HEADER VIRAL PROTEIN/IMMUNE SYSTEM 08-AUG-21 7RR0 TITLE SARS-COV-2 RECEPTOR BINDING DOMAIN BOUND TO FAB PDI 222 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RBD DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PDI 222 FAB HEAVY CHAIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: PDI 222 FAB LIGHT CHAIN; COMPND 12 CHAIN: C; COMPND 13 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 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 22 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS ANTIBODY, SARS-COV-2 RBD, COMPLEX, VIRAL PROTEIN, VIRAL PROTEIN- KEYWDS 2 IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR P.PYMM,A.GLUKHOVA,K.A.BLACK,W.H.THAM REVDAT 3 27-OCT-21 7RR0 1 JRNL REVDAT 2 20-OCT-21 7RR0 1 JRNL REVDAT 1 06-OCT-21 7RR0 0 JRNL AUTH A.K.WHEATLEY,P.PYMM,R.ESTERBAUER,M.H.DIETRICH,W.S.LEE, JRNL AUTH 2 D.DREW,H.G.KELLY,L.J.CHAN,F.L.MORDANT,K.A.BLACK,A.ADAIR, JRNL AUTH 3 H.X.TAN,J.A.JUNO,K.M.WRAGG,T.AMARASENA,E.LOPEZ,K.J.SELVA, JRNL AUTH 4 E.R.HAYCROFT,J.P.COONEY,H.VENUGOPAL,L.L.TAN,M.T.O NEILL, JRNL AUTH 5 C.C.ALLISON,D.CROMER,M.P.DAVENPORT,R.A.BOWEN,A.W.CHUNG, JRNL AUTH 6 M.PELLEGRINI,M.T.LIDDAMENT,A.GLUKHOVA,K.SUBBARAO,S.J.KENT, JRNL AUTH 7 W.H.THAM JRNL TITL LANDSCAPE OF HUMAN ANTIBODY RECOGNITION OF THE SARS-COV-2 JRNL TITL 2 RECEPTOR BINDING DOMAIN. JRNL REF CELL REP V. 37 09822 2021 JRNL REFN ESSN 2211-1247 JRNL PMID 34610292 JRNL DOI 10.1016/J.CELREP.2021.109822 REMARK 2 REMARK 2 RESOLUTION. 3.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GAUTOMATCH 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) : 3.120 REMARK 3 NUMBER OF PARTICLES : 182255 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 7RR0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000257318. 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 RECEPTOR BINDING REMARK 245 DOMAIN- FAB PDI 222 COMPLEX; REMARK 245 SARS-COV-2 RECEPTOR BINDING REMARK 245 DOMAIN; FAB PDI 222 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 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, B, C 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 ASP A 405 CG OD1 OD2 REMARK 470 HIS A 519 CG ND1 CD2 CE1 NE2 REMARK 470 GLU C 1 CG CD OE1 OE2 REMARK 470 GLU C 69 CG CD OE1 OE2 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 ASP A 428 51.53 -95.36 REMARK 500 ALA C 52 -53.74 71.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24649 RELATED DB: EMDB REMARK 900 SARS-COV-2 RECEPTOR BINDING DOMAIN BOUND TO FAB PDI 222 DBREF 7RR0 A 334 527 UNP P0DTC2 SPIKE_SARS2 334 527 DBREF 7RR0 B 1 121 PDB 7RR0 7RR0 1 121 DBREF 7RR0 C 1 107 PDB 7RR0 7RR0 1 107 SEQRES 1 A 194 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 A 194 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 A 194 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 A 194 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 A 194 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 A 194 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 A 194 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 A 194 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 A 194 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 A 194 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 A 194 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 A 194 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 A 194 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 A 194 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 A 194 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 1 B 121 GLN VAL GLN LEU VAL GLN SER GLY PRO GLU VAL LYS LYS SEQRES 2 B 121 PRO GLY THR SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 B 121 PHE THR PHE SER SER SER ALA VAL GLN TRP VAL ARG GLN SEQRES 4 B 121 ALA ARG GLY GLN ARG LEU GLU TRP ILE GLY TRP ILE VAL SEQRES 5 B 121 VAL GLY SER GLY ASN ALA ASN TYR ALA PRO ARG PHE GLN SEQRES 6 B 121 GLU ARG VAL THR ILE THR ARG ASP MET SER THR ASN THR SEQRES 7 B 121 ALA TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 B 121 ALA VAL TYR TYR CYS ALA ALA PRO ASN CYS SER ARG THR SEQRES 9 B 121 LEU CYS TYR ASP GLY PHE ASN MET TRP GLY GLN GLY THR SEQRES 10 B 121 MET VAL THR VAL SEQRES 1 C 107 GLU ILE VAL LEU THR GLN SER PRO GLY SER LEU SER LEU SEQRES 2 C 107 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 C 107 GLN SER VAL ARG SER SER TYR LEU GLY TRP TYR GLN GLN SEQRES 4 C 107 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 C 107 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 C 107 SER GLY SER GLU THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 C 107 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 C 107 TYR ASP SER SER PRO TRP THR PHE GLY GLN GLY THR LYS SEQRES 9 C 107 VAL GLU ILE 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 TYR A 365 ASN A 370 1 6 HELIX 3 AA3 ASP A 405 ILE A 410 5 6 HELIX 4 AA4 GLY A 416 ASN A 422 1 7 HELIX 5 AA5 SER A 438 SER A 443 1 6 HELIX 6 AA6 GLY A 502 TYR A 505 5 4 HELIX 7 AA7 ARG B 87 THR B 91 5 5 HELIX 8 AA8 GLU C 80 PHE C 84 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O SER A 514 N TYR A 396 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 TYR A 380 -1 N LYS A 378 O VAL A 433 SHEET 1 AA2 2 CYS A 391 PHE A 392 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 -1 O VAL A 524 N PHE A 392 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 B 3 GLN B 6 0 SHEET 2 AA4 4 VAL B 18 SER B 25 -1 O LYS B 23 N VAL B 5 SHEET 3 AA4 4 THR B 78 LEU B 83 -1 O MET B 81 N VAL B 20 SHEET 4 AA4 4 VAL B 68 ASP B 73 -1 N ASP B 73 O THR B 78 SHEET 1 AA5 6 GLU B 10 VAL B 11 0 SHEET 2 AA5 6 THR B 117 THR B 120 1 O THR B 120 N GLU B 10 SHEET 3 AA5 6 ALA B 92 ALA B 98 -1 N TYR B 94 O THR B 117 SHEET 4 AA5 6 ALA B 33 GLN B 39 -1 N VAL B 37 O TYR B 95 SHEET 5 AA5 6 LEU B 45 VAL B 52 -1 O GLU B 46 N ARG B 38 SHEET 6 AA5 6 ALA B 58 TYR B 60 -1 O ASN B 59 N TRP B 50 SHEET 1 AA6 4 GLU B 10 VAL B 11 0 SHEET 2 AA6 4 THR B 117 THR B 120 1 O THR B 120 N GLU B 10 SHEET 3 AA6 4 ALA B 92 ALA B 98 -1 N TYR B 94 O THR B 117 SHEET 4 AA6 4 MET B 112 TRP B 113 -1 O MET B 112 N ALA B 98 SHEET 1 AA7 4 LEU C 4 SER C 7 0 SHEET 2 AA7 4 ALA C 19 ALA C 25 -1 O ARG C 24 N THR C 5 SHEET 3 AA7 4 ASP C 71 ILE C 76 -1 O LEU C 74 N LEU C 21 SHEET 4 AA7 4 PHE C 63 SER C 66 -1 N SER C 66 O THR C 73 SHEET 1 AA8 6 SER C 10 SER C 12 0 SHEET 2 AA8 6 THR C 103 GLU C 106 1 O LYS C 104 N LEU C 11 SHEET 3 AA8 6 VAL C 86 GLN C 91 -1 N TYR C 87 O THR C 103 SHEET 4 AA8 6 LEU C 34 GLN C 39 -1 N GLN C 39 O VAL C 86 SHEET 5 AA8 6 PRO C 45 TYR C 50 -1 O LEU C 48 N TRP C 36 SHEET 6 AA8 6 SER C 54 ARG C 55 -1 O SER C 54 N TYR C 50 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.04 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 2.02 SSBOND 5 CYS B 22 CYS B 96 1555 1555 2.03 SSBOND 6 CYS B 101 CYS B 106 1555 1555 2.03 SSBOND 7 CYS C 23 CYS C 89 1555 1555 2.04 CISPEP 1 SER C 7 PRO C 8 0 -9.73 CISPEP 2 SER C 95 PRO C 96 0 -5.47 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