HEADER VIRAL PROTEIN/IMMUNE SYSTEM 25-JUL-22 8DTK TITLE STRUCTURE OF RBD DIRECTED ANTIBODY DH1047 IN COMPLEX WITH SARS-COV-2 TITLE 2 SPIKE: LOCAL REFINEMENT OF RBD-FAB INTERACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DH1047 FAB LIGHT CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DH1047 FAB HEAVY CHAIN; COMPND 11 CHAIN: C; 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 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS RBD, FAB, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR A.J.MAY,K.MANNE,P.ACHARYA REVDAT 2 28-FEB-24 8DTK 1 JRNL REMARK REVDAT 1 02-AUG-23 8DTK 0 JRNL AUTH R.D.MALEWANA,V.STALLS,A.MAY,X.LU,D.R.MARTINEZ,A.SCHAFER, JRNL AUTH 2 D.LI,M.BARR,L.L.SUTHERLAND,E.LEE,R.PARKS,W.E.BECK,A.NEWMAN, JRNL AUTH 3 K.W.BOCK,M.MINAI,B.M.NAGATA,C.T.DEMARCO,T.N.DENNY, JRNL AUTH 4 T.H.OGUIN 3RD,W.ROUNTREE,Y.WANG,K.MANSOURI,R.J.EDWARDS, JRNL AUTH 5 G.D.SEMPOWSKI,A.EATON,H.MURAMATSU,R.HENDERSON,Y.TAM, JRNL AUTH 6 C.BARBOSA,J.TANG,D.W.CAIN,S.SANTRA,I.N.MOORE,H.ANDERSEN, JRNL AUTH 7 M.G.LEWIS,H.GOLDING,R.SEDER,S.KHURANA,D.C.MONTEFIORI, JRNL AUTH 8 N.PARDI,D.WEISSMAN,R.S.BARIC,P.ACHARYA,B.F.HAYNES, JRNL AUTH 9 K.O.SAUNDERS JRNL TITL BROADLY NEUTRALIZING ANTIBODY INDUCTION BY NON-STABILIZED JRNL TITL 2 SARS-COV-2 SPIKE MRNA VACCINATION IN NONHUMAN PRIMATES. JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL PMID 38187726 JRNL DOI 10.1101/2023.12.18.572191 REMARK 2 REMARK 2 RESOLUTION. 3.77 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 : 7LD1 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) : 3.770 REMARK 3 NUMBER OF PARTICLES : 398238 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 8DTK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267346. 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 DIRECTED ANTIBODY DH1047 IN REMARK 245 COMPLEX WITH SARS-COV-2 SPIKE 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 6677.00 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, B, C 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 O ASN A 439 OG SER A 443 2.10 REMARK 500 O TYR B 49 OH TYR B 91 2.12 REMARK 500 OD1 ASP C 86 OH TYR C 90 2.12 REMARK 500 O VAL C 96 OG1 THR C 100L 2.14 REMARK 500 OG SER B 63 OG1 THR B 74 2.19 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 LEU C 4 CB - CG - CD2 ANGL. DEV. = 10.7 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 ASN A 331 -179.18 -170.30 REMARK 500 PRO A 337 47.85 -82.88 REMARK 500 ASP A 389 17.96 -142.00 REMARK 500 TRP B 50 -164.76 -79.46 REMARK 500 PRO B 95 37.96 -95.34 REMARK 500 GLU C 81 42.76 -141.06 REMARK 500 THR C 100L -131.47 64.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27703 RELATED DB: EMDB REMARK 900 STRUCTURE OF RBD DIRECTED ANTIBODY DH1047 IN COMPLEX WITH SARS-COV- REMARK 900 2 SPIKE: LOCAL REFINEMENT OF RBD-FAB INTERACE DBREF 8DTK A 330 532 UNP P0DTC2 SPIKE_SARS2 330 532 DBREF 8DTK B 1 107 PDB 8DTK 8DTK 1 107 DBREF 8DTK C 1 115 PDB 8DTK 8DTK 1 115 SEQRES 1 A 203 PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE SEQRES 2 A 203 ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG SEQRES 3 A 203 LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU SEQRES 4 A 203 TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY SEQRES 5 A 203 VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN SEQRES 6 A 203 VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL SEQRES 7 A 203 ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP SEQRES 8 A 203 TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL SEQRES 9 A 203 ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY SEQRES 10 A 203 GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER SEQRES 11 A 203 ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE SEQRES 12 A 203 TYR GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY SEQRES 13 A 203 PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN SEQRES 14 A 203 PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL SEQRES 15 A 203 VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL SEQRES 16 A 203 CYS GLY PRO LYS LYS SER THR ASN SEQRES 1 B 113 ASP ILE VAL MET THR GLN SER PRO ASP SER LEU ALA VAL SEQRES 2 B 113 SER LEU GLY GLU ARG ALA THR ILE ASN CYS ARG SER SER SEQRES 3 B 113 GLN SER VAL LEU TYR SER SER ASN ASN GLU ASN TYR LEU SEQRES 4 B 113 ALA TRP TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU SEQRES 5 B 113 LEU ILE TYR TRP ALA SER THR ARG GLU SER GLY ILE PRO SEQRES 6 B 113 ASP ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR SEQRES 7 B 113 LEU THR ILE SER ARG LEU GLN ALA GLU ASP VAL ALA VAL SEQRES 8 B 113 TYR TYR CYS GLN GLN TYR TYR SER LEU PRO ARG THR PHE SEQRES 9 B 113 GLY GLN GLY THR LYS VAL GLU ILE LYS SEQRES 1 C 133 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 C 133 PRO GLY ALA SER VAL GLN VAL SER CYS GLN ALA SER ALA SEQRES 3 C 133 ASN THR PHE THR ASN HIS TYR ILE HIS TRP VAL ARG GLN SEQRES 4 C 133 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ILE ILE TYR SEQRES 5 C 133 PRO THR GLY GLY ASN THR ILE TYR ALA GLN GLY PHE GLN SEQRES 6 C 133 GLY ARG VAL THR MET THR ARG ASP THR SER LEU ASN THR SEQRES 7 C 133 ILE TYR LEU GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 C 133 ALA VAL TYR TYR CYS ALA ARG ASP VAL ARG VAL ASP ASP SEQRES 9 C 133 SER TRP SER GLY TYR ASP LEU LEU SER GLY GLY THR TYR SEQRES 10 C 133 PHE ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SEQRES 11 C 133 SER ALA SER HET NAG A 601 28 HET NAG A 602 28 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 A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 TYR A 365 ASN A 370 1 6 HELIX 4 AA4 PRO A 384 LEU A 390 5 7 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 GLY A 502 TYR A 505 5 4 HELIX 8 AA8 GLN C 61 GLN C 64 5 4 HELIX 9 AA9 ARG C 83 THR C 87 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 VAL A 511 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 ILE A 434 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 PHE A 374 THR A 376 -1 N THR A 376 O ALA A 435 SHEET 1 AA2 3 ASN A 354 ILE A 358 0 SHEET 2 AA2 3 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA2 3 SER A 514 GLU A 516 -1 O SER A 514 N TYR A 396 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 MET B 4 THR B 5 0 SHEET 2 AA5 4 ALA B 19 SER B 25 -1 O ARG B 24 N THR B 5 SHEET 3 AA5 4 ASP B 70 ILE B 75 -1 O PHE B 71 N CYS B 23 SHEET 4 AA5 4 PHE B 62 SER B 67 -1 N SER B 63 O THR B 74 SHEET 1 AA6 5 SER B 10 VAL B 13 0 SHEET 2 AA6 5 THR B 102 ILE B 106 1 O GLU B 105 N VAL B 13 SHEET 3 AA6 5 VAL B 85 GLN B 89 -1 N TYR B 86 O THR B 102 SHEET 4 AA6 5 ALA B 34 GLN B 38 -1 N TYR B 36 O TYR B 87 SHEET 5 AA6 5 LYS B 45 ILE B 48 -1 O LEU B 47 N TRP B 35 SHEET 1 AA7 3 LEU C 4 GLN C 6 0 SHEET 2 AA7 3 SER C 21 ALA C 24 -1 O GLN C 23 N VAL C 5 SHEET 3 AA7 3 ILE C 78 TYR C 79 -1 O ILE C 78 N CYS C 22 SHEET 1 AA8 6 GLU C 10 LYS C 12 0 SHEET 2 AA8 6 LEU C 108 VAL C 111 1 O THR C 110 N LYS C 12 SHEET 3 AA8 6 ALA C 88 TYR C 91 -1 N ALA C 88 O VAL C 109 SHEET 4 AA8 6 ILE C 34 GLN C 39 -1 N VAL C 37 O TYR C 91 SHEET 5 AA8 6 LEU C 45 ILE C 51 -1 O GLU C 46 N ARG C 38 SHEET 6 AA8 6 THR C 57 TYR C 59 -1 O ILE C 58 N ILE C 50 SHEET 1 AA9 2 SER C 17 VAL C 18 0 SHEET 2 AA9 2 LEU C 82 SER C 82A-1 O LEU C 82 N VAL C 18 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.04 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS B 23 CYS B 88 1555 1555 2.04 SSBOND 6 CYS C 22 CYS C 92 1555 1555 2.03 LINK ND2 ASN A 331 C1 NAG A 601 1555 1555 1.44 LINK ND2 ASN A 343 C1 NAG A 602 1555 1555 1.44 CISPEP 1 LEU B 94 PRO B 95 0 1.95 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