HEADER VIRAL PROTEIN 02-JUL-22 7YD1 TITLE LOCAL REFINEMENT OF SARS-COV-2 OMICRON S TRIMER COMPLEXED WITH XG005 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: C; COMPND 4 FRAGMENT: RBD; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: XG005-VH; COMPND 8 CHAIN: A; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: XG005-VL; COMPND 11 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS SARS-COV-2, SPIKE, ANTIBODY, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR W.Q.ZHAN,X.ZHANG,Z.G.CHEN,L.SUN REVDAT 1 12-JUL-23 7YD1 0 JRNL AUTH W.Q.ZHAN,X.ZHANG JRNL TITL OS-XG005 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.99 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 313560 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 7YD1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030441. 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 : OMICRON RBD WITH 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 : 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 K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 6100.00 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, A, B 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 THR C 333 OG1 CG2 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 ILE C 332 -50.78 -125.69 REMARK 500 ALA C 348 -179.71 -178.85 REMARK 500 SER C 383 75.78 54.23 REMARK 500 LEU C 390 119.36 -160.99 REMARK 500 GLN C 414 148.31 -171.05 REMARK 500 ASP C 427 44.85 -88.66 REMARK 500 ASP C 428 17.05 -142.03 REMARK 500 PRO A 89 45.00 -76.06 REMARK 500 ASP B 52 137.45 -35.50 REMARK 500 ALA B 70 -57.26 -121.55 REMARK 500 ASN B 71 18.81 -142.23 REMARK 500 GLU B 83 53.49 -91.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33745 RELATED DB: EMDB REMARK 900 LOCAL REFINEMENT OF SARS-COV-2 OMICRON S TRIMER COMPLEXED WITH XG005 DBREF 7YD1 C 331 528 UNP P0DTC2 SPIKE_SARS2 331 528 DBREF 7YD1 A 1 122 PDB 7YD1 7YD1 1 122 DBREF 7YD1 B 3 110 PDB 7YD1 7YD1 3 110 SEQADV 7YD1 ASP C 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7YD1 LEU C 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7YD1 PRO C 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7YD1 PHE C 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7YD1 ASN C 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7YD1 LYS C 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7YD1 SER C 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7YD1 ASN C 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7YD1 LYS C 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7YD1 ALA C 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7YD1 ARG C 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7YD1 SER C 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7YD1 ARG C 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7YD1 TYR C 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7YD1 HIS C 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 C 198 ASN ILE THR ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN SEQRES 2 C 198 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 3 C 198 ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR SEQRES 4 C 198 ASN LEU ALA PRO PHE PHE THR PHE LYS CYS TYR GLY VAL SEQRES 5 C 198 SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL SEQRES 6 C 198 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 7 C 198 GLN ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR SEQRES 8 C 198 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 9 C 198 ALA TRP ASN SER ASN LYS LEU ASP SER LYS VAL SER GLY SEQRES 10 C 198 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 11 C 198 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 12 C 198 GLN ALA GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY PHE SEQRES 13 C 198 ASN CYS TYR PHE PRO LEU ARG SER TYR SER PHE ARG PRO SEQRES 14 C 198 THR TYR GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL SEQRES 15 C 198 LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS SEQRES 16 C 198 GLY PRO LYS SEQRES 1 A 122 GLN VAL THR LEU ARG GLU SER GLY PRO THR LEU VAL LYS SEQRES 2 A 122 PRO LYS GLN THR LEU THR LEU THR CYS THR PHE SER GLY SEQRES 3 A 122 PHE SER LEU SER THR PRO GLY GLY GLY VAL GLY TRP ILE SEQRES 4 A 122 ARG GLN PRO PRO GLY LYS ALA LEU GLU TRP LEU ALA LEU SEQRES 5 A 122 ILE TYR TRP ASP ASP ASP LYS ARG TYR SER PRO SER LEU SEQRES 6 A 122 LYS SER SER LEU THR ILE THR LYS ASP THR SER LYS ASN SEQRES 7 A 122 GLN VAL VAL LEU THR MET THR ASN MET ASP PRO VAL ASP SEQRES 8 A 122 THR ALA THR TYR TYR CYS ALA ARG LEU THR ALA ALA ASP SEQRES 9 A 122 THR ILE PHE ASP CYS TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 A 122 VAL SER SER ALA SER SEQRES 1 B 108 ALA LEU THR GLN PRO ALA SER VAL SER GLY SER PRO GLY SEQRES 2 B 108 LEU SER ILE THR ILE SER CYS THR ALA THR SER SER ASP SEQRES 3 B 108 VAL GLY ALA TYR ASN TYR VAL SER TRP TYR GLN GLN HIS SEQRES 4 B 108 PRO GLY GLN ALA PRO LYS LEU MET ILE TYR ASP VAL SER SEQRES 5 B 108 LYS ARG PRO SER GLY VAL SER ASN ARG PHE SER GLY SER SEQRES 6 B 108 LYS SER ALA ASN THR ALA SER LEU THR ILE SER GLY LEU SEQRES 7 B 108 GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS SER SER TYR SEQRES 8 B 108 THR THR THR SER VAL VAL PHE GLY GLY GLY THR LYS LEU SEQRES 9 B 108 THR VAL LEU GLY HELIX 1 AA1 PHE C 338 ASN C 343 1 6 HELIX 2 AA2 ASP C 364 ASN C 370 5 7 HELIX 3 AA3 GLU C 406 ILE C 410 5 5 HELIX 4 AA4 ASN C 417 ASN C 422 1 6 HELIX 5 AA5 GLN B 81 GLU B 85 5 5 SHEET 1 AA1 5 ASN C 354 ILE C 358 0 SHEET 2 AA1 5 VAL C 395 ILE C 402 -1 O ALA C 397 N LYS C 356 SHEET 3 AA1 5 TYR C 508 PHE C 515 -1 O VAL C 512 N ASP C 398 SHEET 4 AA1 5 GLY C 431 ASN C 437 -1 N ILE C 434 O VAL C 511 SHEET 5 AA1 5 THR C 376 CYS C 379 -1 N THR C 376 O ALA C 435 SHEET 1 AA2 2 CYS C 361 VAL C 362 0 SHEET 2 AA2 2 VAL C 524 CYS C 525 1 O CYS C 525 N CYS C 361 SHEET 1 AA3 2 TYR C 473 GLN C 474 0 SHEET 2 AA3 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SHEET 1 AA4 4 THR A 3 GLU A 6 0 SHEET 2 AA4 4 LEU A 20 SER A 25 -1 O THR A 23 N ARG A 5 SHEET 3 AA4 4 GLN A 79 THR A 83 -1 O VAL A 80 N CYS A 22 SHEET 4 AA4 4 THR A 70 LYS A 73 -1 N THR A 70 O THR A 83 SHEET 1 AA5 3 LEU A 11 VAL A 12 0 SHEET 2 AA5 3 THR A 114 VAL A 118 1 O THR A 117 N VAL A 12 SHEET 3 AA5 3 ALA A 93 TYR A 95 -1 N ALA A 93 O VAL A 116 SHEET 1 AA6 3 GLY A 37 ARG A 40 0 SHEET 2 AA6 3 GLU A 48 ILE A 53 -1 O GLU A 48 N ARG A 40 SHEET 3 AA6 3 LYS A 59 TYR A 61 -1 O ARG A 60 N LEU A 52 SHEET 1 AA7 2 SER B 9 GLY B 12 0 SHEET 2 AA7 2 LYS B 105 VAL B 108 1 O LYS B 105 N VAL B 10 SHEET 1 AA8 3 ILE B 18 THR B 23 0 SHEET 2 AA8 3 THR B 72 ILE B 77 -1 O ILE B 77 N ILE B 18 SHEET 3 AA8 3 PHE B 64 LYS B 68 -1 N SER B 67 O SER B 74 SHEET 1 AA9 4 LYS B 47 ILE B 50 0 SHEET 2 AA9 4 VAL B 35 GLN B 40 -1 N GLN B 39 O LYS B 47 SHEET 3 AA9 4 ASP B 87 TYR B 93 -1 O SER B 91 N SER B 36 SHEET 4 AA9 4 VAL B 98 VAL B 99 -1 O VAL B 99 N SER B 92 SSBOND 1 CYS C 336 CYS C 361 1555 1555 2.03 SSBOND 2 CYS C 379 CYS C 432 1555 1555 2.03 SSBOND 3 CYS C 391 CYS C 525 1555 1555 2.03 SSBOND 4 CYS C 480 CYS C 488 1555 1555 2.03 SSBOND 5 CYS A 22 CYS A 97 1555 1555 2.03 SSBOND 6 CYS B 22 CYS B 90 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