HEADER VIRAL PROTEIN 27-JAN-22 7WRL TITLE LOCAL STRUCTURE OF BD55-1239 FAB AND SARS-COV2 OMICRON RBD COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: BD55-1239H; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BD55-1239L; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: R; COMPND 12 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, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Z.Z.ZHANG,J.J.XIAO REVDAT 3 31-AUG-22 7WRL 1 JRNL REVDAT 2 13-JUL-22 7WRL 1 JRNL REVDAT 1 22-JUN-22 7WRL 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. 3.51 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) : 3.510 REMARK 3 NUMBER OF PARTICLES : 3300 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 7WRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300027300. 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 STRUCTURE OF BD55-1239 REMARK 245 FAB AND SARS-COV2 OMICRON RBD REMARK 245 COMPLEX 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 : OTHER 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: A, B, R 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 R 516 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 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 -166.44 -78.74 REMARK 500 TYR A 105 -167.42 -164.68 REMARK 500 SER B 26 48.20 -86.16 REMARK 500 SER B 27 -11.89 -145.44 REMARK 500 ASP B 28 -62.61 -95.83 REMARK 500 ASP B 52 -72.98 -85.17 REMARK 500 VAL B 53 -51.19 -134.49 REMARK 500 ASN B 55 -168.84 -79.50 REMARK 500 SER B 92 147.58 -171.25 REMARK 500 SER B 96 20.12 -144.11 REMARK 500 ASN B 97 -3.25 70.37 REMARK 500 PRO R 337 54.13 -90.65 REMARK 500 ASN R 343 55.27 -93.49 REMARK 500 PHE R 377 49.82 -141.47 REMARK 500 ALA R 411 144.66 -172.91 REMARK 500 ASP R 428 32.87 -92.75 REMARK 500 ASN R 477 -177.55 -171.35 REMARK 500 LYS R 478 78.06 53.43 REMARK 500 PRO R 479 6.49 -64.42 REMARK 500 PHE R 486 -10.72 71.78 REMARK 500 ASN R 487 -39.28 -133.60 REMARK 500 THR R 500 56.48 -95.21 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 LYS A 13 PRO A 14 -145.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32732 RELATED DB: EMDB REMARK 900 LOCAL STRUCTURE OF BD55-1239 FAB AND SARS-COV2 OMICRON RBD COMPLEX DBREF 7WRL A 1 127 PDB 7WRL 7WRL 1 127 DBREF 7WRL B 2 106 PDB 7WRL 7WRL 2 106 DBREF 7WRL R 334 526 UNP P0DTC2 SPIKE_SARS2 334 526 SEQADV 7WRL ASP R 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7WRL LEU R 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7WRL PRO R 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7WRL PHE R 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7WRL ASN R 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7WRL LYS R 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7WRL SER R 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7WRL ASN R 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7WRL LYS R 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7WRL ALA R 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7WRL ARG R 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7WRL SER R 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7WRL ARG R 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7WRL TYR R 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7WRL HIS R 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 127 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 A 127 PRO GLY SER SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 A 127 ASP ILE TYR SER THR TYR ALA SER SER TRP VAL ARG GLN SEQRES 4 A 127 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ARG ILE ILE SEQRES 5 A 127 PRO VAL SER GLY THR VAL ASN TYR ALA ASP ASN PHE GLN SEQRES 6 A 127 GLY ARG VAL THR ILE THR ALA ASP LYS SER THR SER THR SEQRES 7 A 127 ALA TYR MET GLU LEU ARG SER LEU THR SER GLU ASP THR SEQRES 8 A 127 ALA VAL TYR TYR CYS ALA ARG ASP VAL ALA ARG GLY GLY SEQRES 9 A 127 TYR SER GLY THR ASP PHE PHE ASP TYR TYR TYR GLY MET SEQRES 10 A 127 ASP VAL TRP GLY GLN GLY THR THR VAL THR SEQRES 1 B 105 SER ALA LEU THR GLN PRO ALA SER VAL SER GLY SER PRO SEQRES 2 B 105 GLY GLN SER ILE THR ILE SER CYS THR GLY THR SER SER SEQRES 3 B 105 ASP VAL GLY GLY TYR ASN TYR VAL SER TRP TYR GLN GLN SEQRES 4 B 105 HIS PRO ASP LYS ALA PRO LYS LEU LEU ILE TYR ASP VAL SEQRES 5 B 105 ASN ASN ARG PRO SER GLY VAL SER THR ARG PHE SER GLY SEQRES 6 B 105 SER LYS SER GLY ASN THR ALA SER LEU THR ILE SER ARG SEQRES 7 B 105 LEU GLN THR ASP ASP GLU ALA ASP TYR SER CYS SER SER SEQRES 8 B 105 TYR THR SER SER ASN THR TRP VAL PHE GLY GLY GLY THR SEQRES 9 B 105 LYS SEQRES 1 R 193 ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA THR ARG SEQRES 2 R 193 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 R 193 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN LEU ALA SEQRES 4 R 193 PRO PHE PHE THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 R 193 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 R 193 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 R 193 PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR LYS SEQRES 8 R 193 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 R 193 SER ASN LYS LEU ASP SER LYS VAL SER GLY ASN TYR ASN SEQRES 10 R 193 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 R 193 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 R 193 ASN LYS PRO CYS ASN GLY VAL ALA GLY PHE ASN CYS TYR SEQRES 13 R 193 PHE PRO LEU ARG SER TYR SER PHE ARG PRO THR TYR GLY SEQRES 14 R 193 VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 R 193 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY HELIX 1 AA1 ASP A 62 GLN A 65 5 4 HELIX 2 AA2 THR A 87 THR A 91 5 5 HELIX 3 AA3 PRO R 384 LEU R 390 5 7 HELIX 4 AA4 ARG R 498 GLY R 502 5 5 SHEET 1 AA1 2 LEU A 4 GLN A 6 0 SHEET 2 AA1 2 CYS A 22 ALA A 24 -1 O LYS A 23 N VAL A 5 SHEET 1 AA2 3 SER A 17 LYS A 19 0 SHEET 2 AA2 3 GLU A 82 ARG A 84 -1 O LEU A 83 N VAL A 18 SHEET 3 AA2 3 VAL A 68 THR A 69 -1 N THR A 69 O GLU A 82 SHEET 1 AA3 3 SER A 34 GLN A 39 0 SHEET 2 AA3 3 LEU A 45 ILE A 51 -1 O MET A 48 N TRP A 36 SHEET 3 AA3 3 VAL A 58 TYR A 60 -1 O ASN A 59 N ARG A 50 SHEET 1 AA4 2 ALA A 72 ASP A 73 0 SHEET 2 AA4 2 THR A 78 ALA A 79 -1 O THR A 78 N ASP A 73 SHEET 1 AA5 2 ALA A 92 VAL A 93 0 SHEET 2 AA5 2 THR A 125 VAL A 126 -1 O VAL A 126 N ALA A 92 SHEET 1 AA6 2 ALA A 97 ALA A 101 0 SHEET 2 AA6 2 TYR A 113 TRP A 120 -1 O VAL A 119 N ARG A 98 SHEET 1 AA7 3 ILE B 18 CYS B 22 0 SHEET 2 AA7 3 ALA B 73 ILE B 77 -1 O LEU B 75 N ILE B 20 SHEET 3 AA7 3 SER B 65 SER B 67 -1 N SER B 67 O SER B 74 SHEET 1 AA8 3 PRO B 46 ILE B 50 0 SHEET 2 AA8 3 SER B 36 GLN B 40 -1 N GLN B 39 O LYS B 47 SHEET 3 AA8 3 ASP B 87 SER B 91 -1 O SER B 89 N TYR B 38 SHEET 1 AA9 5 LYS R 356 ILE R 358 0 SHEET 2 AA9 5 VAL R 395 SER R 399 -1 O VAL R 395 N ILE R 358 SHEET 3 AA9 5 VAL R 511 SER R 514 -1 O VAL R 512 N ASP R 398 SHEET 4 AA9 5 CYS R 432 ALA R 435 -1 N CYS R 432 O LEU R 513 SHEET 5 AA9 5 THR R 376 CYS R 379 -1 N LYS R 378 O VAL R 433 SHEET 1 AB1 2 CYS R 361 VAL R 362 0 SHEET 2 AB1 2 VAL R 524 CYS R 525 1 O CYS R 525 N CYS R 361 SHEET 1 AB2 2 LEU R 452 ARG R 454 0 SHEET 2 AB2 2 LEU R 492 SER R 494 -1 O ARG R 493 N TYR R 453 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.03 SSBOND 2 CYS R 379 CYS R 432 1555 1555 2.03 SSBOND 3 CYS R 391 CYS R 525 1555 1555 2.03 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