE GLY GLY GLY THR LYS LEU THR SEQRES 9 J 108 VAL LEU GLY GLN SEQRES 1 C 201 PRO ASN ILE THR ASN LEU CYS PRO PHE ASP GLU VAL PHE SEQRES 2 C 201 ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG SEQRES 3 C 201 LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU SEQRES 4 C 201 TYR ASN LEU ALA PRO PHE PHE THR PHE LYS CYS TYR GLY SEQRES 5 C 201 VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN SEQRES 6 C 201 VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL SEQRES 7 C 201 ARG GLN ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP SEQRES 8 C 201 TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL SEQRES 9 C 201 ILE ALA TRP ASN SER ASN LYS LEU ASP SER LYS VAL SER SEQRES 10 C 201 GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER SEQRES 11 C 201 ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE SEQRES 12 C 201 TYR GLN ALA GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY SEQRES 13 C 201 PHE ASN CYS TYR PHE PRO LEU ARG SER TYR SER PHE ARG SEQRES 14 C 201 PRO THR TYR GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL SEQRES 15 C 201 VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL SEQRES 16 C 201 CYS GLY PRO LYS LYS SER 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 4 NAG C8 H15 N O6 HELIX 1 AA1 SER H 28 ALA H 32 5 5 HELIX 2 AA2 TYR C 365 ASN C 370 1 6 HELIX 3 AA3 ASP C 405 ARG C 408 5 4 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 SER H 17 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA1 4 THR H 80 SER H 86 -1 O LEU H 83 N LEU H 20 SHEET 4 AA1 4 PHE H 70 ASP H 75 -1 N THR H 71 O GLN H 84 SHEET 1 AA2 4 LEU H 45 ARG H 50 0 SHEET 2 AA2 4 MET H 34 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 3 AA2 4 ALA H 94 THR H 100 -1 O TYR H 97 N VAL H 37 SHEET 4 AA2 4 THR H 121 VAL H 123 -1 O THR H 121 N TYR H 96 SHEET 1 AA3 2 ILE H 104 VAL H 106 0 SHEET 2 AA3 2 GLU C 465 ASP C 467 -1 O ARG C 466 N VAL H 105 SHEET 1 AA4 5 ALA J 9 VAL J 10 0 SHEET 2 AA4 5 THR J 103 LEU J 105 1 O LYS J 104 N VAL J 10 SHEET 3 AA4 5 ALA J 83 THR J 88 -1 N TYR J 85 O THR J 103 SHEET 4 AA4 5 SER J 33 GLN J 37 -1 N GLN J 37 O ASP J 84 SHEET 5 AA4 5 VAL J 44 ILE J 47 -1 O VAL J 44 N GLN J 36 SHEET 1 AA5 3 VAL J 18 GLN J 23 0 SHEET 2 AA5 3 THR J 69 ILE J 74 -1 O LEU J 72 N ILE J 20 SHEET 3 AA5 3 PHE J 61 SER J 66 -1 N SER J 62 O THR J 73 SHEET 1 AA6 5 ASN C 354 ILE C 358 0 SHEET 2 AA6 5 ASN C 394 ARG C 403 -1 O SER C 399 N ASN C 354 SHEET 3 AA6 5 PRO C 507 GLU C 516 -1 O TYR C 508 N ILE C 402 SHEET 4 AA6 5 GLY C 431 ASN C 437 -1 N CYS C 432 O LEU C 513 SHEET 5 AA6 5 PHE C 374 CYS C 379 -1 N LYS C 378 O VAL C 433 SHEET 1 AA7 2 LEU C 452 ARG C 454 0 SHEET 2 AA7 2 LEU C 492 SER C 494 -1 O ARG C 493 N TYR C 453 SSBOND 1 CYS H 22 CYS H 98 1555 1555 2.03 SSBOND 2 CYS J 22 CYS J 87 1555 1555 2.04 SSBOND 3 CYS C 336 CYS C 361 1555 1555 2.02 SSBOND 4 CYS C 379 CYS C 432 1555 1555 2.05 SSBOND 5 CYS C 391 CYS C 525 1555 1555 2.04 SSBOND 6 CYS C 480 CYS C 488 1555 1555 2.03 LINK ND2 ASN C 343 C1 NAG C 601 1555 1555 1.45 CISPEP 1 ASN C 331 ILE C 332 0 0.38 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