HEADER VIRAL PROTEIN/IMMUNE SYSTEM 29-SEP-20 7K9I TITLE SARS-COV-2 SPIKE RBD IN COMPLEX WITH NEUTRALIZING FAB 2B04 (LOCAL TITLE 2 REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN (UNP RESIDUES 333-527); COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN,SPIKE GLYCOPROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 2B04 HEAVY CHAIN; COMPND 9 CHAIN: H; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 2B04 LIGHT CHAIN; COMPND 13 CHAIN: L; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 21 ORGANISM_COMMON: MOUSE; SOURCE 22 ORGANISM_TAXID: 10090; SOURCE 23 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 24 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 26 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS COMPLEX, NEUTRALIZING ANTIBODY, ACE2-COMPETITIVE, RECEPTOR-BINDING KEYWDS 2 DOMAIN, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF KEYWDS 3 INFECTIOUS DISEASES, CSGID, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR J.M.ERRICO,D.H.FREMONT,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS AUTHOR 2 DISEASES (CSGID) REVDAT 3 10-NOV-21 7K9I 1 JRNL REVDAT 2 03-NOV-21 7K9I 1 JRNL REVDAT 1 29-SEP-21 7K9I 0 JRNL AUTH J.M.ERRICO,H.ZHAO,R.E.CHEN,Z.LIU,J.B.CASE,M.MA,A.J.SCHMITZ, JRNL AUTH 2 M.J.RAU,J.A.J.FITZPATRICK,P.Y.SHI,M.S.DIAMOND,S.P.J.WHELAN, JRNL AUTH 3 A.H.ELLEBEDY,D.H.FREMONT JRNL TITL STRUCTURAL MECHANISM OF SARS-COV-2 NEUTRALIZATION BY TWO JRNL TITL 2 MURINE ANTIBODIES TARGETING THE RBD. JRNL REF CELL REP V. 37 09881 2021 JRNL REFN ESSN 2211-1247 JRNL PMID 34655519 JRNL DOI 10.1016/J.CELREP.2021.109881 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, GCTF, RELION, RELION, RELION, REMARK 3 CRYOSPARC 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 262342 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: C3 EXPANDED PARTICLES REMARK 4 REMARK 4 7K9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000251986. 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 : COMPLEX OF SARS-COV-2 SPIKE REMARK 245 WITH FAB FRAGMENT OF MONOCLONAL REMARK 245 ANTIBODY 2B04; SARS-COV-2 SPIKE; REMARK 245 FAB FRAGMENT OF MONOCLONAL REMARK 245 ANTIBODY 2B04 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00; 0.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50; 7.50 REMARK 245 SAMPLE DETAILS : FAB FRAGMENTS GENERATED BY REMARK 245 PROTEOLYTIC 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 K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 0.01 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6700.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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: A, H, L 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O THR A 393 OG1 THR A 523 2.12 REMARK 500 O ILE H 30 OG1 THR H 53 2.14 REMARK 500 NH1 ARG A 457 OD2 ASP A 467 2.17 REMARK 500 OG1 THR L 12 O GLU L 16 2.19 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 TYR H 105 5.70 -66.81 REMARK 500 THR L 53 -11.01 72.99 REMARK 500 ASN L 54 -13.73 -140.57 REMARK 500 SER L 67 -173.21 -172.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-22749 RELATED DB: EMDB REMARK 900 RELATED ID: IDP51002 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: EMD-22748 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-22750 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-22751 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-22752 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-22753 RELATED DB: EMDB REMARK 900 RELATED ID: 7K9H RELATED DB: PDB REMARK 900 RELATED ID: 7K9J RELATED DB: PDB REMARK 900 RELATED ID: 7K9K RELATED DB: PDB DBREF 7K9I A 333 527 UNP P0DTC2 SPIKE_SARS2 333 527 DBREF 7K9I H 1 119 PDB 7K9I 7K9I 1 119 DBREF 7K9I L 1 109 PDB 7K9I 7K9I 1 109 SEQRES 1 A 195 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 195 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 195 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 195 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 195 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 195 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 195 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 195 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 195 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 195 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 195 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 195 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 195 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 195 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 195 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 1 H 119 GLN VAL GLN LEU LYS GLN SER GLY PRO GLY LEU VAL ALA SEQRES 2 H 119 PRO SER GLN SER LEU SER ILE THR CYS THR VAL SER GLY SEQRES 3 H 119 PHE SER LEU ILE ASN TYR ALA ILE SER TRP VAL ARG GLN SEQRES 4 H 119 PRO PRO GLY LYS GLY LEU GLU TRP LEU GLY VAL ILE TRP SEQRES 5 H 119 THR GLY GLY GLY THR ASN TYR ASN SER ALA LEU LYS SER SEQRES 6 H 119 ARG LEU SER ILE SER LYS ASP ASN SER LYS SER GLN VAL SEQRES 7 H 119 PHE LEU LYS MET ASN SER LEU GLN THR ASP ASP THR ALA SEQRES 8 H 119 ARG TYR TYR CYS ALA ARG LYS ASP TYR TYR GLY ARG TYR SEQRES 9 H 119 TYR GLY MET ASP TYR TRP GLY GLN GLY THR SER VAL THR SEQRES 10 H 119 VAL SER SEQRES 1 L 109 GLN ALA VAL VAL THR GLN GLU SER ALA LEU THR THR SER SEQRES 2 L 109 PRO GLY GLU THR VAL THR LEU THR CYS ARG SER SER THR SEQRES 3 L 109 GLY ALA VAL THR THR SER ASN TYR ALA ASN TRP VAL GLN SEQRES 4 L 109 GLU LYS PRO ASP HIS LEU PHE THR GLY LEU ILE GLY GLY SEQRES 5 L 109 THR ASN ASN ARG ALA PRO GLY VAL PRO ALA ARG PHE SER SEQRES 6 L 109 GLY SER LEU ILE GLY ASP LYS ALA ALA LEU THR ILE THR SEQRES 7 L 109 GLY ALA GLN THR GLU ASP GLU ALA ILE TYR PHE CYS ALA SEQRES 8 L 109 LEU TRP TYR ASN ASN HIS TRP VAL PHE GLY GLY GLY THR SEQRES 9 L 109 LYS LEU THR VAL LEU HET NAG A 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 C8 H15 N O6 HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 ASP A 364 SER A 371 1 8 HELIX 3 AA3 THR A 385 ASP A 389 5 5 HELIX 4 AA4 ASP A 405 ILE A 410 5 6 HELIX 5 AA5 GLY A 416 ASN A 422 1 7 HELIX 6 AA6 GLY A 502 TYR A 505 5 4 HELIX 7 AA7 GLN H 86 THR H 90 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 VAL A 395 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 5 PRO A 507 SER A 514 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 CYS A 379 -1 N LYS A 378 O VAL A 433 SHEET 1 AA2 2 CYS A 361 VAL A 362 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 4 GLN H 3 SER H 7 0 SHEET 2 AA4 4 SER H 19 SER H 25 -1 O THR H 23 N LYS H 5 SHEET 3 AA4 4 GLN H 77 MET H 82 -1 O VAL H 78 N CYS H 22 SHEET 4 AA4 4 LEU H 67 ASP H 72 -1 N SER H 70 O PHE H 79 SHEET 1 AA5 5 THR H 57 TYR H 59 0 SHEET 2 AA5 5 GLU H 46 ILE H 51 -1 N VAL H 50 O ASN H 58 SHEET 3 AA5 5 ALA H 33 GLN H 39 -1 N TRP H 36 O LEU H 48 SHEET 4 AA5 5 ALA H 91 LYS H 98 -1 O LYS H 98 N ALA H 33 SHEET 5 AA5 5 MET H 107 TRP H 110 -1 O TYR H 109 N ARG H 97 SHEET 1 AA6 5 THR H 57 TYR H 59 0 SHEET 2 AA6 5 GLU H 46 ILE H 51 -1 N VAL H 50 O ASN H 58 SHEET 3 AA6 5 ALA H 33 GLN H 39 -1 N TRP H 36 O LEU H 48 SHEET 4 AA6 5 ALA H 91 LYS H 98 -1 O LYS H 98 N ALA H 33 SHEET 5 AA6 5 THR H 114 VAL H 116 -1 O VAL H 116 N ALA H 91 SHEET 1 AA7 4 THR L 5 GLN L 6 0 SHEET 2 AA7 4 VAL L 18 ARG L 23 -1 O ARG L 23 N THR L 5 SHEET 3 AA7 4 ALA L 73 ILE L 77 -1 O ALA L 73 N CYS L 22 SHEET 4 AA7 4 PHE L 64 SER L 67 -1 N SER L 65 O THR L 76 SHEET 1 AA8 5 ASN L 55 ARG L 56 0 SHEET 2 AA8 5 LEU L 45 GLY L 51 -1 N GLY L 51 O ASN L 55 SHEET 3 AA8 5 ALA L 35 LYS L 41 -1 N TRP L 37 O LEU L 49 SHEET 4 AA8 5 ILE L 87 TRP L 93 -1 O ILE L 87 N GLU L 40 SHEET 5 AA8 5 TRP L 98 PHE L 100 -1 O VAL L 99 N LEU L 92 SHEET 1 AA9 5 ASN L 55 ARG L 56 0 SHEET 2 AA9 5 LEU L 45 GLY L 51 -1 N GLY L 51 O ASN L 55 SHEET 3 AA9 5 ALA L 35 LYS L 41 -1 N TRP L 37 O LEU L 49 SHEET 4 AA9 5 ILE L 87 TRP L 93 -1 O ILE L 87 N GLU L 40 SHEET 5 AA9 5 THR L 104 LYS L 105 -1 O THR L 104 N TYR L 88 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS H 22 CYS H 95 1555 1555 2.04 SSBOND 6 CYS L 22 CYS L 90 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG A 601 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