HEADER PROTEIN BINDING 22-APR-22 7URV TITLE FMC63 SCFV IN COMPLEX WITH SOLUBLE CD19 COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-LYMPHOCYTE ANTIGEN CD19; COMPND 3 CHAIN: C; COMPND 4 SYNONYM: B-LYMPHOCYTE SURFACE ANTIGEN B4,DIFFERENTIATION ANTIGEN COMPND 5 CD19,T-CELL SURFACE ANTIGEN LEU-12; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: FMC63 SINGLE-CHAIN VARIABLE FRAGMENT; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD19; 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: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 14 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS COMPLEX, CAR-T, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR J.MEYERSON,C.HE REVDAT 2 15-MAR-23 7URV 1 JRNL REVDAT 1 15-FEB-23 7URV 0 JRNL AUTH C.HE,J.MANSILLA-SOTO,N.KHANRA,M.HAMIEH,V.BUSTOS, JRNL AUTH 2 A.J.PAQUETTE,A.GARCIA ANGUS,D.M.SHORE,W.J.RICE, JRNL AUTH 3 G.KHELASHVILI,M.SADELAIN,J.R.MEYERSON JRNL TITL CD19 CAR ANTIGEN ENGAGEMENT MECHANISMS AND AFFINITY TUNING. JRNL REF SCI IMMUNOL V. 8 F1426 2023 JRNL REFN ESSN 2470-9468 JRNL PMID 36867678 JRNL DOI 10.1126/SCIIMMUNOL.ADF1426 REMARK 2 REMARK 2 RESOLUTION. 3.05 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) : 3.050 REMARK 3 NUMBER OF PARTICLES : 442863 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 7URV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264639. 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 : FMC63 SCFV IN COMPLEX WITH REMARK 245 SOLUBLE CD19; B-LYMPHOCYTE REMARK 245 ANTIGEN CD19; FMC63 SINGLE- REMARK 245 CHAIN VARIABLE FRAGMENT 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 : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2900.00 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) : 5082.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 C 21 REMARK 465 GLU C 22 REMARK 465 LYS C 40 REMARK 465 GLY C 41 REMARK 465 THR C 42 REMARK 465 SER C 43 REMARK 465 ASP C 44 REMARK 465 GLY C 45 REMARK 465 PRO C 46 REMARK 465 GLY C 133 REMARK 465 CYS C 134 REMARK 465 GLY C 135 REMARK 465 LEU C 136 REMARK 465 LYS C 137 REMARK 465 ASN C 138 REMARK 465 ARG C 139 REMARK 465 SER C 140 REMARK 465 SER C 141 REMARK 465 GLU C 142 REMARK 465 GLY C 143 REMARK 465 PRO C 144 REMARK 465 SER C 145 REMARK 465 SER C 146 REMARK 465 PRO C 147 REMARK 465 SER C 148 REMARK 465 GLY C 149 REMARK 465 LYS C 150 REMARK 465 LEU C 151 REMARK 465 MET C 152 REMARK 465 PRO C 175 REMARK 465 PRO C 176 REMARK 465 ARG C 177 REMARK 465 ASP C 178 REMARK 465 SER C 179 REMARK 465 LEU C 180 REMARK 465 ASN C 181 REMARK 465 GLN C 182 REMARK 465 SER C 183 REMARK 465 LEU C 184 REMARK 465 GLY D 146 REMARK 465 GLY D 147 REMARK 465 GLY D 148 REMARK 465 GLY D 149 REMARK 465 SER D 150 REMARK 465 GLY D 151 REMARK 465 GLY D 152 REMARK 465 GLY D 153 REMARK 465 GLY D 154 REMARK 465 SER D 155 REMARK 465 GLY D 156 REMARK 465 GLY D 157 REMARK 465 GLY D 158 REMARK 465 GLY D 159 REMARK 465 SER D 160 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 ALA C 106 31.52 -140.15 REMARK 500 GLU C 116 -105.91 41.56 REMARK 500 ASP C 128 -169.31 -79.91 REMARK 500 LYS C 161 -7.56 64.07 REMARK 500 ASP C 162 -18.55 -141.59 REMARK 500 PRO C 171 64.69 -103.04 REMARK 500 MET C 242 -146.17 -99.13 REMARK 500 THR C 244 -50.34 -126.27 REMARK 500 LEU C 246 71.35 -119.91 REMARK 500 THR D 89 -12.40 74.13 REMARK 500 LEU D 223 53.12 -93.37 REMARK 500 SER D 225 -1.43 69.83 REMARK 500 ALA D 256 115.51 -162.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26719 RELATED DB: EMDB REMARK 900 FMC63 SCFV IN COMPLEX WITH SOLUBLE CD19 DBREF 7URV C 21 277 UNP P15391 CD19_HUMAN 21 277 DBREF 7URV D 39 280 PDB 7URV 7URV 39 280 SEQADV 7URV VAL C 75 UNP P15391 MET 75 CONFLICT SEQADV 7URV SER C 76 UNP P15391 ARG 76 CONFLICT SEQADV 7URV SER C 85 UNP P15391 PHE 85 CONFLICT SEQRES 1 C 257 GLU GLU PRO LEU VAL VAL LYS VAL GLU GLU GLY ASP ASN SEQRES 2 C 257 ALA VAL LEU GLN CYS LEU LYS GLY THR SER ASP GLY PRO SEQRES 3 C 257 THR GLN GLN LEU THR TRP SER ARG GLU SER PRO LEU LYS SEQRES 4 C 257 PRO PHE LEU LYS LEU SER LEU GLY LEU PRO GLY LEU GLY SEQRES 5 C 257 ILE HIS VAL SER PRO LEU ALA ILE TRP LEU PHE ILE SER SEQRES 6 C 257 ASN VAL SER GLN GLN MET GLY GLY PHE TYR LEU CYS GLN SEQRES 7 C 257 PRO GLY PRO PRO SER GLU LYS ALA TRP GLN PRO GLY TRP SEQRES 8 C 257 THR VAL ASN VAL GLU GLY SER GLY GLU LEU PHE ARG TRP SEQRES 9 C 257 ASN VAL SER ASP LEU GLY GLY LEU GLY CYS GLY LEU LYS SEQRES 10 C 257 ASN ARG SER SER GLU GLY PRO SER SER PRO SER GLY LYS SEQRES 11 C 257 LEU MET SER PRO LYS LEU TYR VAL TRP ALA LYS ASP ARG SEQRES 12 C 257 PRO GLU ILE TRP GLU GLY GLU PRO PRO CYS LEU PRO PRO SEQRES 13 C 257 ARG ASP SER LEU ASN GLN SER LEU SER GLN ASP LEU THR SEQRES 14 C 257 MET ALA PRO GLY SER THR LEU TRP LEU SER CYS GLY VAL SEQRES 15 C 257 PRO PRO ASP SER VAL SER ARG GLY PRO LEU SER TRP THR SEQRES 16 C 257 HIS VAL HIS PRO LYS GLY PRO LYS SER LEU LEU SER LEU SEQRES 17 C 257 GLU LEU LYS ASP ASP ARG PRO ALA ARG ASP MET TRP VAL SEQRES 18 C 257 MET GLU THR GLY LEU LEU LEU PRO ARG ALA THR ALA GLN SEQRES 19 C 257 ASP ALA GLY LYS TYR TYR CYS HIS ARG GLY ASN LEU THR SEQRES 20 C 257 MET SER PHE HIS LEU GLU ILE THR ALA ARG SEQRES 1 D 242 ASP ILE GLN MET THR GLN THR THR SER SER LEU SER ALA SEQRES 2 D 242 SER LEU GLY ASP ARG VAL THR ILE SER CYS ARG ALA SER SEQRES 3 D 242 GLN ASP ILE SER LYS TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 D 242 PRO ASP GLY THR VAL LYS LEU LEU ILE TYR HIS THR SER SEQRES 5 D 242 ARG LEU HIS SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 D 242 GLY SER GLY THR ASP TYR SER LEU THR ILE SER ASN LEU SEQRES 7 D 242 GLU GLN GLU ASP ILE ALA THR TYR PHE CYS GLN GLN GLY SEQRES 8 D 242 ASN THR LEU PRO TYR THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 D 242 GLU ILE THR GLY GLY GLY GLY SER GLY GLY GLY GLY SER SEQRES 10 D 242 GLY GLY GLY GLY SER GLU VAL LYS LEU GLN GLU SER GLY SEQRES 11 D 242 PRO GLY LEU VAL ALA PRO SER GLN SER LEU SER VAL THR SEQRES 12 D 242 CYS THR VAL SER GLY VAL SER LEU PRO ASP TYR GLY VAL SEQRES 13 D 242 SER TRP ILE ARG GLN PRO PRO ARG LYS GLY LEU GLU TRP SEQRES 14 D 242 LEU GLY VAL ILE TRP GLY SER GLU THR THR TYR TYR ASN SEQRES 15 D 242 SER ALA LEU LYS SER ARG LEU THR ILE ILE LYS ASP ASN SEQRES 16 D 242 SER LYS SER GLN VAL PHE LEU LYS MET ASN SER LEU GLN SEQRES 17 D 242 THR ASP ASP THR ALA ILE TYR TYR CYS ALA LYS HIS TYR SEQRES 18 D 242 TYR TYR GLY GLY SER TYR ALA MET ASP TYR TRP GLY GLN SEQRES 19 D 242 GLY THR SER VAL THR VAL SER SER HELIX 1 AA1 SER C 88 GLY C 92 5 5 HELIX 2 AA2 VAL C 202 SER C 206 5 5 HELIX 3 AA3 GLU D 117 ILE D 121 5 5 HELIX 4 AA4 GLN D 246 THR D 250 5 5 SHEET 1 AA110 LEU C 24 GLU C 29 0 SHEET 2 AA110 THR C 267 THR C 275 1 O HIS C 271 N VAL C 26 SHEET 3 AA110 GLY C 257 HIS C 262 -1 N TYR C 259 O PHE C 270 SHEET 4 AA110 LEU C 50 SER C 56 -1 N SER C 53 O TYR C 260 SHEET 5 AA110 LYS C 59 LEU C 66 -1 O LEU C 64 N LEU C 50 SHEET 6 AA110 GLY C 221 LEU C 230 -1 O GLU C 229 N LYS C 63 SHEET 7 AA110 LEU C 212 HIS C 218 -1 N HIS C 216 O LYS C 223 SHEET 8 AA110 GLY C 93 CYS C 97 -1 N PHE C 94 O VAL C 217 SHEET 9 AA110 GLN C 108 VAL C 115 -1 O GLN C 108 N CYS C 97 SHEET 10 AA110 ASP C 187 MET C 190 1 O MET C 190 N ASN C 114 SHEET 1 AA2 5 THR C 195 LEU C 198 0 SHEET 2 AA2 5 ILE C 80 SER C 85 -1 N LEU C 82 O LEU C 198 SHEET 3 AA2 5 LEU C 71 VAL C 75 -1 N HIS C 74 O TRP C 81 SHEET 4 AA2 5 MET C 239 VAL C 241 -1 O MET C 239 N VAL C 75 SHEET 5 AA2 5 LEU C 246 LEU C 247 -1 O LEU C 247 N TRP C 240 SHEET 1 AA3 3 GLU C 120 ARG C 123 0 SHEET 2 AA3 3 LYS C 155 TRP C 159 1 O TYR C 157 N LEU C 121 SHEET 3 AA3 3 PRO C 164 ILE C 166 -1 O GLU C 165 N VAL C 158 SHEET 1 AA4 4 MET D 42 THR D 43 0 SHEET 2 AA4 4 VAL D 57 ALA D 63 -1 O ARG D 62 N THR D 43 SHEET 3 AA4 4 ASP D 108 ILE D 113 -1 O LEU D 111 N ILE D 59 SHEET 4 AA4 4 PHE D 100 SER D 105 -1 N SER D 101 O THR D 112 SHEET 1 AA5 5 SER D 48 ALA D 51 0 SHEET 2 AA5 5 THR D 140 ILE D 144 1 O LYS D 141 N LEU D 49 SHEET 3 AA5 5 ALA D 122 GLN D 128 -1 N ALA D 122 O LEU D 142 SHEET 4 AA5 5 LEU D 71 GLN D 76 -1 N GLN D 76 O THR D 123 SHEET 5 AA5 5 VAL D 82 LEU D 84 -1 O LYS D 83 N GLN D 75 SHEET 1 AA6 4 SER D 48 ALA D 51 0 SHEET 2 AA6 4 THR D 140 ILE D 144 1 O LYS D 141 N LEU D 49 SHEET 3 AA6 4 ALA D 122 GLN D 128 -1 N ALA D 122 O LEU D 142 SHEET 4 AA6 4 THR D 135 PHE D 136 -1 O THR D 135 N GLN D 128 SHEET 1 AA7 2 ILE D 86 TYR D 87 0 SHEET 2 AA7 2 ARG D 91 LEU D 92 -1 O ARG D 91 N TYR D 87 SHEET 1 AA8 4 LYS D 163 SER D 167 0 SHEET 2 AA8 4 THR D 181 SER D 185 -1 O THR D 181 N SER D 167 SHEET 3 AA8 4 GLN D 237 MET D 242 -1 O VAL D 238 N CYS D 182 SHEET 4 AA8 4 LEU D 227 ASP D 232 -1 N ILE D 230 O PHE D 239 SHEET 1 AA9 5 THR D 217 TYR D 219 0 SHEET 2 AA9 5 GLU D 206 ILE D 211 -1 N VAL D 210 O TYR D 218 SHEET 3 AA9 5 VAL D 194 ARG D 198 -1 N ARG D 198 O GLU D 206 SHEET 4 AA9 5 ALA D 251 HIS D 258 -1 O TYR D 254 N ILE D 197 SHEET 5 AA9 5 MET D 267 TRP D 270 -1 O ASP D 268 N LYS D 257 SHEET 1 AB1 5 THR D 217 TYR D 219 0 SHEET 2 AB1 5 GLU D 206 ILE D 211 -1 N VAL D 210 O TYR D 218 SHEET 3 AB1 5 VAL D 194 ARG D 198 -1 N ARG D 198 O GLU D 206 SHEET 4 AB1 5 ALA D 251 HIS D 258 -1 O TYR D 254 N ILE D 197 SHEET 5 AB1 5 THR D 274 VAL D 276 -1 O VAL D 276 N ALA D 251 SSBOND 1 CYS C 38 CYS C 261 1555 1555 2.03 SSBOND 2 CYS C 97 CYS C 200 1555 1555 2.03 SSBOND 3 CYS D 61 CYS D 126 1555 1555 2.03 SSBOND 4 CYS D 182 CYS D 255 1555 1555 2.03 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