HEADER VIRAL PROTEIN 03-SEP-20 7CYH TITLE BINDING INTERFACE OF SARS-COV-2 RBD AND ITS NEUTRALIZING ANTIBODY HB27 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: LIGHT CHAIN OF HB27; COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: HEAVY CHAIN OF HB27; COMPND 12 CHAIN: E; 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_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: HEK293T KEYWDS SARS-COV-2, SPIKE TRIMER, NEUTRALIZING ANTIBODY, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.WANG,L.ZHU REVDAT 1 09-JUN-21 7CYH 0 JRNL AUTH X.WANG,L.ZHU JRNL TITL BINDING INTERFACE OF SARS-COV-2 RBD AND ITS NEUTRALIZING JRNL TITL 2 ANTIBODY HB27 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.90 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 393321 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 7CYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018421. 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 RBD AND REMARK 245 ITS NEUTRALIZING ANTIBODY HB27; REMARK 245 SARS-COV-2 RBD; HB27 ANTIBODY 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 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 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 APPLY THE FOLLOWING TO CHAINS: A, D, E 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 ILE D 2 CG1 CG2 CD1 REMARK 470 VAL D 28 CG1 CG2 REMARK 470 MET D 36 CG SD CE REMARK 470 ASP D 73 CG OD1 OD2 REMARK 470 PHE D 74 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP D 85 CG OD1 OD2 REMARK 470 LYS D 95 CG CD CE NZ REMARK 470 GLN D 103 CG CD OE1 NE2 REMARK 470 LYS D 106 CG CD CE NZ REMARK 470 GLU E 50 CG CD OE1 OE2 REMARK 470 PHE E 68 CG CD1 CD2 CE1 CE2 CZ 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 OG1 THR A 393 OE1 GLU A 516 2.09 REMARK 500 O THR E 30 OG SER E 53 2.09 REMARK 500 O SER E 52 NH1 ARG E 72 2.14 REMARK 500 NH1 ARG A 457 OG SER A 459 2.17 REMARK 500 O THR D 5 N ARG D 23 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 498 C - N - CA ANGL. DEV. = -16.6 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 PRO A 337 48.75 -86.78 REMARK 500 THR A 345 -74.12 -80.34 REMARK 500 LEU A 368 -74.35 -86.80 REMARK 500 ALA A 372 19.83 57.24 REMARK 500 PHE A 377 164.50 173.71 REMARK 500 TYR A 380 -75.89 -121.48 REMARK 500 THR A 393 -71.47 -131.07 REMARK 500 ALA A 411 177.08 174.50 REMARK 500 ILE A 418 -72.67 -82.61 REMARK 500 TYR A 421 -72.71 -98.91 REMARK 500 LEU A 441 -64.55 -96.37 REMARK 500 LEU A 455 -64.41 -101.11 REMARK 500 LEU A 517 -117.39 62.40 REMARK 500 GLU D 26 -137.23 51.57 REMARK 500 ASP D 29 -112.99 56.30 REMARK 500 ILE D 33 -20.58 74.82 REMARK 500 MET D 36 -153.21 60.77 REMARK 500 ASN D 37 175.08 174.66 REMARK 500 LEU D 50 -77.23 -119.44 REMARK 500 ALA D 53 19.63 56.79 REMARK 500 ALA D 54 -11.87 62.08 REMARK 500 GLN D 57 -160.28 59.40 REMARK 500 SER D 80 72.12 50.85 REMARK 500 SER D 94 175.27 179.42 REMARK 500 LYS D 95 -15.97 66.77 REMARK 500 VAL D 97 167.76 69.84 REMARK 500 ILE D 100 -150.93 47.81 REMARK 500 SER E 52 -167.78 -75.32 REMARK 500 SER E 53 -64.72 -96.26 REMARK 500 ASP E 62 -73.89 -81.45 REMARK 500 THR E 63 -119.51 46.61 REMARK 500 ALA E 92 179.91 179.90 REMARK 500 ASP E 108 -78.52 -102.04 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 SER A 383 PRO A 384 -149.34 REMARK 500 GLN D 92 GLN D 93 149.00 REMARK 500 GLY E 55 SER E 56 -149.77 REMARK 500 THR E 63 VAL E 64 146.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30500 RELATED DB: EMDB REMARK 900 BINDING INTERFACE OF SARS-COV-2 RBD AND ITS NEUTRALIZING ANTIBODY REMARK 900 HB27 DBREF 7CYH A 334 527 UNP P0DTC2 SPIKE_SARS2 334 527 DBREF 7CYH D 2 111 PDB 7CYH 7CYH 2 111 DBREF 7CYH E 2 120 PDB 7CYH 7CYH 2 120 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 D 110 ILE VAL LEU THR GLN SER PRO THR LEU SER LEU SER PRO SEQRES 2 D 110 GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER GLU SER SEQRES 3 D 110 VAL ASP ASN TYR GLY ILE SER PHE MET ASN TRP PHE GLN SEQRES 4 D 110 GLN LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR ALA SEQRES 5 D 110 ALA SER ASN GLN GLY SER GLY ILE PRO SER ARG PHE SER SEQRES 6 D 110 GLY SER GLY SER GLY THR ASP PHE SER LEU THR ILE SER SEQRES 7 D 110 SER LEU GLU PRO GLU ASP PHE ALA VAL TYR PHE CYS GLN SEQRES 8 D 110 GLN SER LYS GLU VAL PRO ARG ILE PHE GLY GLN GLY THR SEQRES 9 D 110 LYS VAL GLU ILE LEU LYS SEQRES 1 E 119 VAL LYS LEU VAL GLU SER GLY GLY GLY LEU VAL LYS PRO SEQRES 2 E 119 GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY PHE SEQRES 3 E 119 THR PHE THR ASN TYR GLY MET SER TRP VAL ARG GLN ALA SEQRES 4 E 119 PRO GLY LYS ARG LEU GLU TRP VAL ALA GLU ILE SER SER SEQRES 5 E 119 GLY GLY SER TYR THR TYR TYR PRO ASP THR VAL THR GLY SEQRES 6 E 119 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR LEU SEQRES 7 E 119 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 E 119 VAL TYR TYR CYS ALA ARG PHE ARG TYR GLY GLY GLY GLY SEQRES 9 E 119 THR VAL ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 E 119 SER SER 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 THR A 385 LEU A 390 5 6 HELIX 4 AA4 ASP A 405 ILE A 410 5 6 HELIX 5 AA5 GLY A 416 TYR A 421 1 6 HELIX 6 AA6 ILE D 51 SER D 55 5 5 HELIX 7 AA7 ARG E 87 THR E 91 5 5 SHEET 1 AA1 2 LYS A 356 ARG A 357 0 SHEET 2 AA1 2 TYR A 396 ALA A 397 -1 O ALA A 397 N LYS A 356 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 3 PHE A 400 ARG A 403 0 SHEET 2 AA3 3 PRO A 507 VAL A 512 -1 O TYR A 508 N ILE A 402 SHEET 3 AA3 3 VAL A 433 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 1 AA4 2 LEU A 452 ARG A 454 0 SHEET 2 AA4 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA5 2 TYR A 473 GLN A 474 0 SHEET 2 AA5 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA6 4 LEU D 4 GLN D 6 0 SHEET 2 AA6 4 SER D 21 ALA D 24 -1 O ARG D 23 N THR D 5 SHEET 3 AA6 4 ASP D 73 THR D 77 -1 O PHE D 74 N CYS D 22 SHEET 4 AA6 4 SER D 66 SER D 70 -1 N SER D 68 O SER D 75 SHEET 1 AA7 2 PHE D 39 GLN D 41 0 SHEET 2 AA7 2 VAL D 88 PHE D 90 -1 O PHE D 90 N PHE D 39 SHEET 1 AA8 4 LYS E 3 GLU E 6 0 SHEET 2 AA8 4 LEU E 18 SER E 25 -1 O ALA E 23 N VAL E 5 SHEET 3 AA8 4 THR E 78 MET E 83 -1 O LEU E 81 N LEU E 20 SHEET 4 AA8 4 ILE E 70 ASP E 73 -1 N ASP E 73 O THR E 78 SHEET 1 AA9 2 LEU E 11 VAL E 12 0 SHEET 2 AA9 2 THR E 117 VAL E 118 1 O THR E 117 N VAL E 12 SHEET 1 AB1 4 LEU E 45 GLU E 50 0 SHEET 2 AB1 4 MET E 34 GLN E 39 -1 N ARG E 38 O GLU E 46 SHEET 3 AB1 4 VAL E 93 PHE E 99 -1 O TYR E 95 N VAL E 37 SHEET 4 AB1 4 VAL E 107 TRP E 110 -1 O ASP E 108 N ARG E 98 SHEET 1 AB2 4 LEU E 45 GLU E 50 0 SHEET 2 AB2 4 MET E 34 GLN E 39 -1 N ARG E 38 O GLU E 46 SHEET 3 AB2 4 VAL E 93 PHE E 99 -1 O TYR E 95 N VAL E 37 SHEET 4 AB2 4 THR E 114 LEU E 115 -1 O THR E 114 N TYR E 94 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.02 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 4 CYS D 22 CYS D 91 1555 1555 2.03 SSBOND 5 CYS E 22 CYS E 96 1555 1555 2.04 CISPEP 1 GLN D 57 GLY D 58 0 -28.27 CISPEP 2 GLY E 105 THR E 106 0 10.62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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