HEADER TRANSPORT PROTEIN 05-NOV-19 6UWL TITLE GLTPH IN COMPLEX WITH L-ASPARTATE AND SODIUM IONS IN INTERMEDIATE TITLE 2 OUTWARD-FACING 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 6UWL 1 JRNL REVDAT 1 22-APR-20 6UWL 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. 3.62 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) : 3.620 REMARK 3 NUMBER OF PARTICLES : 120280 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 6UWL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245328. 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 ILE A 113 REMARK 465 HIS A 114 REMARK 465 LEU A 115 REMARK 465 ALA A 116 REMARK 465 VAL A 117 REMARK 465 GLY A 118 REMARK 465 GLY A 119 REMARK 465 GLN A 120 REMARK 465 GLN A 121 REMARK 465 PHE A 122 REMARK 465 GLN A 123 REMARK 465 PRO A 124 REMARK 465 HIS A 125 REMARK 465 GLN A 126 REMARK 465 ALA A 127 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 CZ TYR A 7 C08 6OU A 502 2.15 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 LEU A 228 CA - CB - CG ANGL. DEV. = 17.3 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 LEU A 130 -13.21 73.44 REMARK 500 ILE A 294 -71.32 -80.93 REMARK 500 SER A 295 147.44 179.53 REMARK 500 SER A 331 -72.72 -65.91 REMARK 500 HIS A 332 -170.83 -172.25 REMARK 500 GLN A 337 70.91 58.63 REMARK 500 LEU A 372 73.11 50.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 294 SER A 295 143.05 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-20923 RELATED DB: EMDB REMARK 900 GLTPH IN COMPLEX WITH L-ASPARTATE AND SODIUM IONS IN INTERMEDIATE REMARK 900 OUTWARD-FACING STATE DBREF 6UWL A 1 422 PDB 6UWL 6UWL 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 39 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 C39 H76 N O8 P HELIX 1 AA1 GLY A 2 ILE A 8 1 7 HELIX 2 AA2 PRO A 11 GLN A 14 5 4 HELIX 3 AA3 LYS A 15 HIS A 32 1 18 HELIX 4 AA4 TYR A 35 VAL A 43 1 9 HELIX 5 AA5 VAL A 43 LEU A 57 1 15 HELIX 6 AA6 LEU A 57 ALA A 70 1 14 HELIX 7 AA7 PRO A 75 MET A 103 1 29 HELIX 8 AA8 VAL A 131 ASP A 136 1 6 HELIX 9 AA9 PHE A 143 ASN A 148 1 6 HELIX 10 AB1 GLN A 150 MET A 169 1 20 HELIX 11 AB2 ASN A 173 GLN A 220 1 48 HELIX 12 AB3 GLY A 221 VAL A 224 5 4 HELIX 13 AB4 LEU A 228 TYR A 254 1 27 HELIX 14 AB5 ASP A 257 ARG A 276 1 20 HELIX 15 AB6 THR A 281 GLY A 293 1 13 HELIX 16 AB7 SER A 295 SER A 300 1 6 HELIX 17 AB8 PHE A 301 ASN A 310 1 10 HELIX 18 AB9 MET A 311 ASN A 327 1 17 HELIX 19 AC1 GLN A 337 GLY A 351 1 15 HELIX 20 AC2 ALA A 358 GLY A 371 1 14 HELIX 21 AC3 VAL A 379 THR A 415 1 37 LINK C FME A 1 N GLY A 2 1555 1555 1.33 LINK CE2 TYR A 7 C08 6OU A 502 1555 1555 1.49 SITE 1 AC1 12 SER A 278 MET A 311 THR A 314 ALA A 353 SITE 2 AC1 12 GLY A 354 VAL A 355 PRO A 356 ALA A 358 SITE 3 AC1 12 GLY A 359 ASP A 394 ARG A 397 THR A 398 SITE 1 AC2 6 TYR A 4 TYR A 7 LYS A 196 ASN A 199 SITE 2 AC2 6 GLY A 200 GLN A 203 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 1 119.793 167.846 154.536 1.00107.19 N HETATM 2 CN FME A 1 120.807 167.691 155.454 1.00107.19 C HETATM 3 O1 FME A 1 120.632 167.285 156.613 1.00107.19 O HETATM 4 CA FME A 1 120.023 168.319 153.199 1.00107.19 C HETATM 5 CB FME A 1 120.376 167.175 152.230 1.00107.19 C HETATM 6 CG FME A 1 121.850 167.174 151.926 1.00107.19 C HETATM 7 SD FME A 1 122.303 165.513 151.519 1.00107.19 S HETATM 8 CE FME A 1 122.398 164.771 153.102 1.00107.19 C HETATM 9 C FME A 1 118.827 169.068 152.611 1.00107.19 C HETATM 10 O FME A 1 118.879 169.713 151.561 1.00107.19 O