HEADER VIRAL PROTEIN 07-AUG-21 7V27 TITLE RBD/XG005 LOCAL REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: XG005-VH; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: XG005-VL; COMPND 11 CHAIN: A; 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; 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 EXPRESSION_SYSTEM_PLASMID: PCDNA3.1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 22 EXPRESSION_SYSTEM_CELL_LINE: HEK293T KEYWDS SARS-COV-2, SPIKE, RBD DOMAIN, ANTIBODIES, INTERFACE REGION, VIRAL KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.Q.ZHAN,X.ZHANG,L.SUN,Z.G.CHEN REVDAT 2 20-NOV-24 7V27 1 REMARK REVDAT 1 10-AUG-22 7V27 0 JRNL AUTH W.Q.ZHAN JRNL TITL RBD/XG005 LOCAL REFINEMENT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.18 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) : 4.180 REMARK 3 NUMBER OF PARTICLES : 70995 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 7V27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1300022018. 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 : INTERFACE OF RBD AND XG005; REMARK 245 RBD; XG005 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 : 7.00 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 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 : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5300.00 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: C, B, 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 GLN A 1 REMARK 465 SER A 2 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 ASN C 343 36.26 -99.58 REMARK 500 ASP C 364 59.30 -96.36 REMARK 500 ASN C 370 31.92 -97.95 REMARK 500 ASP C 389 49.06 -88.63 REMARK 500 LEU C 390 143.65 -171.60 REMARK 500 ALA C 411 149.45 -170.74 REMARK 500 PRO C 412 47.80 -80.51 REMARK 500 TYR C 423 116.46 -160.68 REMARK 500 THR C 478 74.38 52.85 REMARK 500 ASN C 481 61.63 60.03 REMARK 500 SER A 69 -62.32 -93.03 REMARK 500 SER A 78 -167.58 -77.96 REMARK 500 ASP A 84 -175.70 -173.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-31638 RELATED DB: EMDB REMARK 900 RBD/XG005 LOCAL REFINEMENT REMARK 900 RELATED ID: EMD-31637 RELATED DB: EMDB DBREF 7V27 C 334 527 UNP P0DTC2 SPIKE_SARS2 334 527 DBREF 7V27 B 1 120 PDB 7V27 7V27 1 120 DBREF 7V27 A 1 109 PDB 7V27 7V27 1 109 SEQRES 1 C 194 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 C 194 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 C 194 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 C 194 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 C 194 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 C 194 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 C 194 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 C 194 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 C 194 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 C 194 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 C 194 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 C 194 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 C 194 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 C 194 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 C 194 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 1 B 120 GLN VAL THR LEU ARG GLU SER GLY PRO THR LEU VAL LYS SEQRES 2 B 120 PRO LYS GLN THR LEU THR LEU THR CYS THR PHE SER GLY SEQRES 3 B 120 PHE SER LEU SER THR PRO GLY GLY GLY VAL GLY TRP ILE SEQRES 4 B 120 ARG GLN PRO PRO GLY LYS ALA LEU GLU TRP LEU ALA LEU SEQRES 5 B 120 ILE TYR TRP ASP ASP ASP LYS ARG TYR SER PRO SER LEU SEQRES 6 B 120 LYS SER SER LEU THR ILE THR LYS ASP THR SER LYS ASN SEQRES 7 B 120 GLN VAL VAL LEU THR MET THR ASN MET ASP PRO VAL ASP SEQRES 8 B 120 THR ALA THR TYR TYR CYS ALA ARG LEU THR ALA ALA ASP SEQRES 9 B 120 THR ILE PHE ASP CYS TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 B 120 VAL SER SER SEQRES 1 A 109 GLN SER ALA LEU THR GLN PRO ALA SER VAL SER GLY SER SEQRES 2 A 109 PRO GLY LEU SER ILE THR ILE SER CYS THR ALA THR SER SEQRES 3 A 109 SER ASP VAL GLY ALA TYR ASN TYR VAL SER TRP TYR GLN SEQRES 4 A 109 GLN HIS PRO GLY GLN ALA PRO LYS LEU MET ILE TYR ASP SEQRES 5 A 109 VAL SER LYS ARG PRO SER GLY VAL SER ASN ARG PHE SER SEQRES 6 A 109 GLY SER LYS SER ALA ASN THR ALA SER LEU THR ILE SER SEQRES 7 A 109 GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS SER SEQRES 8 A 109 SER TYR THR THR THR SER VAL VAL PHE GLY GLY GLY THR SEQRES 9 A 109 LYS LEU THR VAL LEU HET NAG C 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 C 337 ASN C 343 1 7 HELIX 2 AA2 SER C 349 TRP C 353 5 5 HELIX 3 AA3 TYR C 365 ASN C 370 1 6 HELIX 4 AA4 ASP B 88 THR B 92 5 5 SHEET 1 AA1 4 LYS C 356 ARG C 357 0 SHEET 2 AA1 4 TYR C 396 ILE C 402 -1 O ALA C 397 N LYS C 356 SHEET 3 AA1 4 TYR C 508 VAL C 512 -1 O VAL C 510 N PHE C 400 SHEET 4 AA1 4 ALA C 435 ASN C 437 -1 N TRP C 436 O ARG C 509 SHEET 1 AA2 2 CYS C 379 TYR C 380 0 SHEET 2 AA2 2 GLY C 431 CYS C 432 -1 O GLY C 431 N TYR C 380 SHEET 1 AA3 2 LEU C 452 ARG C 454 0 SHEET 2 AA3 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AA4 4 THR B 3 SER B 7 0 SHEET 2 AA4 4 THR B 17 SER B 25 -1 O THR B 21 N SER B 7 SHEET 3 AA4 4 VAL B 81 THR B 85 -1 O MET B 84 N LEU B 18 SHEET 4 AA4 4 THR B 70 ILE B 71 -1 N THR B 70 O THR B 83 SHEET 1 AA5 6 LEU B 11 VAL B 12 0 SHEET 2 AA5 6 THR B 114 VAL B 118 1 O THR B 117 N VAL B 12 SHEET 3 AA5 6 ALA B 93 TYR B 96 -1 N TYR B 95 O THR B 114 SHEET 4 AA5 6 GLY B 35 GLN B 41 -1 N ILE B 39 O TYR B 96 SHEET 5 AA5 6 GLU B 48 TYR B 54 -1 O LEU B 50 N TRP B 38 SHEET 6 AA5 6 ARG B 60 TYR B 61 -1 O ARG B 60 N LEU B 52 SHEET 1 AA6 5 LEU B 11 VAL B 12 0 SHEET 2 AA6 5 THR B 114 VAL B 118 1 O THR B 117 N VAL B 12 SHEET 3 AA6 5 ALA B 93 TYR B 96 -1 N TYR B 95 O THR B 114 SHEET 4 AA6 5 GLY B 35 GLN B 41 -1 N ILE B 39 O TYR B 96 SHEET 5 AA6 5 ARG B 99 LEU B 100 -1 O LEU B 100 N GLY B 35 SHEET 1 AA7 2 SER A 11 GLY A 12 0 SHEET 2 AA7 2 THR A 107 VAL A 108 1 O THR A 107 N GLY A 12 SHEET 1 AA8 3 THR A 19 CYS A 22 0 SHEET 2 AA8 3 ALA A 73 THR A 76 -1 O ALA A 73 N CYS A 22 SHEET 3 AA8 3 SER A 65 LYS A 68 -1 N SER A 65 O THR A 76 SHEET 1 AA9 4 LEU A 48 ILE A 50 0 SHEET 2 AA9 4 VAL A 35 GLN A 40 -1 N TRP A 37 O ILE A 50 SHEET 3 AA9 4 ASP A 87 TYR A 93 -1 O SER A 91 N SER A 36 SHEET 4 AA9 4 VAL A 98 VAL A 99 -1 O VAL A 99 N SER A 92 SHEET 1 AB1 4 LEU A 48 ILE A 50 0 SHEET 2 AB1 4 VAL A 35 GLN A 40 -1 N TRP A 37 O ILE A 50 SHEET 3 AB1 4 ASP A 87 TYR A 93 -1 O SER A 91 N SER A 36 SHEET 4 AB1 4 THR A 104 LYS A 105 -1 O THR A 104 N TYR A 88 SSBOND 1 CYS C 336 CYS C 361 1555 1555 2.03 SSBOND 2 CYS C 379 CYS C 432 1555 1555 2.04 SSBOND 3 CYS C 391 CYS C 525 1555 1555 2.04 SSBOND 4 CYS C 480 CYS C 488 1555 1555 2.03 SSBOND 5 CYS B 22 CYS B 97 1555 1555 2.03 SSBOND 6 CYS A 22 CYS A 90 1555 1555 2.03 LINK ND2 ASN C 343 C1 NAG C 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