HEADER VIRAL PROTEIN 17-AUG-21 7PHG TITLE MAP OF P5C3RBD INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SURFACE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN VARIABLE; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS RBD, ANTIBODY, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.PEREZ REVDAT 2 27-OCT-21 7PHG 1 JRNL REVDAT 1 13-OCT-21 7PHG 0 JRNL AUTH C.FENWICK,P.TURELLI,L.PEREZ,C.PELLATON, JRNL AUTH 2 L.ESTEVES-LEUENBERGER,A.FARINA,J.CAMPOS,E.LANA,F.FISCALINI, JRNL AUTH 3 C.RACLOT,F.POJER,K.LAU,D.DEMURTAS,M.DESCATOIRE,V.S.JOO, JRNL AUTH 4 M.FOGLIERINI,A.NOTO,R.ABDELNABI,C.S.FOO,L.VANGEEL,J.NEYTS, JRNL AUTH 5 W.DU,B.J.BOSCH,G.VELDMAN,P.LEYSSEN,V.THIEL,R.LEGRAND,Y.LEVY, JRNL AUTH 6 D.TRONO,G.PANTALEO JRNL TITL A HIGHLY POTENT ANTIBODY EFFECTIVE AGAINST SARS-COV-2 JRNL TITL 2 VARIANTS OF CONCERN. JRNL REF CELL REP V. 37 09814 2021 JRNL REFN ESSN 2211-1247 JRNL PMID 34599871 JRNL DOI 10.1016/J.CELREP.2021.109814 REMARK 2 REMARK 2 RESOLUTION. 4.30 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) : 4.300 REMARK 3 NUMBER OF PARTICLES : 585005 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 7PHG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1292117337. 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 : RBD FAB REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.30 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 QUANTUM (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 : NULL REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3800.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 H TYR A 453 O GLN A 493 1.47 REMARK 500 HH22 ARG H 66 OD2 ASP H 86 1.59 REMARK 500 OH TYR A 473 O GLY H 100 1.92 REMARK 500 O TYR L 86 OG1 THR L 102 1.94 REMARK 500 OG1 THR A 376 O ALA A 435 2.00 REMARK 500 OG SER L 65 OG1 THR L 72 2.01 REMARK 500 O VAL H 52 NH1 ARG H 71 2.03 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 THR A 333 -150.26 57.33 REMARK 500 ALA A 348 -132.50 35.44 REMARK 500 SER A 373 30.16 -99.57 REMARK 500 GLN A 414 -120.29 43.68 REMARK 500 THR A 415 -175.83 -170.60 REMARK 500 ALA A 419 -3.78 73.77 REMARK 500 ASN A 450 -169.24 -80.00 REMARK 500 PHE A 456 66.79 60.38 REMARK 500 SER A 459 -169.51 -125.49 REMARK 500 LEU A 461 167.66 64.06 REMARK 500 PHE A 464 -5.25 72.59 REMARK 500 ASN A 481 32.29 -95.69 REMARK 500 ASN A 487 -150.13 54.50 REMARK 500 PHE H 29 48.22 -92.60 REMARK 500 THR H 30 -30.13 -130.86 REMARK 500 TRP H 47 153.92 -47.84 REMARK 500 TYR H 100C 154.62 -47.84 REMARK 500 ASP L 60 6.33 -68.59 REMARK 500 GLN L 100 -14.38 -140.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13415 RELATED DB: EMDB REMARK 900 MAP OF P5C3RBD INTERFACE DBREF1 7PHG A 332 527 UNP A0A7S6Y2X1_SARS2 DBREF2 7PHG A A0A7S6Y2X1 291 486 DBREF 7PHG H 1 113 PDB 7PHG 7PHG 1 113 DBREF 7PHG L 1 107 PDB 7PHG 7PHG 1 107 SEQRES 1 A 196 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 2 A 196 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 3 A 196 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 4 A 196 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 5 A 196 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 6 A 196 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 7 A 196 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 8 A 196 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 9 A 196 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 10 A 196 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 11 A 196 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 12 A 196 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 13 A 196 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 14 A 196 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 15 A 196 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 16 A 196 PRO SEQRES 1 H 123 GLN MET GLN LEU VAL GLN SER GLY PRO GLU VAL LYS LYS SEQRES 2 H 123 PRO GLY THR SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 H 123 PHE THR PHE THR SER SER ALA VAL GLN TRP VAL ARG GLN SEQRES 4 H 123 ALA ARG GLY GLN ARG LEU GLU TRP ILE GLY TRP ILE VAL SEQRES 5 H 123 VAL GLY SER GLY ASN THR ASP TYR ALA GLN GLN PHE GLN SEQRES 6 H 123 GLU ARG VAL THR ILE THR ARG ASP MET SER THR SER THR SEQRES 7 H 123 ALA TYR MET GLU LEU SER SER LEU GLY SER GLU ASP THR SEQRES 8 H 123 ALA VAL TYR TYR CYS ALA ALA PRO ASN CYS SER GLY GLY SEQRES 9 H 123 SER CYS TYR ASP GLY PHE ASP LEU TRP GLY GLN GLY THR SEQRES 10 H 123 MET VAL THR VAL SER SER SEQRES 1 L 108 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 108 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG GLY SER SEQRES 3 L 108 GLN SER VAL ARG SER SER TYR LEU GLY TRP TYR GLN GLN SEQRES 4 L 108 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 L 108 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 L 108 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 L 108 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 L 108 TYR GLY SER SER PRO TRP THR PHE GLY GLN GLY THR LYS SEQRES 9 L 108 VAL GLU ILE LYS HELIX 1 AA1 PRO A 337 PHE A 342 1 6 HELIX 2 AA2 TYR A 365 ASN A 370 1 6 HELIX 3 AA3 LYS A 386 LEU A 390 5 5 HELIX 4 AA4 GLY A 404 ILE A 410 5 7 HELIX 5 AA5 ALA H 60 GLN H 64 5 5 HELIX 6 AA6 GLY H 83 THR H 87 5 5 HELIX 7 AA7 ARG L 29 SER L 31 5 3 SHEET 1 AA1 2 LYS A 356 ILE A 358 0 SHEET 2 AA1 2 VAL A 395 ALA A 397 -1 O ALA A 397 N LYS A 356 SHEET 1 AA2 3 PHE A 377 TYR A 380 0 SHEET 2 AA2 3 GLY A 431 ASN A 437 -1 O GLY A 431 N TYR A 380 SHEET 3 AA2 3 TYR A 508 SER A 514 -1 O VAL A 511 N ILE A 434 SHEET 1 AA3 4 LEU H 4 GLN H 6 0 SHEET 2 AA3 4 VAL H 20 ALA H 24 -1 O LYS H 23 N VAL H 5 SHEET 3 AA3 4 THR H 77 LEU H 82 -1 O ALA H 78 N CYS H 22 SHEET 4 AA3 4 VAL H 67 ASP H 72 -1 N THR H 70 O TYR H 79 SHEET 1 AA4 6 GLU H 10 VAL H 11 0 SHEET 2 AA4 6 MET H 108 THR H 110 1 O THR H 110 N GLU H 10 SHEET 3 AA4 6 ALA H 88 TYR H 90 -1 N ALA H 88 O VAL H 109 SHEET 4 AA4 6 ALA H 33 GLN H 39 -1 N GLN H 39 O VAL H 89 SHEET 5 AA4 6 GLU H 46 VAL H 52 -1 O ILE H 51 N VAL H 34 SHEET 6 AA4 6 ASN H 56 ASP H 58 -1 O ASP H 58 N TRP H 50 SHEET 1 AA5 2 ALA H 93 ALA H 94 0 SHEET 2 AA5 2 LEU H 102 TRP H 103 -1 O LEU H 102 N ALA H 94 SHEET 1 AA6 5 LEU L 11 LEU L 13 0 SHEET 2 AA6 5 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AA6 5 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AA6 5 LEU L 33 GLN L 38 -1 N GLY L 34 O GLN L 89 SHEET 5 AA6 5 ARG L 45 LEU L 46 -1 O ARG L 45 N GLN L 37 SHEET 1 AA7 3 ALA L 19 CYS L 23 0 SHEET 2 AA7 3 ASP L 70 ILE L 75 -1 O ILE L 75 N ALA L 19 SHEET 3 AA7 3 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 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 2.03 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.03 SSBOND 6 CYS H 97 CYS H 100B 1555 1555 2.04 SSBOND 7 CYS L 23 CYS L 88 1555 1555 2.03 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