HEADER TRANSPORT PROTEIN 05-NOV-19 6UWF TITLE GLTPH IN COMPLEX WITH L-ASPARTATE AND SODIUM IONS IN OUTWARD-FACING TITLE 2 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE TRANSPORTER HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLTPH,GLT(PH),SODIUM-ASPARTATE SYMPORTER GLT(PH),SODIUM- COMPND 5 DEPENDENT ASPARTATE TRANSPORTER; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ASPARTATE TRANSPORTER, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.WANG,O.BOUDKER REVDAT 2 18-NOV-20 6UWF 1 JRNL REVDAT 1 03-JUN-20 6UWF 0 JRNL AUTH Y.HUANG,X.WANG,G.LV,A.M.RAZAVI,G.H.M.HUYSMANS,H.WEINSTEIN, JRNL AUTH 2 C.BRACKEN,D.ELIEZER,O.BOUDKER JRNL TITL USE OF PARAMAGNETIC 19 F NMR TO MONITOR DOMAIN MOVEMENT IN A JRNL TITL 2 GLUTAMATE TRANSPORTER HOMOLOG. JRNL REF NAT.CHEM.BIOL. V. 16 1006 2020 JRNL REFN ESSN 1552-4469 JRNL PMID 32514183 JRNL DOI 10.1038/S41589-020-0561-6 REMARK 2 REMARK 2 RESOLUTION. 3.08 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) : 3.080 REMARK 3 NUMBER OF PARTICLES : 94731 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 6UWF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245298. 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 OF GLTPH WITH L REMARK 245 -ASPARTATE AND SODIUM IONS IN REMARK 245 MSP1E3 NANODISC 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) : 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) : 50.16 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 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 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 CE LYS A 196 N29 6OU A 503 1.88 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 TYR A 35 35.09 -98.75 REMARK 500 ALA A 70 55.05 -93.50 REMARK 500 PHE A 122 -72.49 -64.41 REMARK 500 LEU A 130 -7.22 71.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 6OU A 502 REMARK 610 6OU A 503 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ASP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6OU A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6OU A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-20922 RELATED DB: EMDB REMARK 900 GLTPH IN COMPLEX WITH L-ASPARTATE AND SODIUM IONS IN OUTWARD-FACING REMARK 900 STATE DBREF 6UWF A 1 422 PDB 6UWF 6UWF 1 422 SEQRES 1 A 422 FME 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 HET FME A 1 10 HET ASP A 501 9 HET 6OU A 502 30 HET 6OU A 503 43 HETNAM FME N-FORMYLMETHIONINE HETNAM ASP ASPARTIC ACID HETNAM 6OU [(2~{R})-1-[2-AZANYLETHOXY(OXIDANYL)PHOSPHORYL]OXY-3- HETNAM 2 6OU HEXADECANOYLOXY-PROPAN-2-YL] (~{Z})-OCTADEC-9-ENOATE FORMUL 1 FME C6 H11 N O3 S FORMUL 2 ASP C4 H7 N O4 FORMUL 3 6OU 2(C39 H76 N O8 P) HELIX 1 AA1 GLY A 2 GLU A 9 1 8 HELIX 2 AA2 PRO A 11 TYR A 33 1 23 HELIX 3 AA3 TYR A 35 VAL A 43 1 9 HELIX 4 AA4 LYS A 44 LEU A 57 1 14 HELIX 5 AA5 LEU A 57 GLY A 69 1 13 HELIX 6 AA6 PRO A 75 PHE A 107 1 33 HELIX 7 AA7 LEU A 130 ASP A 136 1 7 HELIX 8 AA8 ASN A 141 ASN A 148 1 8 HELIX 9 AA9 GLN A 150 MET A 169 1 20 HELIX 10 AB1 ASN A 173 GLY A 221 1 49 HELIX 11 AB2 GLY A 226 LEU A 245 1 20 HELIX 12 AB3 VAL A 246 ILE A 253 1 8 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 ALA A 307 1 13 HELIX 16 AB7 MET A 311 LEU A 329 1 19 HELIX 17 AB8 THR A 334 THR A 352 1 19 HELIX 18 AB9 GLY A 357 GLY A 371 1 15 HELIX 19 AC1 ASP A 376 ILE A 389 1 14 HELIX 20 AC2 ILE A 389 GLU A 416 1 28 LINK C FME A 1 N GLY A 2 1555 1555 1.33 LINK CD LYS A 196 N29 6OU A 503 1555 1555 1.43 SITE 1 AC1 12 ARG A 276 SER A 278 THR A 314 GLY A 354 SITE 2 AC1 12 VAL A 355 GLY A 357 ALA A 358 GLY A 359 SITE 3 AC1 12 ASP A 394 ARG A 397 THR A 398 ASN A 401 SITE 1 AC2 5 PRO A 128 ILE A 133 LEU A 347 GLY A 351 SITE 2 AC2 5 MET A 362 SITE 1 AC3 4 TYR A 4 TYR A 7 LYS A 196 GLY A 200 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 HETATM 1 N FME A 1 119.984 166.877 154.530 1.00102.06 N HETATM 2 CN FME A 1 119.857 167.151 155.873 1.00102.06 C HETATM 3 O1 FME A 1 119.152 166.484 156.645 1.00102.06 O HETATM 4 CA FME A 1 120.808 167.659 153.650 1.00102.06 C HETATM 5 CB FME A 1 121.826 166.800 152.874 1.00102.06 C HETATM 6 CG FME A 1 122.261 165.598 153.669 1.00102.06 C HETATM 7 SD FME A 1 123.910 165.195 153.164 1.00102.06 S HETATM 8 CE FME A 1 124.657 164.755 154.687 1.00102.06 C HETATM 9 C FME A 1 120.007 168.450 152.615 1.00102.06 C HETATM 10 O FME A 1 120.304 168.497 151.421 1.00102.06 O