HEADER VIRAL PROTEIN/IMMUNE SYSTEM 08-NOV-22 8HED TITLE LOCAL REFINEMENT OF THE SARS-COV-2 SPIKE TRIMER IN COMPLEX WITH RMAB TITLE 2 9H1 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: RBD; COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RABBIT ANTIBODY 9H1 LIGHT CHAIN; COMPND 9 CHAIN: F; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RABBIT ANTIBODY 9H1 HEAVY CHAIN; COMPND 13 CHAIN: G; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 11 ORGANISM_TAXID: 9986; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 17 ORGANISM_TAXID: 9986; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.GUO,Y.GAO,Y.LU,H.YANG,X.JI REVDAT 1 26-APR-23 8HED 0 JRNL AUTH X.CHU,X.DING,Y.YANG,Y.LU,T.LI,Y.GAO,L.ZHENG,H.XIAO,T.YANG, JRNL AUTH 2 H.CHENG,H.HUANG,Y.LIU,Y.LOU,C.WU,Y.CHEN,H.YANG,X.JI,H.GUO JRNL TITL MECHANISM OF AN RBM-TARGETED RABBIT MONOCLONAL ANTIBODY 9H1 JRNL TITL 2 NEUTRALIZING SARS-COV-2. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 660 43 2023 JRNL REFN ESSN 1090-2104 JRNL PMID 37062240 JRNL DOI 10.1016/J.BBRC.2023.04.002 REMARK 2 REMARK 2 RESOLUTION. 3.59 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) : 3.590 REMARK 3 NUMBER OF PARTICLES : 111153 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 8HED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033180. 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 WT SPIKE REMARK 245 GLYCOPROTEIN RBD COMPLEX WITH REMARK 245 9H1 FABS; SARS-COV-2 SPIKE REMARK 245 GLYCOPROTEIN RBD; 9H1 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 : 7.40 REMARK 245 SAMPLE DETAILS : SARS-COV-2 WT SPIKE PROTEIN REMARK 245 RECEPTOR-BINDING DOMAIN; FAB FRAGMENT GENERATED BY PROTEOLYTIC REMARK 245 CLEAVAGE OF IGG ANTIBODY 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) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2800.00 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 : SPOT SCAN 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: B, F, G, O 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 HIS B 519 CG ND1 CD2 CE1 NE2 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 PHE B 338 -8.22 66.67 REMARK 500 ASP B 428 36.63 -98.46 REMARK 500 ASN B 481 11.87 59.84 REMARK 500 LYS B 528 -149.24 58.08 REMARK 500 TYR F 29 -122.81 59.52 REMARK 500 ALA F 50 -4.75 68.70 REMARK 500 ALA F 83 -168.41 -165.16 REMARK 500 PHE F 91 63.03 -152.62 REMARK 500 SER F 92 -143.42 52.75 REMARK 500 CYS F 93 -91.96 -141.58 REMARK 500 ASP F 97 52.76 -140.36 REMARK 500 CYS F 98 -87.93 53.10 REMARK 500 SER G 29 7.17 -64.13 REMARK 500 LYS G 63 -4.61 67.52 REMARK 500 THR G 73 29.76 -141.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34688 RELATED DB: EMDB REMARK 900 TO BE PUBLISHED DBREF 8HED B 331 530 UNP P0DTC2 SPIKE_SARS2 331 530 DBREF 8HED F 1 110 PDB 8HED 8HED 1 110 DBREF 8HED G 1 117 PDB 8HED 8HED 1 117 SEQRES 1 B 200 ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN SEQRES 2 B 200 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 3 B 200 ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR SEQRES 4 B 200 ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SEQRES 5 B 200 SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL SEQRES 6 B 200 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 7 B 200 GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR SEQRES 8 B 200 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 9 B 200 ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY SEQRES 10 B 200 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 11 B 200 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 12 B 200 GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE SEQRES 13 B 200 ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO SEQRES 14 B 200 THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL SEQRES 15 B 200 LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS SEQRES 16 B 200 GLY PRO LYS LYS SER SEQRES 1 F 110 GLN VAL LEU THR GLN THR PRO SER SER VAL SER ALA ALA SEQRES 2 F 110 VAL GLY GLY THR VAL THR ILE ASN CYS GLN ALA SER GLU SEQRES 3 F 110 ASP ILE TYR ASP ASN LEU VAL TRP TYR GLN GLN LYS PRO SEQRES 4 F 110 GLY GLN PRO PRO LYS LEU LEU ILE TYR ASP ALA SER THR SEQRES 5 F 110 LEU ALA PHE GLY VAL SER SER ARG PHE ARG GLY SER GLY SEQRES 6 F 110 SER GLY THR HIS PHE THR LEU THR MET ARG ASP VAL GLN SEQRES 7 F 110 CYS ASP ASP ALA ALA THR TYR TYR CYS GLN GLY GLU PHE SEQRES 8 F 110 SER CYS SER SER GLY ASP CYS THR ALA PHE GLY GLY GLY SEQRES 9 F 110 THR GLU VAL VAL VAL LYS SEQRES 1 G 117 GLN SER VAL GLU GLU SER GLY GLY ARG LEU VAL THR PRO SEQRES 2 G 117 GLY THR PRO LEU THR LEU THR CYS THR VAL SER GLY PHE SEQRES 3 G 117 SER LEU SER ARG TYR ALA MET SER TRP VAL ARG GLN ALA SEQRES 4 G 117 PRO GLY LYS GLY LEU GLU TRP ILE GLY ILE ILE VAL ASP SEQRES 5 G 117 SER GLY HIS THR ALA TYR ALA SER TRP ALA LYS GLY ARG SEQRES 6 G 117 PHE THR ILE SER ARG THR SER THR THR VAL ASP LEU LYS SEQRES 7 G 117 MET THR SER LEU THR THR GLU ASP THR ALA THR TYR PHE SEQRES 8 G 117 CYS ALA ARG GLU THR GLY GLY GLY ALA PHE TYR VAL PHE SEQRES 9 G 117 GLU PHE TRP GLY PRO GLY THR VAL VAL THR VAL SER SER HET NAG O 1 14 HET NAG O 2 14 HET NAG B 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 3(C8 H15 N O6) HELIX 1 AA1 PHE B 338 ASN B 343 1 6 HELIX 2 AA2 SER B 349 TRP B 353 5 5 HELIX 3 AA3 TYR B 365 SER B 371 1 7 HELIX 4 AA4 ASP B 405 ILE B 410 5 6 HELIX 5 AA5 LYS B 417 ASN B 422 1 6 HELIX 6 AA6 SER B 438 SER B 443 1 6 HELIX 7 AA7 GLY B 502 TYR B 505 5 4 HELIX 8 AA8 GLN F 78 ALA F 82 5 5 HELIX 9 AA9 SER G 27 TYR G 31 5 5 SHEET 1 AA1 5 ASN B 354 ILE B 358 0 SHEET 2 AA1 5 ASN B 394 ARG B 403 -1 O VAL B 395 N ILE B 358 SHEET 3 AA1 5 PRO B 507 GLU B 516 -1 O SER B 514 N TYR B 396 SHEET 4 AA1 5 GLY B 431 ASN B 437 -1 N ILE B 434 O VAL B 511 SHEET 5 AA1 5 THR B 376 TYR B 380 -1 N TYR B 380 O GLY B 431 SHEET 1 AA2 2 LEU B 452 ARG B 454 0 SHEET 2 AA2 2 LEU B 492 SER B 494 -1 O GLN B 493 N TYR B 453 SHEET 1 AA3 2 TYR B 473 GLN B 474 0 SHEET 2 AA3 2 CYS B 488 TYR B 489 -1 O TYR B 489 N TYR B 473 SHEET 1 AA4 4 LEU F 3 THR F 6 0 SHEET 2 AA4 4 VAL F 18 ALA F 24 -1 O ASN F 21 N THR F 6 SHEET 3 AA4 4 HIS F 69 MET F 74 -1 O LEU F 72 N ILE F 20 SHEET 4 AA4 4 PHE F 61 SER F 66 -1 N ARG F 62 O THR F 73 SHEET 1 AA5 6 SER F 9 ALA F 13 0 SHEET 2 AA5 6 THR F 105 LYS F 110 1 O GLU F 106 N VAL F 10 SHEET 3 AA5 6 THR F 84 GLU F 90 -1 N TYR F 85 O THR F 105 SHEET 4 AA5 6 LEU F 32 GLN F 37 -1 N VAL F 33 O GLN F 88 SHEET 5 AA5 6 LYS F 44 TYR F 48 -1 O ILE F 47 N TRP F 34 SHEET 6 AA5 6 THR F 52 LEU F 53 -1 O THR F 52 N TYR F 48 SHEET 1 AA6 4 SER F 9 ALA F 13 0 SHEET 2 AA6 4 THR F 105 LYS F 110 1 O GLU F 106 N VAL F 10 SHEET 3 AA6 4 THR F 84 GLU F 90 -1 N TYR F 85 O THR F 105 SHEET 4 AA6 4 THR F 99 PHE F 101 -1 O ALA F 100 N GLY F 89 SHEET 1 AA7 4 GLU G 4 SER G 6 0 SHEET 2 AA7 4 THR G 18 THR G 22 -1 O THR G 22 N GLU G 4 SHEET 3 AA7 4 THR G 74 MET G 79 -1 O LEU G 77 N LEU G 19 SHEET 4 AA7 4 PHE G 66 SER G 69 -1 N THR G 67 O LYS G 78 SHEET 1 AA8 6 LEU G 10 VAL G 11 0 SHEET 2 AA8 6 THR G 111 VAL G 115 1 O THR G 114 N VAL G 11 SHEET 3 AA8 6 ALA G 88 ARG G 94 -1 N TYR G 90 O THR G 111 SHEET 4 AA8 6 MET G 33 GLN G 38 -1 N SER G 34 O ALA G 93 SHEET 5 AA8 6 LEU G 44 ILE G 50 -1 O GLU G 45 N ARG G 37 SHEET 6 AA8 6 THR G 56 TYR G 58 -1 O ALA G 57 N ILE G 49 SHEET 1 AA9 4 LEU G 10 VAL G 11 0 SHEET 2 AA9 4 THR G 111 VAL G 115 1 O THR G 114 N VAL G 11 SHEET 3 AA9 4 ALA G 88 ARG G 94 -1 N TYR G 90 O THR G 111 SHEET 4 AA9 4 PHE G 106 TRP G 107 -1 O PHE G 106 N ARG G 94 SSBOND 1 CYS B 336 CYS B 361 1555 1555 2.03 SSBOND 2 CYS B 379 CYS B 432 1555 1555 2.04 SSBOND 3 CYS B 391 CYS B 525 1555 1555 2.04 SSBOND 4 CYS B 480 CYS B 488 1555 1555 2.03 SSBOND 5 CYS F 22 CYS F 87 1555 1555 2.04 SSBOND 6 CYS G 21 CYS G 92 1555 1555 2.03 LINK ND2 ASN B 331 C1 NAG B 601 1555 1555 1.45 LINK ND2 ASN B 343 C1 NAG O 1 1555 1555 1.44 LINK O4 NAG O 1 C1 NAG O 2 1555 1555 1.45 CISPEP 1 THR F 6 PRO F 7 0 -3.95 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