HEADER TRANSPORT PROTEIN 09-JAN-24 8XSM TITLE TRANSPORTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUTE CARRIER FAMILY 52, RIBOFLAVIN TRANSPORTER, MEMBER 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PORCINE ENDOGENOUS RETROVIRUS A RECEPTOR 1,PERV-A RECEPTOR COMPND 5 1,PROTEIN GPR172A,RIBOFLAVIN TRANSPORTER 3,HRFT3; COMPND 6 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: SLC52A2, GPR172A, PAR1, RFT3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TRANSPORTER, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.H.JIANG,K.WANG REVDAT 1 15-JAN-25 8XSM 0 JRNL AUTH D.H.JIANG,K.WANG JRNL TITL STRUCTURE OF TRANSPORTER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.01 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) : 3.010 REMARK 3 NUMBER OF PARTICLES : 143636 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 8XSM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044094. 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 WITH A 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 : 7.50 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 K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 6000.00 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 THR A 5 REMARK 465 PRO A 6 REMARK 465 GLU A 171 REMARK 465 CYS A 172 REMARK 465 PRO A 173 REMARK 465 PRO A 174 REMARK 465 ALA A 175 REMARK 465 PRO A 176 REMARK 465 ILE A 177 REMARK 465 ASN A 178 REMARK 465 GLY A 179 REMARK 465 THR A 180 REMARK 465 PRO A 181 REMARK 465 GLY A 182 REMARK 465 PRO A 183 REMARK 465 PRO A 184 REMARK 465 LEU A 185 REMARK 465 PRO A 222 REMARK 465 SER A 223 REMARK 465 VAL A 224 REMARK 465 PRO A 225 REMARK 465 THR A 226 REMARK 465 GLY A 227 REMARK 465 GLU A 228 REMARK 465 LEU A 229 REMARK 465 GLY A 230 REMARK 465 SER A 231 REMARK 465 GLY A 232 REMARK 465 LEU A 233 REMARK 465 GLN A 234 REMARK 465 VAL A 235 REMARK 465 GLY A 236 REMARK 465 ALA A 237 REMARK 465 PRO A 238 REMARK 465 GLY A 239 REMARK 465 ALA A 240 REMARK 465 GLU A 241 REMARK 465 GLU A 242 REMARK 465 GLU A 243 REMARK 465 VAL A 244 REMARK 465 GLU A 245 REMARK 465 GLU A 246 REMARK 465 SER A 247 REMARK 465 SER A 248 REMARK 465 PRO A 249 REMARK 465 LEU A 250 REMARK 465 GLN A 251 REMARK 465 GLU A 252 REMARK 465 PRO A 253 REMARK 465 PRO A 254 REMARK 465 SER A 255 REMARK 465 GLN A 256 REMARK 465 ALA A 257 REMARK 465 ALA A 258 REMARK 465 GLY A 259 REMARK 465 THR A 260 REMARK 465 THR A 261 REMARK 465 PRO A 262 REMARK 465 GLY A 263 REMARK 465 PRO A 264 REMARK 465 ASP A 265 REMARK 465 PRO A 266 REMARK 465 LYS A 267 REMARK 465 CYS A 443 REMARK 465 ASP A 444 REMARK 465 SER A 445 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 LEU A 170 CG CD1 CD2 REMARK 470 PHE A 187 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 269 CG CD1 CD2 CE1 CE2 CZ OH REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLN A 270 OG SER A 276 2.16 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 ASN A 59 3.54 -67.97 REMARK 500 PRO A 192 -175.61 -69.56 REMARK 500 LEU A 359 41.12 -101.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38622 RELATED DB: EMDB REMARK 900 TRANSPORTER DBREF 8XSM A 1 445 UNP Q9HAB3 S52A2_HUMAN 1 445 SEQRES 1 A 445 MET ALA ALA PRO THR PRO ALA ARG PRO VAL LEU THR HIS SEQRES 2 A 445 LEU LEU VAL ALA LEU PHE GLY MET GLY SER TRP ALA ALA SEQRES 3 A 445 VAL ASN GLY ILE TRP VAL GLU LEU PRO VAL VAL VAL LYS SEQRES 4 A 445 GLU LEU PRO GLU GLY TRP SER LEU PRO SER TYR VAL SER SEQRES 5 A 445 VAL LEU VAL ALA LEU GLY ASN LEU GLY LEU LEU VAL VAL SEQRES 6 A 445 THR LEU TRP ARG ARG LEU ALA PRO GLY LYS ASP GLU GLN SEQRES 7 A 445 VAL PRO ILE ARG VAL VAL GLN VAL LEU GLY MET VAL GLY SEQRES 8 A 445 THR ALA LEU LEU ALA SER LEU TRP HIS HIS VAL ALA PRO SEQRES 9 A 445 VAL ALA GLY GLN LEU HIS SER VAL ALA PHE LEU ALA LEU SEQRES 10 A 445 ALA PHE VAL LEU ALA LEU ALA CYS CYS ALA SER ASN VAL SEQRES 11 A 445 THR PHE LEU PRO PHE LEU SER HIS LEU PRO PRO ARG PHE SEQRES 12 A 445 LEU ARG SER PHE PHE LEU GLY GLN GLY LEU SER ALA LEU SEQRES 13 A 445 LEU PRO CYS VAL LEU ALA LEU VAL GLN GLY VAL GLY ARG SEQRES 14 A 445 LEU GLU CYS PRO PRO ALA PRO ILE ASN GLY THR PRO GLY SEQRES 15 A 445 PRO PRO LEU ASP PHE LEU GLU ARG PHE PRO ALA SER THR SEQRES 16 A 445 PHE PHE TRP ALA LEU THR ALA LEU LEU VAL ALA SER ALA SEQRES 17 A 445 ALA ALA PHE GLN GLY LEU LEU LEU LEU LEU PRO PRO PRO SEQRES 18 A 445 PRO SER VAL PRO THR GLY GLU LEU GLY SER GLY LEU GLN SEQRES 19 A 445 VAL GLY ALA PRO GLY ALA GLU GLU GLU VAL GLU GLU SER SEQRES 20 A 445 SER PRO LEU GLN GLU PRO PRO SER GLN ALA ALA GLY THR SEQRES 21 A 445 THR PRO GLY PRO ASP PRO LYS ALA TYR GLN LEU LEU SER SEQRES 22 A 445 ALA ARG SER ALA CYS LEU LEU GLY LEU LEU ALA ALA THR SEQRES 23 A 445 ASN ALA LEU THR ASN GLY VAL LEU PRO ALA VAL GLN SER SEQRES 24 A 445 PHE SER CYS LEU PRO TYR GLY ARG LEU ALA TYR HIS LEU SEQRES 25 A 445 ALA VAL VAL LEU GLY SER ALA ALA ASN PRO LEU ALA CYS SEQRES 26 A 445 PHE LEU ALA MET GLY VAL LEU CYS ARG SER LEU ALA GLY SEQRES 27 A 445 LEU GLY GLY LEU SER LEU LEU GLY VAL PHE CYS GLY GLY SEQRES 28 A 445 TYR LEU MET ALA LEU ALA VAL LEU SER PRO CYS PRO PRO SEQRES 29 A 445 LEU VAL GLY THR SER ALA GLY VAL VAL LEU VAL VAL LEU SEQRES 30 A 445 SER TRP VAL LEU CYS LEU GLY VAL PHE SER TYR VAL LYS SEQRES 31 A 445 VAL ALA ALA SER SER LEU LEU HIS GLY GLY GLY ARG PRO SEQRES 32 A 445 ALA LEU LEU ALA ALA GLY VAL ALA ILE GLN VAL GLY SER SEQRES 33 A 445 LEU LEU GLY ALA VAL ALA MET PHE PRO PRO THR SER ILE SEQRES 34 A 445 TYR HIS VAL PHE HIS SER ARG LYS ASP CYS ALA ASP PRO SEQRES 35 A 445 CYS ASP SER HET RBF A 501 27 HET RBF A 502 27 HETNAM RBF RIBOFLAVIN HETSYN RBF RIBOFLAVINE; VITAMIN B2 FORMUL 2 RBF 2(C17 H20 N4 O6) HELIX 1 AA1 ARG A 8 GLY A 22 1 15 HELIX 2 AA2 TRP A 24 LYS A 39 1 16 HELIX 3 AA3 SER A 46 GLY A 58 1 13 HELIX 4 AA4 ASN A 59 ALA A 72 1 14 HELIX 5 AA5 GLU A 77 LEU A 98 1 22 HELIX 6 AA6 VAL A 112 LEU A 133 1 22 HELIX 7 AA7 PRO A 134 LEU A 139 5 6 HELIX 8 AA8 PRO A 140 ARG A 142 5 3 HELIX 9 AA9 PHE A 143 GLY A 166 1 24 HELIX 10 AB1 PRO A 192 LEU A 218 1 27 HELIX 11 AB2 SER A 273 VAL A 293 1 21 HELIX 12 AB3 VAL A 293 LEU A 303 1 11 HELIX 13 AB4 GLY A 306 VAL A 331 1 26 HELIX 14 AB5 SER A 335 LEU A 359 1 25 HELIX 15 AB6 THR A 368 HIS A 398 1 31 HELIX 16 AB7 GLY A 401 ILE A 429 1 29 SHEET 1 AA1 2 VAL A 102 VAL A 105 0 SHEET 2 AA1 2 GLN A 108 SER A 111 -1 O GLN A 108 N VAL A 105 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