HEADER VIRAL PROTEIN 27-JAN-22 7WRY TITLE LOCAL STRUCTURE OF BD55-3546 FAB AND SARS-COV2 DELTA RBD COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: R; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BD55-3546L; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: BD55-3546H; COMPND 11 CHAIN: H; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS B012; SOURCE 3 ORGANISM_TAXID: 305406; SOURCE 4 GENE: S, 2; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS B012; SOURCE 9 ORGANISM_TAXID: 305406; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS B012; SOURCE 14 ORGANISM_TAXID: 305406; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV2 DELTA RBD, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Z.Z.ZHANG,J.J.XIAO REVDAT 3 30-OCT-24 7WRY 1 REMARK REVDAT 2 12-APR-23 7WRY 1 JRNL REVDAT 1 28-SEP-22 7WRY 0 JRNL AUTH Y.CAO,F.JIAN,Z.ZHANG,A.YISIMAYI,X.HAO,L.BAO,F.YUAN,Y.YU, JRNL AUTH 2 S.DU,J.WANG,T.XIAO,W.SONG,Y.ZHANG,P.LIU,R.AN,P.WANG,Y.WANG, JRNL AUTH 3 S.YANG,X.NIU,Y.ZHANG,Q.GU,F.SHAO,Y.HU,W.YIN,A.ZHENG,Y.WANG, JRNL AUTH 4 C.QIN,R.JIN,J.XIAO,X.S.XIE JRNL TITL RATIONAL IDENTIFICATION OF POTENT AND BROAD JRNL TITL 2 SARBECOVIRUS-NEUTRALIZING ANTIBODY COCKTAILS FROM SARS JRNL TITL 3 CONVALESCENTS. JRNL REF CELL REP V. 41 11845 2022 JRNL REFN ESSN 2211-1247 JRNL PMID 36493787 JRNL DOI 10.1016/J.CELREP.2022.111845 REMARK 2 REMARK 2 RESOLUTION. 3.28 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) : 3.280 REMARK 3 NUMBER OF PARTICLES : 303444 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 7WRY 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_1300027327. 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 BD55-3546 REMARK 245 FAB AND SARS-COV2 DELTA 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 : 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: R, L, H, 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 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: 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 CYS R 432 CA - CB - SG ANGL. DEV. = 14.1 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 R 352 67.04 -103.83 REMARK 500 ASN R 370 56.21 -95.05 REMARK 500 PHE R 377 50.81 -140.34 REMARK 500 TYR R 473 -159.78 -83.50 REMARK 500 SER R 477 -160.00 -81.80 REMARK 500 GLU R 484 -163.72 -78.54 REMARK 500 ASN R 487 21.82 47.79 REMARK 500 PHE H 64 55.38 -97.18 REMARK 500 LEU H 83 76.50 -101.59 REMARK 500 GLU H 89 48.53 -84.80 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 TYR R 473 GLN R 474 -143.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32737 RELATED DB: EMDB REMARK 900 LOCAL STRUCTURE OF BD55-3546 FAB AND SARS-COV2 DELTA RBD COMPLEX DBREF 7WRY R 334 526 UNP P0DTC2 SPIKE_SARS2 334 526 DBREF 7WRY L 1 106 PDB 7WRY 7WRY 1 106 DBREF 7WRY H 1 119 PDB 7WRY 7WRY 1 119 SEQADV 7WRY ARG R 452 UNP P0DTC2 LEU 452 CONFLICT SEQADV 7WRY LYS R 478 UNP P0DTC2 THR 478 CONFLICT SEQRES 1 R 193 ASN LEU CYS PRO PHE GLY 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 SER ALA SEQRES 4 R 193 SER PHE SER 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 LYS 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 ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 R 193 TYR ARG 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 SER LYS PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 R 193 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 R 193 VAL GLY TYR 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 SEQRES 1 L 106 ASP VAL VAL LEU THR GLN SER PRO ALA THR LEU SER VAL SEQRES 2 L 106 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 106 HIS ASN VAL GLY THR SER LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 106 PRO GLY GLN ALA PRO ARG LEU LEU ILE HIS GLY VAL SER SEQRES 5 L 106 THR ARG ALA THR GLY VAL PRO ALA ARG PHE SER ASP SER SEQRES 6 L 106 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 106 GLN SER GLU ASP LEU ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 L 106 ASN TYR TRP PRO LEU THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 L 106 GLU ILE SEQRES 1 H 119 GLN VAL GLN LEU VAL GLN SER GLY SER ALA LEU LYS ARG SEQRES 2 H 119 PRO GLY ALA SER VAL LYS LEU SER CYS LYS ALA SER GLY SEQRES 3 H 119 TYR THR PHE ILE ASN TYR ALA ILE HIS TRP VAL ARG GLN SEQRES 4 H 119 ALA PRO GLY GLN GLY LEU GLN TRP MET GLY TRP ILE ASN SEQRES 5 H 119 PRO ASN THR GLY ILE PRO THR TYR ALA GLN GLY PHE THR SEQRES 6 H 119 GLY ARG PHE VAL PHE SER LEU ASP THR SER VAL SER THR SEQRES 7 H 119 ALA TYR LEU GLN LEU SER SER LEU LYS ILE GLU ASP THR SEQRES 8 H 119 ALA VAL TYR TYR CYS ALA ARG ASP GLN ASP LEU TYR GLU SEQRES 9 H 119 ARG ALA PHE ASP ILE TRP GLY GLN GLY THR MET VAL THR SEQRES 10 H 119 VAL SER HET NAG A 1 14 HET NAG A 2 14 HET BMA A 3 11 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 4 NAG 2(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 HELIX 1 AA1 PRO R 337 VAL R 341 5 5 HELIX 2 AA2 TYR R 365 ASN R 370 1 6 HELIX 3 AA3 SER R 383 LEU R 387 5 5 HELIX 4 AA4 ASP R 405 ILE R 410 5 6 HELIX 5 AA5 LYS R 417 ASN R 422 1 6 HELIX 6 AA6 SER R 438 SER R 443 1 6 HELIX 7 AA7 THR H 28 TYR H 32 5 5 HELIX 8 AA8 LYS H 87 THR H 91 5 5 SHEET 1 AA1 5 LYS R 356 ILE R 358 0 SHEET 2 AA1 5 VAL R 395 ARG R 403 -1 O VAL R 395 N ILE R 358 SHEET 3 AA1 5 PRO R 507 SER R 514 -1 O VAL R 512 N ASP R 398 SHEET 4 AA1 5 GLY R 431 ASN R 437 -1 N ILE R 434 O VAL R 511 SHEET 5 AA1 5 CYS R 379 TYR R 380 -1 N TYR R 380 O GLY R 431 SHEET 1 AA2 2 CYS R 361 VAL R 362 0 SHEET 2 AA2 2 VAL R 524 CYS R 525 1 O CYS R 525 N CYS R 361 SHEET 1 AA3 2 ARG R 452 ARG R 454 0 SHEET 2 AA3 2 LEU R 492 SER R 494 -1 O GLN R 493 N TYR R 453 SHEET 1 AA4 4 LEU L 4 SER L 7 0 SHEET 2 AA4 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA4 4 PHE L 71 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 AA4 4 PHE L 62 SER L 65 -1 N SER L 63 O THR L 74 SHEET 1 AA5 2 THR L 10 SER L 12 0 SHEET 2 AA5 2 LYS L 103 GLU L 105 1 O GLU L 105 N LEU L 11 SHEET 1 AA6 4 ARG L 45 ILE L 48 0 SHEET 2 AA6 4 LEU L 33 GLN L 37 -1 N TRP L 35 O LEU L 47 SHEET 3 AA6 4 CYS L 88 GLN L 90 -1 O GLN L 89 N ALA L 34 SHEET 4 AA6 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AA7 4 GLN H 3 GLN H 6 0 SHEET 2 AA7 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AA7 4 THR H 78 LEU H 83 -1 O ALA H 79 N CYS H 22 SHEET 4 AA7 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 AA8 6 ALA H 10 LYS H 12 0 SHEET 2 AA8 6 THR H 114 VAL H 118 1 O THR H 117 N ALA H 10 SHEET 3 AA8 6 ALA H 92 ASP H 99 -1 N ALA H 92 O VAL H 116 SHEET 4 AA8 6 ILE H 34 GLN H 39 -1 N HIS H 35 O ALA H 97 SHEET 5 AA8 6 LEU H 45 ILE H 51 -1 O GLY H 49 N TRP H 36 SHEET 6 AA8 6 PRO H 58 TYR H 60 -1 O THR H 59 N TRP H 50 SHEET 1 AA9 4 ALA H 10 LYS H 12 0 SHEET 2 AA9 4 THR H 114 VAL H 118 1 O THR H 117 N ALA H 10 SHEET 3 AA9 4 ALA H 92 ASP H 99 -1 N ALA H 92 O VAL H 116 SHEET 4 AA9 4 PHE H 107 TRP H 110 -1 O ILE H 109 N ARG H 98 SSBOND 1 CYS R 336 CYS R 361 1555 1555 2.03 SSBOND 2 CYS R 379 CYS R 432 1555 1555 2.06 SSBOND 3 CYS R 391 CYS R 525 1555 1555 2.03 SSBOND 4 CYS R 480 CYS R 488 1555 1555 2.03 SSBOND 5 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 6 CYS H 22 CYS H 96 1555 1555 2.03 LINK ND2 ASN R 343 C1 NAG A 1 1555 1555 1.44 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.44 LINK O4 NAG A 2 C1 BMA A 3 1555 1555 1.45 CISPEP 1 SER L 7 PRO L 8 0 -2.06 CISPEP 2 TRP L 94 PRO L 95 0 -2.46 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