HEADER VIRAL PROTEIN/IMMUNE SYSTEM 02-SEP-25 9WLA TITLE LOCAL REFINEMENT REGION OF SARS-COV-2 SPIKE RBD IN COMPLEX WITH TITLE 2 ANTIBODIES CT1-5. COMPND MOL_ID: 1; COMPND 2 MOLECULE: S309 FAB LIGHT CHAIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: S309 FAB HEAVY CHAIN; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: R; COMPND 12 FRAGMENT: RBD; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: CT1-5 FAB HEAVY CHAIN; COMPND 16 CHAIN: H; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 5; COMPND 19 MOLECULE: CT1-5 FAB LIGHT CHAIN; COMPND 20 CHAIN: L; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 13 2; SOURCE 14 ORGANISM_TAXID: 2697049; SOURCE 15 STRAIN: WT; SOURCE 16 GENE: S, 2; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 19 MOL_ID: 4; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_TAXID: 9606; SOURCE 22 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 24 MOL_ID: 5; SOURCE 25 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 26 ORGANISM_TAXID: 9606; SOURCE 27 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, RBD, FAB, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN- KEYWDS 2 IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Y.JIANG,H.SUN,Q.ZHENG,S.LI REVDAT 1 03-JUN-26 9WLA 0 JRNL AUTH Y.JIANG,H.SUN,Q.ZHENG,S.LI JRNL TITL LOCAL REFINEMENT REGION OF SARS-COV-2 SPIKE RBD IN COMPLEX JRNL TITL 2 WITH ANTIBODIES CT1-5. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC 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) : 3.600 REMARK 3 NUMBER OF PARTICLES : 49476 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 9WLA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 07-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300060606. 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 IN COMPLEX REMARK 245 WITH S309 AND CT1-5 FAB; SARS- REMARK 245 COV-2 SPIKE; THE FAB OF S309; REMARK 245 THE FAB OF CT1-5 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2100.00 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) : 4800.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : OTHER 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, R, 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 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 GLU B 1 REMARK 465 ARG B 108 REMARK 465 THR B 109 REMARK 465 VAL B 110 REMARK 465 ALA B 111 REMARK 465 ALA B 112 REMARK 465 PRO B 113 REMARK 465 SER B 114 REMARK 465 VAL B 115 REMARK 465 PHE B 116 REMARK 465 ILE B 117 REMARK 465 PHE B 118 REMARK 465 PRO B 119 REMARK 465 PRO B 120 REMARK 465 SER B 121 REMARK 465 ASP B 122 REMARK 465 GLU B 123 REMARK 465 GLN B 124 REMARK 465 LEU B 125 REMARK 465 LYS B 126 REMARK 465 SER B 127 REMARK 465 GLY B 128 REMARK 465 THR B 129 REMARK 465 ALA B 130 REMARK 465 SER B 131 REMARK 465 VAL B 132 REMARK 465 VAL B 133 REMARK 465 CYS B 134 REMARK 465 LEU B 135 REMARK 465 LEU B 136 REMARK 465 ASN B 137 REMARK 465 ASN B 138 REMARK 465 PHE B 139 REMARK 465 TYR B 140 REMARK 465 PRO B 141 REMARK 465 ARG B 142 REMARK 465 GLU B 143 REMARK 465 ALA B 144 REMARK 465 LYS B 145 REMARK 465 VAL B 146 REMARK 465 GLN B 147 REMARK 465 TRP B 148 REMARK 465 LYS B 149 REMARK 465 VAL B 150 REMARK 465 ASP B 151 REMARK 465 ASN B 152 REMARK 465 ALA B 153 REMARK 465 LEU B 154 REMARK 465 GLN B 155 REMARK 465 SER B 156 REMARK 465 GLY B 157 REMARK 465 ASN B 158 REMARK 465 SER B 159 REMARK 465 GLN B 160 REMARK 465 GLU B 161 REMARK 465 SER B 162 REMARK 465 VAL B 163 REMARK 465 THR B 164 REMARK 465 GLU B 165 REMARK 465 GLN B 166 REMARK 465 ASP B 167 REMARK 465 SER B 168 REMARK 465 LYS B 169 REMARK 465 ASP B 170 REMARK 465 SER B 171 REMARK 465 THR B 172 REMARK 465 TYR B 173 REMARK 465 SER B 174 REMARK 465 LEU B 175 REMARK 465 SER B 176 REMARK 465 SER B 177 REMARK 465 THR B 178 REMARK 465 LEU B 179 REMARK 465 THR B 180 REMARK 465 LEU B 181 REMARK 465 SER B 182 REMARK 465 LYS B 183 REMARK 465 ALA B 184 REMARK 465 ASP B 185 REMARK 465 TYR B 186 REMARK 465 GLU B 187 REMARK 465 LYS B 188 REMARK 465 HIS B 189 REMARK 465 LYS B 190 REMARK 465 VAL B 191 REMARK 465 TYR B 192 REMARK 465 ALA B 193 REMARK 465 CYS B 194 REMARK 465 GLU B 195 REMARK 465 VAL B 196 REMARK 465 THR B 197 REMARK 465 HIS B 198 REMARK 465 GLN B 199 REMARK 465 GLY B 200 REMARK 465 LEU B 201 REMARK 465 SER B 202 REMARK 465 SER B 203 REMARK 465 PRO B 204 REMARK 465 VAL B 205 REMARK 465 THR B 206 REMARK 465 LYS B 207 REMARK 465 SER B 208 REMARK 465 PHE B 209 REMARK 465 ASN B 210 REMARK 465 ARG B 211 REMARK 465 GLY B 212 REMARK 465 GLU B 213 REMARK 465 CYS B 214 REMARK 465 ARG R 319 REMARK 465 VAL R 320 REMARK 465 GLN R 321 REMARK 465 PRO R 322 REMARK 465 THR R 323 REMARK 465 GLU R 324 REMARK 465 SER R 325 REMARK 465 ILE R 326 REMARK 465 VAL R 327 REMARK 465 ARG R 328 REMARK 465 PHE R 329 REMARK 465 PRO R 330 REMARK 465 ASN R 331 REMARK 465 ILE R 332 REMARK 465 THR R 333 REMARK 465 LYS R 528 REMARK 465 LYS R 529 REMARK 465 SER R 530 REMARK 465 THR R 531 REMARK 465 ASN R 532 REMARK 465 LEU R 533 REMARK 465 VAL R 534 REMARK 465 LYS R 535 REMARK 465 ASN R 536 REMARK 465 LYS R 537 REMARK 465 CYS R 538 REMARK 465 VAL R 539 REMARK 465 ASN R 540 REMARK 465 PHE R 541 REMARK 465 GLN H 1 REMARK 465 GLU H 82 REMARK 465 LEU H 83 REMARK 465 SER H 84 REMARK 465 SER H 85 REMARK 465 SER H 122 REMARK 465 SER H 123 REMARK 465 ASP L 1 REMARK 465 GLU L 17 REMARK 465 ARG L 18 REMARK 465 ALA L 19 REMARK 465 GLY L 67 REMARK 465 SER L 68 REMARK 465 GLY L 69 REMARK 465 ILE L 108 REMARK 465 LYS L 109 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU B 17 CG CD OE1 OE2 REMARK 470 GLN B 27 CG CD OE1 NE2 REMARK 470 THR B 28 OG1 CG2 REMARK 470 SER B 53 OG REMARK 470 ASP B 61 CG OD1 OD2 REMARK 470 ASP B 71 CG OD1 OD2 REMARK 470 ARG B 78 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 80 CG CD OE1 OE2 REMARK 470 GLU B 82 CG CD OE1 OE2 REMARK 470 THR B 102 OG1 CG2 REMARK 470 GLU B 105 CG CD OE1 OE2 REMARK 470 GLN D 1 CG CD OE1 NE2 REMARK 470 GLU D 10 CG CD OE1 OE2 REMARK 470 VAL D 11 CG1 CG2 REMARK 470 LYS D 12 CG CD CE NZ REMARK 470 LYS D 13 CG CD CE NZ REMARK 470 GLN D 43 CG CD OE1 NE2 REMARK 470 GLN D 62 CG CD OE1 NE2 REMARK 470 LYS D 63 CG CD CE NZ REMARK 470 ASP D 73 CG OD1 OD2 REMARK 470 GLU D 82 CG CD OE1 OE2 REMARK 470 ARG D 85 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 108 CG CD OE1 OE2 REMARK 470 ARG R 346 CG CD NE CZ NH1 NH2 REMARK 470 ASN R 360 CG OD1 ND2 REMARK 470 LYS R 378 CG CD CE NZ REMARK 470 LYS R 386 CG CD CE NZ REMARK 470 LEU R 390 CG CD1 CD2 REMARK 470 ASP R 405 CG OD1 OD2 REMARK 470 GLN R 498 CG CD OE1 NE2 REMARK 470 LEU R 518 CG CD1 CD2 REMARK 470 MET H 2 CG SD CE REMARK 470 GLN H 3 CG CD OE1 NE2 REMARK 470 SER H 7 OG REMARK 470 GLU H 10 CG CD OE1 OE2 REMARK 470 LYS H 13 CG CD CE NZ REMARK 470 THR H 16 OG1 CG2 REMARK 470 SER H 17 OG REMARK 470 LYS H 19 CG CD CE NZ REMARK 470 LYS H 23 CG CD CE NZ REMARK 470 SER H 25 OG REMARK 470 THR H 28 OG1 CG2 REMARK 470 SER H 31 OG REMARK 470 SER H 32 OG REMARK 470 ARG H 38 CG CD NE CZ NH1 NH2 REMARK 470 ARG H 41 CG CD NE CZ NH1 NH2 REMARK 470 GLN H 43 CG CD OE1 NE2 REMARK 470 ARG H 44 CG CD NE CZ NH1 NH2 REMARK 470 SER H 55 OG REMARK 470 ASN H 57 CG OD1 ND2 REMARK 470 GLN H 62 CG CD OE1 NE2 REMARK 470 LYS H 63 CG CD CE NZ REMARK 470 GLN H 65 CG CD OE1 NE2 REMARK 470 GLU H 66 CG CD OE1 OE2 REMARK 470 THR H 71 OG1 CG2 REMARK 470 MET H 74 CG SD CE REMARK 470 SER H 75 OG REMARK 470 THR H 76 OG1 CG2 REMARK 470 SER H 77 OG REMARK 470 THR H 78 OG1 CG2 REMARK 470 LEU H 86C CG CD1 CD2 REMARK 470 ARG H 87 CG CD NE CZ NH1 NH2 REMARK 470 SER H 88 OG REMARK 470 GLU H 89 CG CD OE1 OE2 REMARK 470 THR H 91 OG1 CG2 REMARK 470 SER H 105 OG REMARK 470 ASP H 111 CG OD1 OD2 REMARK 470 MET H 118 CG SD CE REMARK 470 VAL H 119 CG1 CG2 REMARK 470 VAL L 3 CG1 CG2 REMARK 470 THR L 5 OG1 CG2 REMARK 470 GLN L 6 CG CD OE1 NE2 REMARK 470 THR L 7 OG1 CG2 REMARK 470 SER L 12 OG REMARK 470 LEU L 13 CG CD1 CD2 REMARK 470 SER L 22 OG REMARK 470 SER L 26 OG REMARK 470 GLN L 27 CG CD OE1 NE2 REMARK 470 SER L 28 OG REMARK 470 SER L 30 OG REMARK 470 SER L 31 OG REMARK 470 SER L 32 OG REMARK 470 LYS L 40 CG CD CE NZ REMARK 470 LEU L 48 CG CD1 CD2 REMARK 470 SER L 53 OG REMARK 470 SER L 54 OG REMARK 470 ASP L 61 CG OD1 OD2 REMARK 470 SER L 64 OG REMARK 470 SER L 66 OG REMARK 470 THR L 70 OG1 CG2 REMARK 470 ASP L 71 CG OD1 OD2 REMARK 470 THR L 73 OG1 CG2 REMARK 470 THR L 75 OG1 CG2 REMARK 470 SER L 77 OG REMARK 470 ARG L 78 CG CD NE CZ NH1 NH2 REMARK 470 LEU L 79 CG CD1 CD2 REMARK 470 GLU L 80 CG CD OE1 OE2 REMARK 470 GLU L 82 CG CD OE1 OE2 REMARK 470 ASP L 83 CG OD1 OD2 REMARK 470 GLN L 91 CG CD OE1 NE2 REMARK 470 THR L 96 OG1 CG2 REMARK 470 THR L 104 OG1 CG2 REMARK 470 VAL L 106 CG1 CG2 REMARK 470 GLU L 107 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO R 521 CG PRO R 521 CD -0.480 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 ASP B 83 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 PRO R 521 N - CA - CB ANGL. DEV. = -7.6 DEGREES REMARK 500 PRO R 521 CA - CB - CG ANGL. DEV. = -20.1 DEGREES REMARK 500 PRO R 521 N - CD - CG ANGL. DEV. = -24.6 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 ASP B 83 46.31 -100.25 REMARK 500 TYR D 54 -60.53 -94.94 REMARK 500 HIS R 519 57.75 -92.70 REMARK 500 CYS R 525 -167.87 -164.66 REMARK 500 ASP H 73 67.90 36.74 REMARK 500 ALA L 52 -3.34 67.35 REMARK 500 PRO L 60 -178.43 -66.79 REMARK 500 LEU L 74 79.38 -100.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG H 72 0.25 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66051 RELATED DB: EMDB REMARK 900 LOCAL REFINEMENT REGION OF SARS-COV-2 SPIKE RBD IN COMPLEX WITH REMARK 900 ANTIBODIES CT1-5. DBREF 9WLA B 1 214 PDB 9WLA 9WLA 1 214 DBREF 9WLA D 1 127 PDB 9WLA 9WLA 1 127 DBREF 9WLA R 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 9WLA H 1 123 PDB 9WLA 9WLA 1 123 DBREF 9WLA L 1 109 PDB 9WLA 9WLA 1 109 SEQRES 1 B 214 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 B 214 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 B 214 GLN THR VAL SER SER THR SER LEU ALA TRP TYR GLN GLN SEQRES 4 B 214 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 B 214 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 B 214 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 B 214 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 B 214 HIS ASP THR SER LEU THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 B 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 B 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 B 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 B 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 B 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 B 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 B 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 B 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 B 214 PHE ASN ARG GLY GLU CYS SEQRES 1 D 127 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 D 127 PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 D 127 TYR PRO PHE THR SER TYR GLY ILE SER TRP VAL ARG GLN SEQRES 4 D 127 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY TRP ILE SER SEQRES 5 D 127 THR TYR ASN GLY ASN THR ASN TYR ALA GLN LYS PHE GLN SEQRES 6 D 127 GLY ARG VAL THR MET THR THR ASP THR SER THR THR THR SEQRES 7 D 127 GLY TYR MET GLU LEU ARG ARG LEU ARG SER ASP ASP THR SEQRES 8 D 127 ALA VAL TYR TYR CYS ALA ARG ASP TYR THR ARG GLY ALA SEQRES 9 D 127 TRP PHE GLY GLU SER LEU ILE GLY GLY PHE ASP ASN TRP SEQRES 10 D 127 GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 1 R 223 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 R 223 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 R 223 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 R 223 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 R 223 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 R 223 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 R 223 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 R 223 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 R 223 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 R 223 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 R 223 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 R 223 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 R 223 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 R 223 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 R 223 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 R 223 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 R 223 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18 R 223 ASN PHE SEQRES 1 H 123 GLN MET GLN LEU VAL GLN SER GLY PRO GLU VAL LYS LYS SEQRES 2 H 123 PRO GLY THR SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 H 123 PHE THR PHE THR SER SER ALA VAL GLN TRP VAL ARG GLN SEQRES 4 H 123 ALA ARG GLY GLN ARG LEU GLU TRP ILE GLY TRP ILE VAL SEQRES 5 H 123 VAL GLY SER GLY ASN THR ASN TYR ALA GLN LYS PHE GLN SEQRES 6 H 123 GLU ARG VAL THR ILE THR ARG ASP MET SER THR SER THR SEQRES 7 H 123 ALA TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 H 123 ALA VAL TYR TYR CYS ALA ALA PRO TYR CYS SER GLY GLY SEQRES 9 H 123 SER CYS HIS ASP ALA PHE ASP ILE TRP GLY GLN GLY THR SEQRES 10 H 123 MET VAL THR VAL SER SER SEQRES 1 L 109 ASP ILE VAL LEU THR GLN THR PRO GLY THR LEU SER LEU SEQRES 2 L 109 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 109 GLN SER VAL SER SER SER TYR LEU ALA TRP TYR GLN GLN SEQRES 4 L 109 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 L 109 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 L 109 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 L 109 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 L 109 TYR VAL GLY LEU THR GLY TRP THR PHE GLY GLN GLY THR SEQRES 9 L 109 LYS VAL GLU ILE LYS HET CL B 301 1 HETNAM CL CHLORIDE ION FORMUL 6 CL CL 1- HELIX 1 AA1 PRO D 28 TYR D 32 5 5 HELIX 2 AA2 ARG D 87 THR D 91 5 5 HELIX 3 AA3 PHE R 338 ASN R 343 1 6 HELIX 4 AA4 SER R 349 TRP R 353 5 5 HELIX 5 AA5 TYR R 365 SER R 371 1 7 HELIX 6 AA6 LYS R 386 LEU R 390 5 5 HELIX 7 AA7 ASP R 405 VAL R 407 5 3 HELIX 8 AA8 GLY R 416 ASN R 422 1 7 HELIX 9 AA9 SER R 438 SER R 443 1 6 HELIX 10 AB1 THR H 28 SER H 31 5 4 HELIX 11 AB2 ARG H 87 THR H 91 5 5 SHEET 1 AA1 2 THR B 10 SER B 12 0 SHEET 2 AA1 2 LYS B 103 GLU B 105 1 O GLU B 105 N LEU B 11 SHEET 1 AA2 2 ALA B 19 VAL B 29 0 SHEET 2 AA2 2 PHE B 63 ILE B 76 -1 O GLY B 69 N VAL B 29 SHEET 1 AA3 5 SER B 54 ARG B 55 0 SHEET 2 AA3 5 ARG B 46 TYR B 50 -1 N TYR B 50 O SER B 54 SHEET 3 AA3 5 LEU B 34 GLN B 39 -1 N TRP B 36 O LEU B 48 SHEET 4 AA3 5 VAL B 86 GLN B 91 -1 O GLN B 90 N ALA B 35 SHEET 5 AA3 5 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 91 SHEET 1 AA4 4 GLN D 3 GLN D 6 0 SHEET 2 AA4 4 VAL D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AA4 4 THR D 78 LEU D 83 -1 O GLY D 79 N CYS D 22 SHEET 4 AA4 4 VAL D 68 ASP D 73 -1 N THR D 71 O TYR D 80 SHEET 1 AA5 5 GLU D 10 LYS D 12 0 SHEET 2 AA5 5 THR D 121 VAL D 125 1 O THR D 124 N GLU D 10 SHEET 3 AA5 5 ALA D 92 ASP D 99 -1 N TYR D 94 O THR D 121 SHEET 4 AA5 5 GLY D 33 GLN D 39 -1 N GLY D 33 O ASP D 99 SHEET 5 AA5 5 LEU D 45 ILE D 51 -1 O GLU D 46 N ARG D 38 SHEET 1 AA6 4 GLU D 10 LYS D 12 0 SHEET 2 AA6 4 THR D 121 VAL D 125 1 O THR D 124 N GLU D 10 SHEET 3 AA6 4 ALA D 92 ASP D 99 -1 N TYR D 94 O THR D 121 SHEET 4 AA6 4 ASP D 115 TRP D 117 -1 O ASP D 115 N ARG D 98 SHEET 1 AA7 5 ASN R 354 ILE R 358 0 SHEET 2 AA7 5 ASN R 394 ARG R 403 -1 O SER R 399 N ASN R 354 SHEET 3 AA7 5 PRO R 507 GLU R 516 -1 O VAL R 512 N ASP R 398 SHEET 4 AA7 5 GLY R 431 ASN R 437 -1 N ILE R 434 O VAL R 511 SHEET 5 AA7 5 PHE R 374 THR R 376 -1 N SER R 375 O ALA R 435 SHEET 1 AA8 5 ASN R 354 ILE R 358 0 SHEET 2 AA8 5 ASN R 394 ARG R 403 -1 O SER R 399 N ASN R 354 SHEET 3 AA8 5 PRO R 507 GLU R 516 -1 O VAL R 512 N ASP R 398 SHEET 4 AA8 5 GLY R 431 ASN R 437 -1 N ILE R 434 O VAL R 511 SHEET 5 AA8 5 CYS R 379 TYR R 380 -1 N TYR R 380 O GLY R 431 SHEET 1 AA9 2 LEU R 452 ARG R 454 0 SHEET 2 AA9 2 LEU R 492 SER R 494 -1 O GLN R 493 N TYR R 453 SHEET 1 AB1 2 TYR R 473 GLN R 474 0 SHEET 2 AB1 2 CYS R 488 TYR R 489 -1 O TYR R 489 N TYR R 473 SHEET 1 AB2 3 GLN H 3 GLN H 6 0 SHEET 2 AB2 3 VAL H 20 SER H 25 -1 O SER H 25 N GLN H 3 SHEET 3 AB2 3 THR H 78 MET H 81 -1 O ALA H 79 N CYS H 22 SHEET 1 AB3 4 GLU H 46 TRP H 47 0 SHEET 2 AB3 4 ALA H 33 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 3 AB3 4 ALA H 92 ALA H 98 -1 O VAL H 93 N GLN H 39 SHEET 4 AB3 4 ILE H 112 TRP H 113 -1 O ILE H 112 N ALA H 98 SHEET 1 AB4 5 THR H 58 TYR H 60 0 SHEET 2 AB4 5 GLY H 49 VAL H 52 -1 N TRP H 50 O ASN H 59 SHEET 3 AB4 5 ALA H 33 GLN H 39 -1 N VAL H 34 O ILE H 51 SHEET 4 AB4 5 ALA H 92 ALA H 98 -1 O VAL H 93 N GLN H 39 SHEET 5 AB4 5 THR H 117 VAL H 119 -1 O VAL H 119 N ALA H 92 SHEET 1 AB5 3 LEU L 4 THR L 7 0 SHEET 2 AB5 3 SER L 22 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AB5 3 ASP L 71 THR L 73 -1 O PHE L 72 N CYS L 23 SHEET 1 AB6 2 THR L 10 LEU L 11 0 SHEET 2 AB6 2 LYS L 105 VAL L 106 1 O LYS L 105 N LEU L 11 SHEET 1 AB7 4 SER L 54 ARG L 55 0 SHEET 2 AB7 4 ARG L 46 TYR L 50 -1 N TYR L 50 O SER L 54 SHEET 3 AB7 4 ALA L 35 GLN L 39 -1 N TRP L 36 O ILE L 49 SHEET 4 AB7 4 VAL L 86 GLN L 90 -1 O TYR L 88 N TYR L 37 SSBOND 1 CYS B 23 CYS B 89 1555 1555 2.17 SSBOND 2 CYS D 22 CYS D 96 1555 1555 2.03 SSBOND 3 CYS R 336 CYS R 361 1555 1555 2.05 SSBOND 4 CYS R 379 CYS R 432 1555 1555 2.04 SSBOND 5 CYS R 391 CYS R 525 1555 1555 2.11 SSBOND 6 CYS R 480 CYS R 488 1555 1555 2.03 SSBOND 7 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 8 CYS H 101 CYS H 106 1555 1555 2.03 SSBOND 9 CYS L 23 CYS L 89 1555 1555 2.22 CISPEP 1 SER B 7 PRO B 8 0 3.19 CISPEP 2 THR L 7 PRO L 8 0 -1.24 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 CONECT 150 628 CONECT 628 150 CONECT 896 1464 CONECT 1464 896 CONECT 1720 1918 CONECT 1918 1720 CONECT 2054 2457 CONECT 2137 3193 CONECT 2457 2054 CONECT 2848 2905 CONECT 2905 2848 CONECT 3193 2137 CONECT 3333 3818 CONECT 3818 3333 CONECT 3853 3878 CONECT 3878 3853 CONECT 4103 4545 CONECT 4545 4103 MASTER 453 0 1 11 57 0 0 6 4669 5 18 64 END