HEADER VIRAL PROTEIN/IMMUNE SYSTEM 18-JUL-22 8DPZ TITLE LOCAL REFINEMENT OF SARS-COV-2 VACCINE INDUCED ANTIBODY DH1338 BOUND TITLE 2 TO SARS-COV-2 HEXAPRO RBD SPIKE ECTODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DH1338 FAB HEAVY CHAIN; COMPND 7 CHAIN: F; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DH1338 FAB LIGHT CHAIN; COMPND 11 CHAIN: G; COMPND 12 ENGINEERED: YES 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 EXPRESSION_SYSTEM_CELL_LINE: 293F; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 11 ORGANISM_TAXID: 9544; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: MACACA MULATTA; SOURCE 16 ORGANISM_TAXID: 9544; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, VIRAL PROTEIN, ANTIBODY, FAB, RBD, VIRAL PROTEIN-IMMUNE KEYWDS 2 SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR V.STALLS,A.J.MAY,P.ACHARYA REVDAT 1 02-AUG-23 8DPZ 0 JRNL AUTH V.STALLS,P.ACHARYA,A.J.MAY,D.MALEWANA JRNL TITL LOCAL REFINEMENT OF SARS-COV-2 VACCINE INDUCED ANTIBODY JRNL TITL 2 AB026500 BOUND TO SARS-COV-2 HEXAPRO RBD SPIKE ECTODOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CRYOSPARC, COOT, ISOLDE, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7LD1 REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 3.380 REMARK 3 NUMBER OF PARTICLES : 110301 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 8DPZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000266992. 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 : AB026500 FAB BOUND TO SARS-COV REMARK 245 -2 HEXAPRO SPIKE S1 LOCAL REMARK 245 REFINEMENT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.50 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 : 7866 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5940.00 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: B, F, G, 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 ILE B 326 REMARK 465 VAL B 327 REMARK 465 ARG B 328 REMARK 465 PHE B 329 REMARK 465 PRO B 330 REMARK 465 ASN B 331 REMARK 465 ILE B 332 REMARK 465 GLY B 476 REMARK 465 SER B 477 REMARK 465 THR B 478 REMARK 465 PRO B 479 REMARK 465 CYS B 480 REMARK 465 ASN B 481 REMARK 465 GLY B 482 REMARK 465 VAL B 483 REMARK 465 GLU B 484 REMARK 465 GLY B 485 REMARK 465 PHE B 486 REMARK 465 ASN B 487 REMARK 465 CYS B 488 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 B 337 24.06 -77.83 REMARK 500 ALA B 352 59.98 -98.87 REMARK 500 ASP B 428 53.42 -92.53 REMARK 500 ILE F 48 -61.24 -95.08 REMARK 500 TYR G 32 75.31 -102.49 REMARK 500 ALA G 51 -1.23 62.74 REMARK 500 TYR G 91 31.89 -142.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27606 RELATED DB: EMDB REMARK 900 TRIMER MAP REMARK 900 RELATED ID: EMD-27644 RELATED DB: EMDB REMARK 900 LOCAL REFINEMENT OF SARS-COV-2 VACCINE INDUCED ANTIBODY AB026500 REMARK 900 BOUND TO SARS-COV-2 HEXAPRO RBD SPIKE ECTODOMAIN DBREF 8DPZ B 326 530 UNP P0DTC2 SPIKE_SARS2 326 530 DBREF 8DPZ F 1 113 PDB 8DPZ 8DPZ 1 113 DBREF 8DPZ G 1 107 PDB 8DPZ 8DPZ 1 107 SEQRES 1 B 205 ILE VAL ARG PHE PRO ASN ILE THR ASN LEU CYS PRO PHE SEQRES 2 B 205 GLY GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL TYR SEQRES 3 B 205 ALA TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP SEQRES 4 B 205 TYR SER VAL LEU TYR ASN SER ALA SER PHE SER THR PHE SEQRES 5 B 205 LYS CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU SEQRES 6 B 205 CYS PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG SEQRES 7 B 205 GLY ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR GLY SEQRES 8 B 205 LYS ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE SEQRES 9 B 205 THR GLY CYS VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SEQRES 10 B 205 SER LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU SEQRES 11 B 205 PHE ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SEQRES 12 B 205 SER THR GLU ILE TYR GLN ALA GLY SER THR PRO CYS ASN SEQRES 13 B 205 GLY VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU GLN SER SEQRES 14 B 205 TYR GLY PHE GLN PRO THR ASN GLY VAL GLY TYR GLN PRO SEQRES 15 B 205 TYR ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA SEQRES 16 B 205 PRO ALA THR VAL CYS GLY PRO LYS LYS SER SEQRES 1 F 128 GLN LEU GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 F 128 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 F 128 GLY SER ILE SER ARG LYS ASN TRP SER TRP ILE ARG GLN SEQRES 4 F 128 PRO PRO GLY LYS GLY LEU GLY TRP ILE GLY ARG ILE SER SEQRES 5 F 128 GLY SER GLY GLY SER THR ASP TYR ASN PRO SER LEU LYS SEQRES 6 F 128 SER ARG VAL THR ILE SER THR ASP THR SER LYS ASN GLN SEQRES 7 F 128 PHE SER LEU LYS LEU SER SER VAL THR ALA ALA ASP THR SEQRES 8 F 128 ALA VAL TYR TYR CYS ALA ARG VAL ALA TYR TYR GLU ASP SEQRES 9 F 128 ASP TYR GLY TYR TYR TYR THR GLU GLY ALA PHE ASP PHE SEQRES 10 F 128 TRP GLY GLN GLY LEU ARG VAL THR VAL SER SER SEQRES 1 G 107 GLU ILE VAL MET THR GLN SER PRO ALA THR LEU SER LEU SEQRES 2 G 107 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG THR SER SEQRES 3 G 107 GLN SER VAL SER SER TYR VAL ALA TRP TYR GLN GLN LYS SEQRES 4 G 107 PRO GLU GLN THR PRO ARG LEU LEU ILE TYR ASP ALA SER SEQRES 5 G 107 SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY GLY SEQRES 6 G 107 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 G 107 GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 G 107 SER ASN TRP PRO TRP THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 G 107 GLU ILE LYS HET NAG A 1 14 HET NAG A 2 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 2(C8 H15 N O6) HELIX 1 AA1 PRO B 337 ASN B 343 1 7 HELIX 2 AA2 ASP B 364 ASN B 370 1 7 HELIX 3 AA3 THR B 385 LEU B 390 5 6 HELIX 4 AA4 GLU B 406 ILE B 410 5 5 HELIX 5 AA5 GLY B 416 ASN B 422 1 7 HELIX 6 AA6 SER B 438 SER B 443 1 6 HELIX 7 AA7 GLY B 502 TYR B 505 5 4 HELIX 8 AA8 THR F 83 THR F 87 5 5 SHEET 1 AA1 9 ASN B 354 ILE B 358 0 SHEET 2 AA1 9 VAL B 395 ARG B 403 -1 O VAL B 395 N ILE B 358 SHEET 3 AA1 9 PRO B 507 LEU B 513 -1 O TYR B 508 N ILE B 402 SHEET 4 AA1 9 CYS B 432 ASN B 437 -1 N ILE B 434 O VAL B 511 SHEET 5 AA1 9 THR B 376 CYS B 379 -1 N LYS B 378 O VAL B 433 SHEET 6 AA1 9 GLY F 100C TRP F 103 -1 O TYR F 100D N PHE B 377 SHEET 7 AA1 9 ALA F 88 GLU F 99 -1 N ALA F 96 O ALA F 100J SHEET 8 AA1 9 LEU F 107 VAL F 111 -1 O VAL F 109 N ALA F 88 SHEET 9 AA1 9 LEU F 11 VAL F 12 1 N VAL F 12 O THR F 110 SHEET 1 AA210 ASN B 354 ILE B 358 0 SHEET 2 AA210 VAL B 395 ARG B 403 -1 O VAL B 395 N ILE B 358 SHEET 3 AA210 PRO B 507 LEU B 513 -1 O TYR B 508 N ILE B 402 SHEET 4 AA210 CYS B 432 ASN B 437 -1 N ILE B 434 O VAL B 511 SHEET 5 AA210 THR B 376 CYS B 379 -1 N LYS B 378 O VAL B 433 SHEET 6 AA210 GLY F 100C TRP F 103 -1 O TYR F 100D N PHE B 377 SHEET 7 AA210 ALA F 88 GLU F 99 -1 N ALA F 96 O ALA F 100J SHEET 8 AA210 ASN F 33 GLN F 39 -1 N ILE F 37 O TYR F 91 SHEET 9 AA210 GLY F 46 SER F 52 -1 O ILE F 51 N TRP F 34 SHEET 10 AA210 THR F 57 TYR F 59 -1 O ASP F 58 N ARG F 50 SHEET 1 AA3 2 LEU B 452 ARG B 454 0 SHEET 2 AA3 2 LEU B 492 SER B 494 -1 O GLN B 493 N TYR B 453 SHEET 1 AA4 4 GLN F 3 SER F 7 0 SHEET 2 AA4 4 THR F 17 SER F 25 -1 O ALA F 23 N GLN F 5 SHEET 3 AA4 4 GLN F 77 SER F 82A-1 O PHE F 78 N CYS F 22 SHEET 4 AA4 4 VAL F 67 ASP F 72 -1 N SER F 70 O SER F 79 SHEET 1 AA5 4 MET G 4 THR G 5 0 SHEET 2 AA5 4 ALA G 19 THR G 25 -1 O ARG G 24 N THR G 5 SHEET 3 AA5 4 ASP G 70 ILE G 75 -1 O PHE G 71 N CYS G 23 SHEET 4 AA5 4 PHE G 62 SER G 67 -1 N SER G 63 O THR G 74 SHEET 1 AA6 6 THR G 10 LEU G 13 0 SHEET 2 AA6 6 THR G 102 ILE G 106 1 O LYS G 103 N LEU G 11 SHEET 3 AA6 6 VAL G 85 GLN G 90 -1 N TYR G 86 O THR G 102 SHEET 4 AA6 6 VAL G 33 GLN G 38 -1 N GLN G 38 O VAL G 85 SHEET 5 AA6 6 ARG G 45 TYR G 49 -1 O LEU G 47 N TRP G 35 SHEET 6 AA6 6 SER G 53 ARG G 54 -1 O SER G 53 N TYR G 49 SSBOND 1 CYS B 336 CYS B 361 1555 1555 2.03 SSBOND 2 CYS B 379 CYS B 432 1555 1555 2.03 SSBOND 3 CYS B 391 CYS B 525 1555 1555 2.03 SSBOND 4 CYS F 22 CYS F 92 1555 1555 2.03 SSBOND 5 CYS G 23 CYS G 88 1555 1555 2.03 LINK ND2 ASN B 343 C1 NAG A 1 1555 1555 1.44 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 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