HEADER VIRAL PROTEIN 14-APR-22 7XIZ TITLE SARS-COV-2 OMICRON BA.3 VARIANT SPIKE (LOCAL) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, OMICRON, BA.2, SPIKE, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.WANG,L.WANG REVDAT 2 31-AUG-22 7XIZ 1 JRNL REVDAT 1 13-JUL-22 7XIZ 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. 3.74 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) : 3.740 REMARK 3 NUMBER OF PARTICLES : 185916 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 7XIZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-APR-22. REMARK 100 THE DEPOSITION ID IS D_1300028933. 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 OMICRON BA.2 SPIKE REMARK 245 PROTEIN 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 BASE (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 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 : DARK 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO B 384 CG PRO B 384 CD -0.542 REMARK 500 PRO B 384 CD PRO B 384 N 0.100 REMARK 500 REMARK 500 REMARK: NULL 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 PRO B 384 CA - N - CD ANGL. DEV. = -15.4 DEGREES REMARK 500 PRO B 384 CA - CB - CG ANGL. DEV. = -17.5 DEGREES REMARK 500 PRO B 384 N - CD - CG ANGL. DEV. = -24.6 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 ALA B 344 -167.88 52.16 REMARK 500 THR B 345 -52.92 -122.39 REMARK 500 ALA B 348 -179.76 -177.86 REMARK 500 ALA B 372 86.42 -155.15 REMARK 500 PHE B 377 -15.86 70.86 REMARK 500 LYS B 378 60.70 25.78 REMARK 500 ASN B 388 43.56 -85.75 REMARK 500 ARG B 403 -76.83 -63.56 REMARK 500 ASN B 422 -157.68 -147.96 REMARK 500 LYS B 444 163.82 66.62 REMARK 500 SER B 446 19.60 55.65 REMARK 500 LEU B 455 -79.65 60.45 REMARK 500 ALA B 475 -3.20 69.92 REMARK 500 LYS B 478 77.37 52.41 REMARK 500 PRO B 491 -168.72 -74.34 REMARK 500 LEU B 492 61.28 62.63 REMARK 500 VAL B 503 -53.82 62.27 REMARK 500 LEU B 518 -112.86 57.78 REMARK 500 HIS B 519 -140.74 47.70 REMARK 500 ASN B 536 21.12 -143.16 REMARK 500 ASP B 568 -165.58 -124.88 REMARK 500 THR B 581 -5.80 66.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33213 RELATED DB: EMDB REMARK 900 SARS-COV-2 OMICRON BA.3 VARIANT SPIKE (LOCAL) DBREF 7XIZ B 323 589 UNP P0DTC2 SPIKE_SARS2 323 589 SEQADV 7XIZ ASP B 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7XIZ PHE B 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7XIZ PRO B 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7XIZ PHE B 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7XIZ ASN B 405 UNP P0DTC2 ASP 405 VARIANT SEQADV 7XIZ ASN B 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7XIZ LYS B 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7XIZ SER B 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7XIZ ASN B 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7XIZ LYS B 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7XIZ ALA B 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7XIZ ARG B 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7XIZ ARG B 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7XIZ TYR B 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7XIZ HIS B 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 B 267 THR GLU SER ILE VAL ARG PHE PRO ASN ILE THR ASN LEU SEQRES 2 B 267 CYS PRO PHE ASP GLU VAL PHE ASN ALA THR ARG PHE ALA SEQRES 3 B 267 SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER ASN CYS SEQRES 4 B 267 VAL ALA ASP TYR SER VAL LEU TYR ASN PHE ALA PRO PHE SEQRES 5 B 267 PHE THR PHE LYS CYS TYR GLY VAL SER PRO THR LYS LEU SEQRES 6 B 267 ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SER PHE SEQRES 7 B 267 VAL ILE ARG GLY ASN GLU VAL ARG GLN ILE ALA PRO GLY SEQRES 8 B 267 GLN THR GLY ASN ILE ALA ASP TYR ASN TYR LYS LEU PRO SEQRES 9 B 267 ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SER ASN SEQRES 10 B 267 LYS LEU ASP SER LYS VAL SER GLY ASN TYR ASN TYR LEU SEQRES 11 B 267 TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO PHE GLU SEQRES 12 B 267 ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY ASN LYS SEQRES 13 B 267 PRO CYS ASN GLY VAL ALA GLY PHE ASN CYS TYR PHE PRO SEQRES 14 B 267 LEU ARG SER TYR GLY PHE ARG PRO THR TYR GLY VAL GLY SEQRES 15 B 267 HIS GLN PRO TYR ARG VAL VAL VAL LEU SER PHE GLU LEU SEQRES 16 B 267 LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS LYS SER SEQRES 17 B 267 THR ASN LEU VAL LYS ASN LYS CYS VAL ASN PHE ASN PHE SEQRES 18 B 267 ASN GLY LEU THR GLY THR GLY VAL LEU THR GLU SER ASN SEQRES 19 B 267 LYS LYS PHE LEU PRO PHE GLN GLN PHE GLY ARG ASP ILE SEQRES 20 B 267 ALA ASP THR THR ASP ALA VAL ARG ASP PRO GLN THR LEU SEQRES 21 B 267 GLU ILE LEU ASP ILE THR PRO HET NAG B 601 14 HET NAG B 602 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 2 NAG 2(C8 H15 N O6) HELIX 1 AA1 PRO B 337 ASN B 343 1 7 HELIX 2 AA2 LYS B 386 LEU B 390 5 5 SHEET 1 AA1 4 ASN B 354 ILE B 358 0 SHEET 2 AA1 4 VAL B 395 ILE B 402 -1 O VAL B 395 N ILE B 358 SHEET 3 AA1 4 TYR B 508 SER B 514 -1 O SER B 514 N TYR B 396 SHEET 4 AA1 4 GLY B 431 ASN B 437 -1 N ILE B 434 O VAL B 511 SHEET 1 AA2 5 CYS B 538 VAL B 539 0 SHEET 2 AA2 5 GLY B 550 GLU B 554 -1 O GLY B 550 N VAL B 539 SHEET 3 AA2 5 ILE B 584 THR B 588 -1 O THR B 588 N VAL B 551 SHEET 4 AA2 5 THR B 573 ARG B 577 -1 N ASP B 574 O ILE B 587 SHEET 5 AA2 5 PHE B 565 ARG B 567 -1 N GLY B 566 O ALA B 575 SHEET 1 AA3 2 ASN B 542 PHE B 543 0 SHEET 2 AA3 2 LEU B 546 THR B 547 -1 O LEU B 546 N PHE B 543 SSBOND 1 CYS B 336 CYS B 361 1555 1555 2.04 SSBOND 2 CYS B 379 CYS B 432 1555 1555 2.03 SSBOND 3 CYS B 480 CYS B 488 1555 1555 2.03 LINK ND2 ASN B 331 C1 NAG B 601 1555 1555 1.45 LINK ND2 ASN B 343 C1 NAG B 602 1555 1555 1.44 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