HEADER VIRAL PROTEIN 29-NOV-21 7T01 TITLE SARS-COV-2 S-RBD + FAB 54042-4 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: 54042-4 FAB - HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 54042-4 FAB - LIGHT CHAIN; COMPND 11 CHAIN: L; 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, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 22 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, 54042-4, RBD, FAB, COMPLEX, VIRAL PROTEIN-IMMUNE SYSTEM, KEYWDS 2 VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR N.V.JOHNSON,J.S.MCLELLAN REVDAT 1 13-APR-22 7T01 0 JRNL AUTH K.J.KRAMER,N.V.JOHNSON,A.R.SHIAKOLAS,N.SURYADEVARA, JRNL AUTH 2 S.PERIASAMY,N.RAJU,J.K.WILLIAMS,D.WRAPP,S.J.ZOST,L.M.WALKER, JRNL AUTH 3 S.C.WALL,C.M.HOLT,C.L.HSIEH,R.E.SUTTON,A.PAULO,R.S.NARGI, JRNL AUTH 4 E.DAVIDSON,B.J.DORANZ,J.E.CROWE JR.,A.BUKREYEV,R.H.CARNAHAN, JRNL AUTH 5 J.S.MCLELLAN,I.S.GEORGIEV JRNL TITL POTENT NEUTRALIZATION OF SARS-COV-2 VARIANTS OF CONCERN BY JRNL TITL 2 AN ANTIBODY WITH AN UNCOMMON GENETIC SIGNATURE AND JRNL TITL 3 STRUCTURAL MODE OF SPIKE RECOGNITION. JRNL REF CELL REP V. 37 09784 2021 JRNL REFN ESSN 2211-1247 JRNL PMID 34592170 JRNL DOI 10.1016/J.CELREP.2021.109784 REMARK 2 REMARK 2 RESOLUTION. 2.69 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) : 2.690 REMARK 3 NUMBER OF PARTICLES : 214408 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 7T01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000261309. 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 : COMPLEX OF SARS-COV-2 S-ECD REMARK 245 WITH 54042-4 FAB REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : -4 FORCE, 3 S BLOT 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) : 1.50 REMARK 245 MAXIMUM DEFOCUS (NM) : 2.50 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) : 7000.00 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, H, L 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 LEU H 29 CA - CB - CG ANGL. DEV. = 14.1 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 PRO A 337 42.99 -72.88 REMARK 500 THR H 15 54.89 -91.09 REMARK 500 ASN H 86 115.20 -160.53 REMARK 500 PHE L 30 -126.13 55.11 REMARK 500 SER L 52 -0.57 78.16 REMARK 500 SER L 77 107.46 -163.52 REMARK 500 HIS L 92 -59.51 -128.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-25574 RELATED DB: EMDB REMARK 900 SARS-COV-2 S-RBD + FAB 54042-4 DBREF 7T01 A 329 529 UNP P0DTC2 SPIKE_SARS2 329 529 DBREF 7T01 H 1 120 PDB 7T01 7T01 1 120 DBREF 7T01 L 1 107 PDB 7T01 7T01 1 107 SEQRES 1 A 201 PHE PRO ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL SEQRES 2 A 201 PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN SEQRES 3 A 201 ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL SEQRES 4 A 201 LEU TYR ASN SER ALA SER PHE SER THR PHE LYS CYS TYR SEQRES 5 A 201 GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR SEQRES 6 A 201 ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU SEQRES 7 A 201 VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA SEQRES 8 A 201 ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS SEQRES 9 A 201 VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL SEQRES 10 A 201 GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SEQRES 11 A 201 SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU SEQRES 12 A 201 ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU SEQRES 13 A 201 GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE SEQRES 14 A 201 GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL SEQRES 15 A 201 VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR SEQRES 16 A 201 VAL CYS GLY PRO LYS LYS SEQRES 1 H 120 GLN ILE THR LEU LYS GLU SER GLY PRO THR LEU VAL LYS SEQRES 2 H 120 PRO THR GLN THR LEU THR LEU THR CYS THR PHE SER GLY SEQRES 3 H 120 PHE SER LEU SER THR ILE GLY VAL GLY VAL SER TRP ILE SEQRES 4 H 120 ARG GLN PRO PRO GLY LYS ALA LEU ASP TRP LEU ALA LEU SEQRES 5 H 120 ILE TYR TRP ASP ASP ASP LYS ARG TYR SER PRO SER LEU SEQRES 6 H 120 LYS SER ARG LEU THR VAL THR MET ASP THR SER LYS ASN SEQRES 7 H 120 GLN VAL VAL LEU THR LEU THR ASN MET ASP PRO VAL ASP SEQRES 8 H 120 THR ALA THR TYR PHE CYS ALA HIS GLY LEU PHE SER SER SEQRES 9 H 120 SER ASP TRP GLY GLY LEU ASP VAL TRP GLY GLN GLY THR SEQRES 10 H 120 THR VAL THR SEQRES 1 L 107 ASP MET GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 107 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 107 GLN SER VAL PHE THR TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 L 107 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 L 107 ARG LEU GLN SER GLY VAL PRO SER ARG PHE ARG GLY SER SEQRES 6 L 107 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 107 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 L 107 HIS SER THR PRO PHE ILE PHE GLY PRO GLY THR LYS VAL SEQRES 9 L 107 ASP ILE LYS HELIX 1 AA1 PHE A 338 ASN A 343 1 6 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 THR A 385 LEU A 390 5 6 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 SER A 438 SER A 443 1 6 HELIX 8 AA8 PRO H 63 LYS H 66 5 4 HELIX 9 AA9 ASP H 88 THR H 92 5 5 HELIX 10 AB1 GLN L 79 PHE L 83 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 ALA A 397 N LYS A 356 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O VAL A 510 N PHE A 400 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 CYS A 379 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA2 2 CYS A 361 VAL A 362 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 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 LEU H 4 SER H 7 0 SHEET 2 AA5 4 LEU H 20 SER H 25 -1 O THR H 23 N GLU H 6 SHEET 3 AA5 4 GLN H 79 LEU H 84 -1 O VAL H 80 N CYS H 22 SHEET 4 AA5 4 LEU H 69 ASP H 74 -1 N THR H 72 O VAL H 81 SHEET 1 AA6 5 LYS H 59 TYR H 61 0 SHEET 2 AA6 5 ASP H 48 TYR H 54 -1 N LEU H 52 O ARG H 60 SHEET 3 AA6 5 VAL H 34 GLN H 41 -1 N ARG H 40 O ASP H 48 SHEET 4 AA6 5 THR H 94 LEU H 101 -1 O PHE H 96 N ILE H 39 SHEET 5 AA6 5 VAL H 112 TRP H 113 -1 O VAL H 112 N HIS H 99 SHEET 1 AA7 5 LYS H 59 TYR H 61 0 SHEET 2 AA7 5 ASP H 48 TYR H 54 -1 N LEU H 52 O ARG H 60 SHEET 3 AA7 5 VAL H 34 GLN H 41 -1 N ARG H 40 O ASP H 48 SHEET 4 AA7 5 THR H 94 LEU H 101 -1 O PHE H 96 N ILE H 39 SHEET 5 AA7 5 THR H 117 THR H 118 -1 O THR H 117 N TYR H 95 SHEET 1 AA8 4 MET L 4 GLN L 6 0 SHEET 2 AA8 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA8 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 AA8 4 PHE L 62 SER L 67 -1 N SER L 65 O THR L 72 SHEET 1 AA9 6 SER L 10 SER L 12 0 SHEET 2 AA9 6 THR L 102 ASP L 105 1 O ASP L 105 N LEU L 11 SHEET 3 AA9 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA9 6 LEU L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 AA9 6 LYS L 45 ALA L 50 -1 O LYS L 45 N GLN L 37 SHEET 6 AA9 6 ARG L 53 LEU L 54 -1 O ARG L 53 N ALA L 50 SSBOND 1 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 2 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 97 1555 1555 2.04 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