HEADER VIRAL PROTEIN/IMMUNE SYSTEM 21-NOV-21 7SWW TITLE SARS-COV-2 SPIKE NTD IN COMPLEX WITH NEUTRALIZING FAB SARS2-57 (LOCAL TITLE 2 REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 14-304); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SARS2-57 FV HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SARS2-57 FV LIGHT CHAIN; COMPND 11 CHAIN: L 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 EXPRESSION_SYSTEM_CELL_LINE: EXPI293; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 17 ORGANISM_COMMON: MOUSE; SOURCE 18 ORGANISM_TAXID: 10090 KEYWDS GLYCOPROTEIN, ANTIBODY, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS OF INFECTIOUS DISEASES, CSGID, VIRAL PROTEIN-IMMUNE SYSTEM KEYWDS 3 COMPLEX, CENTER FOR STRUCTURAL BIOLOGY OF INFECTIOUS DISEASES, CSBID EXPDTA ELECTRON MICROSCOPY AUTHOR L.J.ADAMS,D.H.FREMONT,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS AUTHOR 2 DISEASES (CSGID),CENTER FOR STRUCTURAL BIOLOGY OF INFECTIOUS AUTHOR 3 DISEASES (CSBID) REVDAT 2 01-FEB-23 7SWW 1 KEYWDS AUTHOR REVDAT 1 23-NOV-22 7SWW 0 JRNL AUTH L.J.ADAMS,L.A.VANBLARGAN,Z.LIU,P.GILCHUK,H.ZHAO,R.E.CHEN, JRNL AUTH 2 S.RAJU,B.WHITENER,S.SHRIHARI,P.N.JETHVA,M.L.GROSS,J.E.CROWE, JRNL AUTH 3 S.P.J.WHELAN,M.S.DIAMOND,D.H.FREMONT JRNL TITL A PROTECTIVE ANTIBODY TARGETING THE N-TERMINAL DOMAIN OF JRNL TITL 2 SARS-COV-2 SPIKE RECOGNIZES MOST EMERGING VARIANTS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.13 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) : 3.130 REMARK 3 NUMBER OF PARTICLES : 241481 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 7SWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000261104. 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 : SARS-COV-2 SPIKE BOUND BY SARS2 REMARK 245 -57 FAB 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 : 7.40 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 K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 6690.00 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, 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 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 LEU A 176 REMARK 465 MET A 177 REMARK 465 ASP A 178 REMARK 465 LEU A 179 REMARK 465 GLU A 180 REMARK 465 GLY A 181 REMARK 465 LYS A 182 REMARK 465 GLN A 183 REMARK 465 GLY A 184 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 LYS A 41 58.53 -98.39 REMARK 500 SER A 98 19.62 59.57 REMARK 500 PRO A 230 57.33 -90.59 REMARK 500 GLN H 43 -0.08 79.31 REMARK 500 ALA L 57 -10.58 74.34 REMARK 500 SER L 73 -169.23 -127.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-25487 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-25488 RELATED DB: EMDB DBREF 7SWW A 14 304 UNP P0DTC2 SPIKE_SARS2 14 304 DBREF 7SWW H 1 117 PDB 7SWW 7SWW 1 117 DBREF 7SWW L 1 112 PDB 7SWW 7SWW 1 112 SEQRES 1 A 291 GLN CYS VAL ASN LEU THR THR ARG THR GLN LEU PRO PRO SEQRES 2 A 291 ALA TYR THR ASN SER PHE THR ARG GLY VAL TYR TYR PRO SEQRES 3 A 291 ASP LYS VAL PHE ARG SER SER VAL LEU HIS SER THR GLN SEQRES 4 A 291 ASP LEU PHE LEU PRO PHE PHE SER ASN VAL THR TRP PHE SEQRES 5 A 291 HIS ALA ILE HIS VAL SER GLY THR ASN GLY THR LYS ARG SEQRES 6 A 291 PHE ASP ASN PRO VAL LEU PRO PHE ASN ASP GLY VAL TYR SEQRES 7 A 291 PHE ALA SER THR GLU LYS SER ASN ILE ILE ARG GLY TRP SEQRES 8 A 291 ILE PHE GLY THR THR LEU ASP SER LYS THR GLN SER LEU SEQRES 9 A 291 LEU ILE VAL ASN ASN ALA THR ASN VAL VAL ILE LYS VAL SEQRES 10 A 291 CYS GLU PHE GLN PHE CYS ASN ASP PRO PHE LEU GLY VAL SEQRES 11 A 291 TYR TYR HIS LYS ASN ASN LYS SER TRP MET GLU SER GLU SEQRES 12 A 291 PHE ARG VAL TYR SER SER ALA ASN ASN CYS THR PHE GLU SEQRES 13 A 291 TYR VAL SER GLN PRO PHE LEU MET ASP LEU GLU GLY LYS SEQRES 14 A 291 GLN GLY ASN PHE LYS ASN LEU ARG GLU PHE VAL PHE LYS SEQRES 15 A 291 ASN ILE ASP GLY TYR PHE LYS ILE TYR SER LYS HIS THR SEQRES 16 A 291 PRO ILE ASN LEU VAL ARG ASP LEU PRO GLN GLY PHE SER SEQRES 17 A 291 ALA LEU GLU PRO LEU VAL ASP LEU PRO ILE GLY ILE ASN SEQRES 18 A 291 ILE THR ARG PHE GLN THR LEU LEU ALA LEU HIS ARG SER SEQRES 19 A 291 TYR LEU THR PRO GLY ASP SER SER SER GLY TRP THR ALA SEQRES 20 A 291 GLY ALA ALA ALA TYR TYR VAL GLY TYR LEU GLN PRO ARG SEQRES 21 A 291 THR PHE LEU LEU LYS TYR ASN GLU ASN GLY THR ILE THR SEQRES 22 A 291 ASP ALA VAL ASP CYS ALA LEU ASP PRO LEU SER GLU THR SEQRES 23 A 291 LYS CYS THR LEU LYS SEQRES 1 H 117 GLU VAL GLN LEU GLN GLN SER GLY ALA GLU LEU VAL ARG SEQRES 2 H 117 PRO GLY ALA LEU VAL LYS LEU SER CYS LYS ALA SER GLY SEQRES 3 H 117 PHE ASN ILE LYS ASP TYR PHE VAL HIS TRP VAL LYS GLN SEQRES 4 H 117 ARG PRO VAL GLN GLY LEU GLU TRP ILE GLY TRP ILE ASP SEQRES 5 H 117 PRO GLU ASN GLY ASN THR ILE TYR GLY PRO LYS PHE GLN SEQRES 6 H 117 GLY LYS ALA SER LEU ALA ALA ASP THR SER SER ASN THR SEQRES 7 H 117 GLY TYR LEU GLN LEU SER SER LEU THR SER GLU ASP THR SEQRES 8 H 117 ALA VAL TYR TYR CYS ALA ARG TRP ASP GLY TYR GLU THR SEQRES 9 H 117 LEU ASP TYR TRP GLY GLN GLY THR SER VAL THR VAL SER SEQRES 1 L 112 ASP ILE VAL MET SER GLN SER PRO SER SER LEU ALA VAL SEQRES 2 L 112 SER VAL GLY GLU LYS VAL THR MET SER CYS GLN SER SER SEQRES 3 L 112 GLN SER LEU LEU TYR SER ASN ASN GLU LYS ASN TYR LEU SEQRES 4 L 112 ALA TRP TYR GLN GLN LYS PRO GLY HIS SER PRO LYS LEU SEQRES 5 L 112 LEU LEU TYR TRP ALA SER THR ARG GLU SER GLY VAL PRO SEQRES 6 L 112 ASP ARG PHE THR GLY SER GLY SER GLY THR ALA PHE THR SEQRES 7 L 112 LEU THR ILE SER SER VAL LYS ALA GLU ASP LEU ALA VAL SEQRES 8 L 112 TYR TYR CYS GLN GLN TYR TYR ASN TYR PRO TYR THR PHE SEQRES 9 L 112 GLY GLY GLY THR LYS LEU GLU ILE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET NAG A 401 14 HET NAG A 402 14 HET NAG A 403 14 HET NAG A 404 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 8(C8 H15 N O6) HELIX 1 AA1 ASP A 294 LYS A 304 1 11 HELIX 2 AA2 ASN H 28 TYR H 32 5 5 SHEET 1 AA1 8 ALA A 27 ASN A 30 0 SHEET 2 AA1 8 ASN A 61 ILE A 68 -1 O TRP A 64 N ALA A 27 SHEET 3 AA1 8 ALA A 262 TYR A 269 -1 O TYR A 265 N PHE A 65 SHEET 4 AA1 8 VAL A 90 GLU A 96 -1 N TYR A 91 O GLY A 268 SHEET 5 AA1 8 ASN A 188 ILE A 197 -1 O PHE A 192 N PHE A 92 SHEET 6 AA1 8 TYR A 200 PRO A 209 -1 O LYS A 202 N LYS A 195 SHEET 7 AA1 8 ALA A 222 LEU A 229 -1 O VAL A 227 N ILE A 203 SHEET 8 AA1 8 VAL A 36 TYR A 37 1 N VAL A 36 O LEU A 223 SHEET 1 AA2 3 LEU A 48 PHE A 55 0 SHEET 2 AA2 3 GLN A 271 TYR A 279 -1 O LEU A 277 N HIS A 49 SHEET 3 AA2 3 ILE A 285 ASP A 290 -1 O ASP A 287 N LYS A 278 SHEET 1 AA3 4 LEU A 84 PRO A 85 0 SHEET 2 AA3 4 ARG A 237 ARG A 246 -1 O PHE A 238 N LEU A 84 SHEET 3 AA3 4 PHE A 140 TYR A 145 1 N VAL A 143 O LEU A 244 SHEET 4 AA3 4 TRP A 152 GLU A 156 -1 O GLU A 156 N GLY A 142 SHEET 1 AA4 6 LEU A 84 PRO A 85 0 SHEET 2 AA4 6 ARG A 237 ARG A 246 -1 O PHE A 238 N LEU A 84 SHEET 3 AA4 6 ILE A 101 GLY A 107 -1 N ILE A 105 O GLN A 239 SHEET 4 AA4 6 GLN A 115 ASN A 122 -1 O LEU A 117 N PHE A 106 SHEET 5 AA4 6 ASN A 125 PHE A 135 -1 O LYS A 129 N LEU A 118 SHEET 6 AA4 6 TYR A 160 SER A 172 -1 O SER A 161 N GLN A 134 SHEET 1 AA5 4 LEU H 4 GLN H 6 0 SHEET 2 AA5 4 VAL H 18 ALA H 24 -1 O LYS H 23 N GLN H 5 SHEET 3 AA5 4 THR H 78 LEU H 83 -1 O GLY H 79 N CYS H 22 SHEET 4 AA5 4 SER H 69 ASP H 73 -1 N SER H 69 O GLN H 82 SHEET 1 AA6 6 GLU H 10 VAL H 12 0 SHEET 2 AA6 6 THR H 112 VAL H 116 1 O SER H 113 N GLU H 10 SHEET 3 AA6 6 VAL H 93 TRP H 99 -1 N TYR H 94 O THR H 112 SHEET 4 AA6 6 PHE H 33 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA6 6 LEU H 45 ASP H 52 -1 O GLU H 46 N LYS H 38 SHEET 6 AA6 6 ASN H 57 TYR H 60 -1 O ASN H 57 N ASP H 52 SHEET 1 AA7 4 GLU H 10 VAL H 12 0 SHEET 2 AA7 4 THR H 112 VAL H 116 1 O SER H 113 N GLU H 10 SHEET 3 AA7 4 VAL H 93 TRP H 99 -1 N TYR H 94 O THR H 112 SHEET 4 AA7 4 LEU H 105 TRP H 108 -1 O ASP H 106 N ARG H 98 SHEET 1 AA8 4 MET L 4 SER L 7 0 SHEET 2 AA8 4 VAL L 19 SER L 25 -1 O SER L 22 N SER L 7 SHEET 3 AA8 4 ALA L 76 ILE L 81 -1 O PHE L 77 N CYS L 23 SHEET 4 AA8 4 THR L 69 GLY L 72 -1 N THR L 69 O THR L 80 SHEET 1 AA9 5 SER L 10 ALA L 12 0 SHEET 2 AA9 5 THR L 108 GLU L 111 1 O GLU L 111 N LEU L 11 SHEET 3 AA9 5 ALA L 90 GLN L 96 -1 N TYR L 92 O THR L 108 SHEET 4 AA9 5 LEU L 39 GLN L 44 -1 N GLN L 44 O VAL L 91 SHEET 5 AA9 5 LYS L 51 LEU L 52 -1 O LYS L 51 N GLN L 43 SHEET 1 AB1 2 LEU L 30 TYR L 31 0 SHEET 2 AB1 2 LYS L 36 ASN L 37 -1 O LYS L 36 N TYR L 31 SSBOND 1 CYS A 15 CYS A 136 1555 1555 2.03 SSBOND 2 CYS A 131 CYS A 166 1555 1555 2.03 SSBOND 3 CYS A 291 CYS A 301 1555 1555 2.03 SSBOND 4 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 5 CYS L 23 CYS L 94 1555 1555 2.04 LINK ND2 ASN A 17 C1 NAG A 401 1555 1555 1.45 LINK ND2 ASN A 61 C1 NAG A 402 1555 1555 1.44 LINK ND2 ASN A 125 C1 NAG A 403 1555 1555 1.45 LINK ND2 ASN A 149 C1 NAG A 404 1555 1555 1.45 LINK ND2 ASN A 165 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 234 C1 NAG C 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 CISPEP 1 SER L 7 PRO L 8 0 -1.34 CISPEP 2 TYR L 100 PRO L 101 0 -5.87 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