HEADER VIRAL PROTEIN/IMMUNE SYSTEM 10-JAN-22 7THE TITLE STRUCTURE OF RBD DIRECTED ANTIBODY DH1042 IN COMPLEX WITH SARS-COV-2 TITLE 2 SPIKE: LOCAL REFINEMENT OF RBD-FAB INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DH1042 FAB HEAVY CHAIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DH1042 FAB LIGHT CHAIN; COMPND 12 CHAIN: C; COMPND 13 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_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 21 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 22 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 3 03-AUG-22 7THE 1 JRNL REVDAT 2 20-APR-22 7THE 1 REMARK REVDAT 1 16-FEB-22 7THE 0 JRNL AUTH S.M.GOBEIL,R.HENDERSON,V.STALLS,K.JANOWSKA,X.HUANG,A.MAY, JRNL AUTH 2 M.SPEAKMAN,E.BEAUDOIN,K.MANNE,D.LI,R.PARKS,M.BARR,M.DEYTON, JRNL AUTH 3 M.MARTIN,K.MANSOURI,R.J.EDWARDS,A.EATON,D.C.MONTEFIORI, JRNL AUTH 4 G.D.SEMPOWSKI,K.O.SAUNDERS,K.WIEHE,W.WILLIAMS,B.KORBER, JRNL AUTH 5 B.F.HAYNES,P.ACHARYA JRNL TITL STRUCTURAL DIVERSITY OF THE SARS-COV-2 OMICRON SPIKE. JRNL REF MOL.CELL V. 82 2050 2022 JRNL REFN ISSN 1097-2765 JRNL PMID 35447081 JRNL DOI 10.1016/J.MOLCEL.2022.03.028 REMARK 2 REMARK 2 RESOLUTION. 3.87 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 : 7EAN 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) : 3.870 REMARK 3 NUMBER OF PARTICLES : 78958 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 7THE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000262231. 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 DH1042 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) : 5402.00 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: 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 ARG A 403 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 457 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 38 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 66 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 83 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 94 NE - CZ - NH1 ANGL. DEV. = 3.8 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 PHE A 377 39.41 -144.19 REMARK 500 PHE A 400 -176.88 -171.69 REMARK 500 PRO A 426 171.58 -59.99 REMARK 500 TYR A 449 4.58 -66.07 REMARK 500 ASN A 481 17.63 55.28 REMARK 500 LEU A 517 -76.60 -110.37 REMARK 500 LEU A 518 -156.94 63.51 REMARK 500 THR B 87 41.75 -145.47 REMARK 500 GLN B 100A 41.27 -78.61 REMARK 500 ALA C 50 -156.19 -155.83 REMARK 500 SER C 60 4.16 -68.29 REMARK 500 SER C 67 88.87 -159.68 REMARK 500 THR C 69 -168.43 -160.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-25893 RELATED DB: EMDB REMARK 900 STRUCTURE OF RBD DIRECTED ANTIBODY DH1042 IN COMPLEX WITH SARS-COV- REMARK 900 2 SPIKE: LOCAL REFINEMENT OF RBD-FAB INTERFACE DBREF 7THE A 333 527 UNP P0DTC2 SPIKE_SARS2 333 527 DBREF 7THE B 1 112 PDB 7THE 7THE 1 112 DBREF 7THE C 1 106 PDB 7THE 7THE 1 106 SEQRES 1 A 195 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 195 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 195 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 195 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 195 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 195 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 195 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 195 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 195 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 195 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 195 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 195 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 195 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 195 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 195 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 1 B 122 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 B 122 PRO GLY SER SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 B 122 GLY THR PHE SER SER TYR ALA ILE SER TRP VAL ARG GLN SEQRES 4 B 122 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ARG ILE ILE SEQRES 5 B 122 PRO MET PHE GLY ILE ALA ASN TYR ALA GLN LYS PHE GLN SEQRES 6 B 122 GLY ARG VAL THR ILE THR ALA ASP LYS SER THR SER THR SEQRES 7 B 122 ALA TYR LEU GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 B 122 ALA VAL TYR TYR CYS ALA ARG TYR MET VAL THR ARG ASP SEQRES 9 B 122 GLN TYR TYR TYR ASP MET ASP VAL TRP GLY GLN GLY THR SEQRES 10 B 122 THR VAL THR VAL SER SEQRES 1 C 106 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 C 106 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 C 106 GLN SER ILE SER ASN TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 C 106 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 C 106 SER LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 C 106 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 C 106 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 C 106 TYR SER PRO PRO PRO THR PHE GLY GLN GLY THR LYS LEU SEQRES 9 C 106 GLU ILE HET NAG A 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 A 337 PHE A 342 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 ASP A 364 ASN A 370 1 7 HELIX 4 AA4 SER A 383 ASP A 389 5 7 HELIX 5 AA5 ASP A 405 ALA A 411 5 7 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 SER A 438 SER A 443 1 6 HELIX 8 AA8 LYS B 73 THR B 75 5 3 HELIX 9 AA9 GLN C 79 PHE C 83 5 5 SHEET 1 AA1 4 ASN A 334 LEU A 335 0 SHEET 2 AA1 4 CYS A 361 VAL A 362 1 O VAL A 362 N ASN A 334 SHEET 3 AA1 4 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 4 AA1 4 CYS A 391 PHE A 392 -1 N PHE A 392 O VAL A 524 SHEET 1 AA2 5 ASN A 354 ILE A 358 0 SHEET 2 AA2 5 ASN A 394 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA2 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA2 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA2 5 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 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 GLN B 3 GLN B 6 0 SHEET 2 AA5 4 VAL B 18 SER B 25 -1 O LYS B 23 N VAL B 5 SHEET 3 AA5 4 THR B 77 LEU B 82 -1 O ALA B 78 N CYS B 22 SHEET 4 AA5 4 VAL B 67 ASP B 72 -1 N THR B 70 O TYR B 79 SHEET 1 AA6 6 GLU B 10 VAL B 11 0 SHEET 2 AA6 6 THR B 107 THR B 110 1 O THR B 110 N GLU B 10 SHEET 3 AA6 6 VAL B 89 TYR B 95 -1 N TYR B 90 O THR B 107 SHEET 4 AA6 6 ALA B 33 GLN B 39 -1 N GLN B 39 O VAL B 89 SHEET 5 AA6 6 LEU B 45 ILE B 51 -1 O MET B 48 N TRP B 36 SHEET 6 AA6 6 ALA B 57 TYR B 59 -1 O ASN B 58 N ARG B 50 SHEET 1 AA7 4 GLU B 10 VAL B 11 0 SHEET 2 AA7 4 THR B 107 THR B 110 1 O THR B 110 N GLU B 10 SHEET 3 AA7 4 VAL B 89 TYR B 95 -1 N TYR B 90 O THR B 107 SHEET 4 AA7 4 VAL B 102 TRP B 103 -1 O VAL B 102 N ARG B 94 SHEET 1 AA8 4 MET C 4 SER C 7 0 SHEET 2 AA8 4 ARG C 18 ALA C 25 -1 O ARG C 24 N THR C 5 SHEET 3 AA8 4 PHE C 71 SER C 76 -1 O ILE C 75 N VAL C 19 SHEET 4 AA8 4 PHE C 62 SER C 65 -1 N SER C 63 O THR C 74 SHEET 1 AA9 5 SER C 10 SER C 12 0 SHEET 2 AA9 5 THR C 102 GLU C 105 1 O GLU C 105 N LEU C 11 SHEET 3 AA9 5 THR C 85 GLN C 90 -1 N TYR C 86 O THR C 102 SHEET 4 AA9 5 LEU C 33 GLN C 38 -1 N TYR C 36 O TYR C 87 SHEET 5 AA9 5 LYS C 45 ILE C 48 -1 O LEU C 47 N TRP C 35 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 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.04 SSBOND 5 CYS B 22 CYS B 92 1555 1555 2.01 SSBOND 6 CYS C 23 CYS C 88 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.46 CISPEP 1 SER C 7 PRO C 8 0 -10.85 CISPEP 2 PRO C 94 PRO C 95 0 -11.14 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