HEADER VIRAL PROTEIN 28-JAN-22 7WRZ TITLE LOCAL RESOLUTION OF BD55-5840 FAB AND SARS-COV2 OMICRON RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: BD55-5840H; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BD55-5840L; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: R; COMPND 12 SYNONYM: OMICRON RBD; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS B012; SOURCE 3 ORGANISM_TAXID: 305406; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS B012; SOURCE 8 ORGANISM_TAXID: 305406; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS B012; SOURCE 13 ORGANISM_TAXID: 305406; SOURCE 14 GENE: S, 2; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV2 OMICRON RBD, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Z.Z.ZHANG,J.J.XIAO REVDAT 3 31-AUG-22 7WRZ 1 JRNL REVDAT 2 13-JUL-22 7WRZ 1 JRNL REVDAT 1 22-JUN-22 7WRZ 0 JRNL AUTH Y.CAO,A.YISIMAYI,F.JIAN,W.SONG,T.XIAO,L.WANG,S.DU,J.WANG, JRNL AUTH 2 Q.LI,X.CHEN,Y.YU,P.WANG,Z.ZHANG,P.LIU,R.AN,X.HAO,Y.WANG, JRNL AUTH 3 J.WANG,R.FENG,H.SUN,L.ZHAO,W.ZHANG,D.ZHAO,J.ZHENG,L.YU,C.LI, JRNL AUTH 4 N.ZHANG,R.WANG,X.NIU,S.YANG,X.SONG,Y.CHAI,Y.HU,Y.SHI, JRNL AUTH 5 L.ZHENG,Z.LI,Q.GU,F.SHAO,W.HUANG,R.JIN,Z.SHEN,Y.WANG,X.WANG, JRNL AUTH 6 J.XIAO,X.S.XIE JRNL TITL BA.2.12.1, BA.4 AND BA.5 ESCAPE ANTIBODIES ELICITED BY JRNL TITL 2 OMICRON INFECTION. JRNL REF NATURE V. 608 593 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35714668 JRNL DOI 10.1038/S41586-022-04980-Y REMARK 2 REMARK 2 RESOLUTION. 3.26 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) : 3.260 REMARK 3 NUMBER OF PARTICLES : 2765 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7WRZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027328. 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 : LOCAL RESOLUTION OF BD55-5840 REMARK 245 FAB AND SARS-COV2 OMICRON RBD 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 : 8.00 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 TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 107.00 REMARK 245 ILLUMINATION MODE : OTHER 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: H, L, R, 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 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 R 517 REMARK 465 LEU R 518 REMARK 465 HIS R 519 REMARK 465 ALA R 520 REMARK 465 PRO R 521 REMARK 465 ALA R 522 REMARK 465 THR R 523 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 R 527 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 H 25 3.28 -64.73 REMARK 500 THR H 30 55.99 -96.07 REMARK 500 SER L 32 63.91 60.41 REMARK 500 TYR L 93 56.46 -99.06 REMARK 500 ASN R 370 49.76 -93.28 REMARK 500 PHE R 377 78.02 -103.71 REMARK 500 PHE R 464 19.15 59.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP L 96 PRO L 97 134.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32738 RELATED DB: EMDB REMARK 900 LOCAL RESOLUTION OF BD55-5840 FAB AND SARS-COV2 OMICRON RBD DBREF 7WRZ H 2 120 PDB 7WRZ 7WRZ 2 120 DBREF 7WRZ L 1 109 PDB 7WRZ 7WRZ 1 109 DBREF 7WRZ R 335 527 UNP P0DTC2 SPIKE_SARS2 335 527 SEQADV 7WRZ ASP R 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7WRZ LEU R 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7WRZ PRO R 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7WRZ PHE R 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7WRZ ASN R 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7WRZ LYS R 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7WRZ SER R 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7WRZ ASN R 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7WRZ LYS R 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7WRZ ALA R 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7WRZ ARG R 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7WRZ SER R 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7WRZ ARG R 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7WRZ TYR R 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7WRZ HIS R 505 UNP P0DTC2 TYR 505 VARIANT SEQADV 7WRZ LYS R 527 UNP P0DTC2 PRO 527 VARIANT SEQRES 1 H 119 VAL GLN LEU ALA GLN SER GLY SER GLU LEU ARG LYS PRO SEQRES 2 H 119 GLY ALA SER VAL LYS VAL SER CYS ASP THR SER GLY HIS SEQRES 3 H 119 SER PHE THR SER ASN ALA ILE HIS TRP VAL ARG GLN ALA SEQRES 4 H 119 PRO GLY GLN GLY LEU GLU TRP MET GLY TRP ILE ASN THR SEQRES 5 H 119 ASP THR GLY THR PRO THR TYR ALA GLN GLY PHE THR GLY SEQRES 6 H 119 ARG PHE VAL PHE SER LEU ASP THR SER ALA ARG THR ALA SEQRES 7 H 119 TYR LEU GLN ILE SER SER LEU LYS ALA ASP ASP THR ALA SEQRES 8 H 119 VAL PHE TYR CYS ALA ARG GLU ARG ASP TYR SER ASP TYR SEQRES 9 H 119 PHE PHE ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 H 119 SER SER SEQRES 1 L 109 GLU VAL VAL MET THR GLN SER PRO ALA SER LEU SER VAL SEQRES 2 L 109 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA ARG SEQRES 3 L 109 ALA SER LEU GLY ILE SER THR ASP LEU ALA TRP TYR GLN SEQRES 4 L 109 GLN ARG PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY SEQRES 5 L 109 ALA SER THR ARG ALA THR GLY ILE PRO ALA ARG PHE SER SEQRES 6 L 109 GLY SER GLY SER GLY THR GLU PHE THR LEU THR ILE SER SEQRES 7 L 109 SER LEU GLN SER GLU ASP SER ALA VAL TYR TYR CYS GLN SEQRES 8 L 109 GLN TYR SER ASN TRP PRO LEU THR PHE GLY GLY GLY THR SEQRES 9 L 109 LYS VAL GLU ILE LYS SEQRES 1 R 193 LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA THR ARG PHE SEQRES 2 R 193 ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER ASN SEQRES 3 R 193 CYS VAL ALA ASP TYR SER VAL LEU TYR ASN LEU ALA PRO SEQRES 4 R 193 PHE PHE THR PHE LYS CYS TYR GLY VAL SER PRO THR LYS SEQRES 5 R 193 LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SER SEQRES 6 R 193 PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA PRO SEQRES 7 R 193 GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR LYS LEU SEQRES 8 R 193 PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SER SEQRES 9 R 193 ASN LYS LEU ASP SER LYS VAL SER GLY ASN TYR ASN TYR SEQRES 10 R 193 LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO PHE SEQRES 11 R 193 GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY ASN SEQRES 12 R 193 LYS PRO CYS ASN GLY VAL ALA GLY PHE ASN CYS TYR PHE SEQRES 13 R 193 PRO LEU ARG SER TYR SER PHE ARG PRO THR TYR GLY VAL SEQRES 14 R 193 GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER PHE GLU SEQRES 15 R 193 LEU LEU HIS ALA PRO ALA THR VAL CYS GLY LYS HET NAG C 1 14 HET NAG C 2 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 2(C8 H15 N O6) HELIX 1 AA1 GLN L 81 SER L 85 5 5 HELIX 2 AA2 PHE R 338 ASN R 343 1 6 HELIX 3 AA3 SER R 349 TRP R 353 5 5 HELIX 4 AA4 TYR R 365 ASN R 370 1 6 HELIX 5 AA5 SER R 383 LEU R 390 5 8 HELIX 6 AA6 ASP R 405 ILE R 410 5 6 HELIX 7 AA7 GLY R 416 ASN R 422 1 7 HELIX 8 AA8 SER R 438 SER R 443 1 6 HELIX 9 AA9 GLY R 502 HIS R 505 5 4 SHEET 1 AA1 6 GLU H 10 ARG H 12 0 SHEET 2 AA1 6 THR H 114 VAL H 118 1 O THR H 117 N GLU H 10 SHEET 3 AA1 6 ALA H 92 ARG H 98 -1 N PHE H 94 O THR H 114 SHEET 4 AA1 6 TYR H 109 GLY H 111 -1 O TYR H 109 N ARG H 98 SHEET 5 AA1 6 GLN H 3 GLN H 6 1 N LEU H 4 O TRP H 110 SHEET 6 AA1 6 CYS H 22 ASP H 23 -1 O ASP H 23 N ALA H 5 SHEET 1 AA2 6 GLU H 10 ARG H 12 0 SHEET 2 AA2 6 THR H 114 VAL H 118 1 O THR H 117 N GLU H 10 SHEET 3 AA2 6 ALA H 92 ARG H 98 -1 N PHE H 94 O THR H 114 SHEET 4 AA2 6 ALA H 33 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA2 6 LEU H 45 ASN H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 PRO H 58 TYR H 60 -1 O THR H 59 N TRP H 50 SHEET 1 AA3 3 VAL H 18 VAL H 20 0 SHEET 2 AA3 3 ALA H 79 ILE H 83 -1 O LEU H 81 N VAL H 20 SHEET 3 AA3 3 PHE H 68 LEU H 72 -1 N VAL H 69 O GLN H 82 SHEET 1 AA4 4 MET L 4 SER L 7 0 SHEET 2 AA4 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA4 4 GLU L 72 ILE L 77 -1 O LEU L 75 N LEU L 21 SHEET 4 AA4 4 PHE L 64 SER L 69 -1 N SER L 65 O THR L 76 SHEET 1 AA5 5 SER L 10 VAL L 13 0 SHEET 2 AA5 5 THR L 104 ILE L 108 1 O GLU L 107 N VAL L 13 SHEET 3 AA5 5 VAL L 87 GLN L 92 -1 N TYR L 88 O THR L 104 SHEET 4 AA5 5 LEU L 35 GLN L 40 -1 N GLN L 40 O VAL L 87 SHEET 5 AA5 5 ARG L 47 TYR L 51 -1 O ILE L 50 N TRP L 37 SHEET 1 AA6 5 LYS R 356 ILE R 358 0 SHEET 2 AA6 5 VAL R 395 ARG R 403 -1 O ALA R 397 N LYS R 356 SHEET 3 AA6 5 PRO R 507 PHE R 515 -1 O TYR R 508 N ILE R 402 SHEET 4 AA6 5 GLY R 431 ASN R 437 -1 N ILE R 434 O VAL R 511 SHEET 5 AA6 5 THR R 376 TYR R 380 -1 N LYS R 378 O VAL R 433 SHEET 1 AA7 2 LEU R 452 ARG R 454 0 SHEET 2 AA7 2 LEU R 492 SER R 494 -1 O ARG R 493 N TYR R 453 SHEET 1 AA8 2 TYR R 473 GLN R 474 0 SHEET 2 AA8 2 CYS R 488 TYR R 489 -1 O TYR R 489 N TYR R 473 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 2 CYS L 23 CYS L 90 1555 1555 2.03 SSBOND 3 CYS R 336 CYS R 361 1555 1555 2.03 SSBOND 4 CYS R 379 CYS R 432 1555 1555 2.03 SSBOND 5 CYS R 391 CYS R 525 1555 1555 2.03 SSBOND 6 CYS R 480 CYS R 488 1555 1555 2.03 LINK ND2 ASN R 343 C1 NAG C 1 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 CISPEP 1 SER L 7 PRO L 8 0 -2.33 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