HEADER IMMUNE SYSTEM/VIRAL PROTEIN 22-JAN-22 7WP2 TITLE CRYO-EM STRUCTURE OF SARS-COV-2 C.1.2 S6P TRIMER IN COMPLEX WITH TITLE 2 NEUTRALIZING ANTIBODY VACW-209 (LOCAL REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACW-209 LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VACW-209 HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: F; COMPND 12 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 15 2; SOURCE 16 ORGANISM_TAXID: 2697049; SOURCE 17 GENE: S, 2; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, C.1.2 VARIANT, SPIKE, NEUTRALIZING ANTIBODY, CRYO-EM, KEYWDS 2 VIRAL PROTEIN, IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Q.ZHENG,H.SUN,B.JU,Z.ZHANG,S.LI,N.XIA REVDAT 2 23-OCT-24 7WP2 1 REMARK REVDAT 1 20-JUL-22 7WP2 0 JRNL AUTH B.JU,Q.ZHENG,H.GUO,Q.FAN,T.LI,S.SONG,H.SUN,S.SHEN,X.ZHOU, JRNL AUTH 2 W.XUE,L.CUI,B.ZHOU,S.LI,N.XIA,Z.ZHANG JRNL TITL IMMUNE ESCAPE BY SARS-COV-2 OMICRON VARIANT AND STRUCTURAL JRNL TITL 2 BASIS OF ITS EFFECTIVE NEUTRALIZATION BY A BROAD JRNL TITL 3 NEUTRALIZING HUMAN ANTIBODY VACW-209. JRNL REF CELL RES. V. 32 491 2022 JRNL REFN ISSN 1001-0602 JRNL PMID 35260792 JRNL DOI 10.1038/S41422-022-00638-6 REMARK 2 REMARK 2 RESOLUTION. 3.52 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) : 3.520 REMARK 3 NUMBER OF PARTICLES : 225574 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 7WP2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300027169. 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 C.1.2 S6P TRIMER IN REMARK 245 COMPLEX WITH NEUTRALIZING REMARK 245 ANTIBODY VACW-209 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) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 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: L, H, F, 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 GLN L 1 REMARK 465 SER L 2 REMARK 465 THR F 333 REMARK 465 ASN F 334 REMARK 465 LEU F 335 REMARK 465 CYS F 336 REMARK 465 HIS F 519 REMARK 465 ALA F 520 REMARK 465 PRO F 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 ASN L 53 -12.70 71.85 REMARK 500 SER L 54 -17.09 -143.99 REMARK 500 PRO L 57 -179.90 -69.85 REMARK 500 ARG H 16 -167.25 -126.49 REMARK 500 SER H 52 -164.09 -79.28 REMARK 500 ALA H 92 -169.04 -164.47 REMARK 500 TYR H 103 51.87 -141.68 REMARK 500 ASP H 113 46.66 -142.22 REMARK 500 TYR F 380 -61.10 -99.02 REMARK 500 LEU F 387 49.45 -85.97 REMARK 500 THR F 500 30.49 -94.96 REMARK 500 SER F 514 119.42 -160.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32667 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SARS-COV-2 C.1.2 S6P TRIMER IN COMPLEX WITH REMARK 900 NEUTRALIZING ANTIBODY VACW-209 (LOCAL REFINEMENT) DBREF1 7WP2 L 1 111 UNP A0A5C2GQT9_HUMAN DBREF2 7WP2 L A0A5C2GQT9 1 111 DBREF 7WP2 H 1 131 PDB 7WP2 7WP2 1 131 DBREF 7WP2 F 333 521 UNP P0DTC2 SPIKE_SARS2 333 521 SEQADV 7WP2 HIS F 449 UNP P0DTC2 TYR 449 VARIANT SEQADV 7WP2 LYS F 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7WP2 TYR F 501 UNP P0DTC2 ASN 501 VARIANT SEQRES 1 L 111 GLN SER VAL LEU THR GLN PRO PRO SER VAL SER GLY ALA SEQRES 2 L 111 PRO GLY GLN ARG VAL THR ILE SER CYS THR GLY SER SER SEQRES 3 L 111 SER ASN ILE GLY ALA GLY TYR ASP VAL HIS TRP TYR GLN SEQRES 4 L 111 GLN LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR GLY SEQRES 5 L 111 ASN SER ASN ARG PRO SER GLY VAL PRO ASP ARG PHE SER SEQRES 6 L 111 GLY SER LYS SER GLY THR SER ALA SER LEU ALA ILE THR SEQRES 7 L 111 GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS GLN SEQRES 8 L 111 SER TYR ASP SER SER LEU SER GLY TRP VAL PHE GLY GLY SEQRES 9 L 111 GLY THR LYS LEU THR VAL LEU SEQRES 1 H 131 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 H 131 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 131 PHE THR PHE SER SER ILE ALA MET HIS TRP VAL ARG GLN SEQRES 4 H 131 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL MET SER SEQRES 5 H 131 PHE ASP GLY SER ILE LYS TYR TYR GLY ASP SER VAL LYS SEQRES 6 H 131 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS SER THR SEQRES 7 H 131 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 131 ALA VAL TYR TYR CYS ALA ARG GLY VAL GLN GLY TYR TYR SEQRES 9 H 131 ASP ARG SER GLY TYR TYR ASN LEU ASP TYR ASN TYR GLY SEQRES 10 H 131 MET ASP VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SEQRES 11 H 131 SER SEQRES 1 F 189 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 F 189 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 F 189 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 F 189 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 F 189 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 F 189 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 F 189 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 F 189 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 F 189 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN HIS SEQRES 10 F 189 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 F 189 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 F 189 GLY SER THR PRO CYS ASN GLY VAL LYS GLY PHE ASN CYS SEQRES 13 F 189 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR TYR SEQRES 14 F 189 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 F 189 PHE GLU LEU LEU HIS ALA PRO HET NAG A 1 14 HET NAG A 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 THR H 28 ILE H 32 5 5 HELIX 2 AA2 ASP F 405 ILE F 410 5 6 SHEET 1 AA1 2 SER L 9 GLY L 12 0 SHEET 2 AA1 2 LYS L 107 VAL L 110 1 O THR L 109 N VAL L 10 SHEET 1 AA2 2 ARG L 17 VAL L 18 0 SHEET 2 AA2 2 ILE L 77 THR L 78 -1 O ILE L 77 N VAL L 18 SHEET 1 AA3 3 CYS L 22 THR L 23 0 SHEET 2 AA3 3 SER L 72 SER L 74 -1 O ALA L 73 N CYS L 22 SHEET 3 AA3 3 SER L 67 SER L 69 -1 N SER L 67 O SER L 74 SHEET 1 AA4 4 LYS L 47 ILE L 50 0 SHEET 2 AA4 4 HIS L 36 GLN L 40 -1 N TRP L 37 O LEU L 49 SHEET 3 AA4 4 ASP L 87 ASP L 94 -1 O ASP L 87 N GLN L 40 SHEET 4 AA4 4 GLY L 99 PHE L 102 -1 O GLY L 99 N ASP L 94 SHEET 1 AA5 4 GLU H 6 SER H 7 0 SHEET 2 AA5 4 LEU H 18 ALA H 23 -1 O SER H 21 N SER H 7 SHEET 3 AA5 4 THR H 78 MET H 83 -1 O LEU H 81 N LEU H 20 SHEET 4 AA5 4 PHE H 68 ASP H 73 -1 N THR H 69 O GLN H 82 SHEET 1 AA6 2 GLY H 10 VAL H 12 0 SHEET 2 AA6 2 VAL H 127 VAL H 129 1 O THR H 128 N VAL H 12 SHEET 1 AA7 4 LYS H 58 TYR H 60 0 SHEET 2 AA7 4 LEU H 45 MET H 51 -1 N VAL H 50 O TYR H 59 SHEET 3 AA7 4 MET H 34 GLN H 39 -1 N MET H 34 O MET H 51 SHEET 4 AA7 4 VAL H 93 ARG H 98 -1 O TYR H 95 N VAL H 37 SHEET 1 AA8 5 ASN F 354 ILE F 358 0 SHEET 2 AA8 5 VAL F 395 ARG F 403 -1 O VAL F 395 N ILE F 358 SHEET 3 AA8 5 PRO F 507 PHE F 515 -1 O TYR F 508 N ILE F 402 SHEET 4 AA8 5 CYS F 432 ASN F 437 -1 N ILE F 434 O VAL F 511 SHEET 5 AA8 5 THR F 376 CYS F 379 -1 N LYS F 378 O VAL F 433 SHEET 1 AA9 2 LEU F 452 ARG F 454 0 SHEET 2 AA9 2 LEU F 492 SER F 494 -1 O GLN F 493 N TYR F 453 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 2 CYS F 379 CYS F 432 1555 1555 2.03 LINK ND2 ASN F 343 C1 NAG A 1 1555 1555 1.44 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 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