HEADER TRANSPORT PROTEIN 19-APR-24 9BH2 TITLE APO GLTPH, OUTWARD-FACING STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE TRANSPORTER HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLT(PH),SODIUM-ASPARTATE SYMPORTER GLT(PH),SODIUM-DEPENDENT COMPND 5 ASPARTATE TRANSPORTER; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: PH1295; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SODIUM-COUPLED ASPARTATE TRANSPORTER, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.D.REDDY,O.BOUDKER REVDAT 1 12-MAR-25 9BH2 0 JRNL AUTH K.D.REDDY,B.RASOOL,F.B.AKHER,N.KUTLESIC,S.PANT,O.BOUDKER JRNL TITL EVOLUTIONARY ANALYSIS REVEALS THE ORIGIN OF SODIUM COUPLING JRNL TITL 2 IN GLUTAMATE TRANSPORTERS. JRNL REF BIORXIV 2024 JRNL REFN ISSN 2692-8205 JRNL PMID 38106174 JRNL DOI 10.1101/2023.12.03.569786 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.700 REMARK 3 NUMBER OF PARTICLES : 148756 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 9BH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000283052. 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 : SODIUM-COUPLED ASPARTATE REMARK 245 TRANSPORTER, APO CONDITIONS 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 K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 900.00 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) : 5342.00 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 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 GLY A 2 REMARK 465 GLY A 417 REMARK 465 THR A 418 REMARK 465 LEU A 419 REMARK 465 VAL A 420 REMARK 465 PRO A 421 REMARK 465 ARG A 422 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 A 181 CG CD OE1 OE2 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 OH TYR A 247 OD2 ASP A 312 2.10 REMARK 500 OD1 ASN A 148 NE2 GLN A 150 2.11 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 ILE A 298 -62.18 -97.38 REMARK 500 LEU A 372 67.19 -115.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-44530 RELATED DB: EMDB REMARK 900 APO GLTPH, OUTWARD-FACING STATE DBREF 9BH2 A 1 417 UNP O59010 GLT_PYRHO 1 417 SEQADV 9BH2 HIS A 37 UNP O59010 ASP 37 CONFLICT SEQADV 9BH2 HIS A 40 UNP O59010 LYS 40 CONFLICT SEQADV 9BH2 HIS A 125 UNP O59010 LYS 125 CONFLICT SEQADV 9BH2 HIS A 132 UNP O59010 LYS 132 CONFLICT SEQADV 9BH2 HIS A 223 UNP O59010 LYS 223 CONFLICT SEQADV 9BH2 HIS A 264 UNP O59010 LYS 264 CONFLICT SEQADV 9BH2 HIS A 368 UNP O59010 GLU 368 CONFLICT SEQADV 9BH2 THR A 418 UNP O59010 EXPRESSION TAG SEQADV 9BH2 LEU A 419 UNP O59010 EXPRESSION TAG SEQADV 9BH2 VAL A 420 UNP O59010 EXPRESSION TAG SEQADV 9BH2 PRO A 421 UNP O59010 EXPRESSION TAG SEQADV 9BH2 ARG A 422 UNP O59010 EXPRESSION TAG SEQRES 1 A 422 MET GLY LEU TYR ARG LYS TYR ILE GLU TYR PRO VAL LEU SEQRES 2 A 422 GLN LYS ILE LEU ILE GLY LEU ILE LEU GLY ALA ILE VAL SEQRES 3 A 422 GLY LEU ILE LEU GLY HIS TYR GLY TYR ALA HIS ALA VAL SEQRES 4 A 422 HIS THR TYR VAL LYS PRO PHE GLY ASP LEU PHE VAL ARG SEQRES 5 A 422 LEU LEU LYS MET LEU VAL MET PRO ILE VAL PHE ALA SER SEQRES 6 A 422 LEU VAL VAL GLY ALA ALA SER ILE SER PRO ALA ARG LEU SEQRES 7 A 422 GLY ARG VAL GLY VAL LYS ILE VAL VAL TYR TYR LEU LEU SEQRES 8 A 422 THR SER ALA PHE ALA VAL THR LEU GLY ILE ILE MET ALA SEQRES 9 A 422 ARG LEU PHE ASN PRO GLY ALA GLY ILE HIS LEU ALA VAL SEQRES 10 A 422 GLY GLY GLN GLN PHE GLN PRO HIS GLN ALA PRO PRO LEU SEQRES 11 A 422 VAL HIS ILE LEU LEU ASP ILE VAL PRO THR ASN PRO PHE SEQRES 12 A 422 GLY ALA LEU ALA ASN GLY GLN VAL LEU PRO THR ILE PHE SEQRES 13 A 422 PHE ALA ILE ILE LEU GLY ILE ALA ILE THR TYR LEU MET SEQRES 14 A 422 ASN SER GLU ASN GLU LYS VAL ARG LYS SER ALA GLU THR SEQRES 15 A 422 LEU LEU ASP ALA ILE ASN GLY LEU ALA GLU ALA MET TYR SEQRES 16 A 422 LYS ILE VAL ASN GLY VAL MET GLN TYR ALA PRO ILE GLY SEQRES 17 A 422 VAL PHE ALA LEU ILE ALA TYR VAL MET ALA GLU GLN GLY SEQRES 18 A 422 VAL HIS VAL VAL GLY GLU LEU ALA LYS VAL THR ALA ALA SEQRES 19 A 422 VAL TYR VAL GLY LEU THR LEU GLN ILE LEU LEU VAL TYR SEQRES 20 A 422 PHE VAL LEU LEU LYS ILE TYR GLY ILE ASP PRO ILE SER SEQRES 21 A 422 PHE ILE LYS HIS ALA LYS ASP ALA MET LEU THR ALA PHE SEQRES 22 A 422 VAL THR ARG SER SER SER GLY THR LEU PRO VAL THR MET SEQRES 23 A 422 ARG VAL ALA LYS GLU MET GLY ILE SER GLU GLY ILE TYR SEQRES 24 A 422 SER PHE THR LEU PRO LEU GLY ALA THR ILE ASN MET ASP SEQRES 25 A 422 GLY THR ALA LEU TYR GLN GLY VAL CYS THR PHE PHE ILE SEQRES 26 A 422 ALA ASN ALA LEU GLY SER HIS LEU THR VAL GLY GLN GLN SEQRES 27 A 422 LEU THR ILE VAL LEU THR ALA VAL LEU ALA SER ILE GLY SEQRES 28 A 422 THR ALA GLY VAL PRO GLY ALA GLY ALA ILE MET LEU ALA SEQRES 29 A 422 MET VAL LEU HIS SER VAL GLY LEU PRO LEU THR ASP PRO SEQRES 30 A 422 ASN VAL ALA ALA ALA TYR ALA MET ILE LEU GLY ILE ASP SEQRES 31 A 422 ALA ILE LEU ASP MET GLY ARG THR MET VAL ASN VAL THR SEQRES 32 A 422 GLY ASP LEU THR GLY THR ALA ILE VAL ALA LYS THR GLU SEQRES 33 A 422 GLY THR LEU VAL PRO ARG HELIX 1 AA1 LEU A 3 TYR A 10 1 8 HELIX 2 AA2 PRO A 11 GLY A 34 1 24 HELIX 3 AA3 TYR A 35 VAL A 43 1 9 HELIX 4 AA4 VAL A 43 ILE A 73 1 31 HELIX 5 AA5 SER A 74 ASN A 108 1 35 HELIX 6 AA6 PRO A 129 ILE A 137 1 9 HELIX 7 AA7 ASN A 141 ASN A 148 1 8 HELIX 8 AA8 GLN A 150 ASN A 170 1 21 HELIX 9 AA9 ASN A 173 GLY A 221 1 49 HELIX 10 AB1 VAL A 222 VAL A 224 5 3 HELIX 11 AB2 GLY A 226 VAL A 246 1 21 HELIX 12 AB3 VAL A 246 TYR A 254 1 9 HELIX 13 AB4 ASP A 257 ARG A 276 1 20 HELIX 14 AB5 THR A 281 MET A 292 1 12 HELIX 15 AB6 SER A 295 ASN A 310 1 16 HELIX 16 AB7 MET A 311 GLY A 330 1 20 HELIX 17 AB8 GLY A 336 ALA A 348 1 13 HELIX 18 AB9 SER A 349 ALA A 353 5 5 HELIX 19 AC1 GLY A 357 GLY A 371 1 15 HELIX 20 AC2 ASP A 376 GLY A 388 1 13 HELIX 21 AC3 ILE A 389 GLU A 416 1 28 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 TER 3079 GLU A 416 MASTER 150 0 0 21 0 0 0 6 3078 1 0 33 END