HEADER TRANSPORT PROTEIN 19-APR-24 9BGY TITLE ANCESTRAL UNCOUPLED ASPARTATE TRANSPORTER, APO CONDITIONS, LOW- TITLE 2 AFFINITY STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTATE TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: C-TERMINAL THROMBIN CLEAVAGE SITE, TWIN-STREP TAG, COMPND 6 ALFA TAG, AND (HIS)10 TAG. ENGINEERED WITH LOOPS AND TAILS FROM NCBI COMPND 7 KJS87745.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSPORTER, ION-UNCOUPLED, ANCESTRAL, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.D.REDDY,O.BOUDKER REVDAT 1 12-MAR-25 9BGY 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. 3.00 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 68420 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 9BGY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000281337. 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 : ANCESTRAL BACTERIAL ASPARTATE REMARK 245 TRANSPORTER, UNCOUPLED 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) : 5029.00 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 GLU A 390 REMARK 465 LEU A 391 REMARK 465 ASN A 392 REMARK 465 ARG A 393 REMARK 465 GLU A 394 REMARK 465 MET A 395 REMARK 465 THR A 396 REMARK 465 ALA A 397 REMARK 465 THR A 398 REMARK 465 PRO A 399 REMARK 465 LEU A 400 REMARK 465 GLU A 401 REMARK 465 VAL A 402 REMARK 465 LEU A 403 REMARK 465 GLU A 404 REMARK 465 SER A 405 REMARK 465 LYS A 406 REMARK 465 THR A 407 REMARK 465 ILE A 408 REMARK 465 ALA A 409 REMARK 465 LEU A 410 REMARK 465 GLY A 411 REMARK 465 SER A 412 REMARK 465 SER A 413 REMARK 465 SER A 414 REMARK 465 LEU A 415 REMARK 465 VAL A 416 REMARK 465 PRO A 417 REMARK 465 ARG A 418 REMARK 465 GLY A 419 REMARK 465 SER A 420 REMARK 465 GLY A 421 REMARK 465 GLY A 422 REMARK 465 GLY A 423 REMARK 465 SER A 424 REMARK 465 GLY A 425 REMARK 465 GLY A 426 REMARK 465 SER A 427 REMARK 465 PRO A 428 REMARK 465 SER A 429 REMARK 465 ARG A 430 REMARK 465 LEU A 431 REMARK 465 GLU A 432 REMARK 465 GLU A 433 REMARK 465 GLU A 434 REMARK 465 LEU A 435 REMARK 465 ARG A 436 REMARK 465 ARG A 437 REMARK 465 ARG A 438 REMARK 465 LEU A 439 REMARK 465 THR A 440 REMARK 465 GLU A 441 REMARK 465 PRO A 442 REMARK 465 GLY A 443 REMARK 465 GLY A 444 REMARK 465 GLY A 445 REMARK 465 SER A 446 REMARK 465 GLY A 447 REMARK 465 GLY A 448 REMARK 465 GLY A 449 REMARK 465 SER A 450 REMARK 465 ALA A 451 REMARK 465 TRP A 452 REMARK 465 SER A 453 REMARK 465 HIS A 454 REMARK 465 PRO A 455 REMARK 465 GLN A 456 REMARK 465 PHE A 457 REMARK 465 GLU A 458 REMARK 465 LYS A 459 REMARK 465 GLY A 460 REMARK 465 GLY A 461 REMARK 465 GLY A 462 REMARK 465 SER A 463 REMARK 465 GLY A 464 REMARK 465 GLY A 465 REMARK 465 GLY A 466 REMARK 465 SER A 467 REMARK 465 GLY A 468 REMARK 465 GLY A 469 REMARK 465 SER A 470 REMARK 465 ALA A 471 REMARK 465 TRP A 472 REMARK 465 SER A 473 REMARK 465 HIS A 474 REMARK 465 PRO A 475 REMARK 465 GLN A 476 REMARK 465 PHE A 477 REMARK 465 GLU A 478 REMARK 465 LYS A 479 REMARK 465 GLY A 480 REMARK 465 GLY A 481 REMARK 465 GLY A 482 REMARK 465 SER A 483 REMARK 465 GLY A 484 REMARK 465 GLY A 485 REMARK 465 GLY A 486 REMARK 465 SER A 487 REMARK 465 HIS A 488 REMARK 465 HIS A 489 REMARK 465 HIS A 490 REMARK 465 HIS A 491 REMARK 465 HIS A 492 REMARK 465 HIS A 493 REMARK 465 HIS A 494 REMARK 465 HIS A 495 REMARK 465 HIS A 496 REMARK 465 HIS A 497 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 OD1 ASP A 366 NH2 ARG A 369 2.19 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 LYS A 233 62.10 60.91 REMARK 500 CYS A 254 36.21 71.03 REMARK 500 THR A 322 -20.37 73.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-44526 RELATED DB: EMDB REMARK 900 ANCESTRAL UNCOUPLED ASPARTATE TRANSPORTER, APO CONDITIONS, LOW- REMARK 900 AFFINITY STATE DBREF 9BGY A 1 497 PDB 9BGY 9BGY 1 497 SEQRES 1 A 497 MET SER LEU TYR HIS LYS ILE LEU ILE GLY PHE VAL LEU SEQRES 2 A 497 GLY VAL ILE VAL GLY LEU ILE PHE GLY ASP LYS ALA GLU SEQRES 3 A 497 PHE ILE LYS PRO LEU GLY ASP ILE PHE LEU ARG LEU LEU SEQRES 4 A 497 LYS MET ILE VAL VAL PRO LEU VAL PHE SER THR ILE VAL SEQRES 5 A 497 THR GLY ILE ALA SER MET GLY ASP VAL LYS LYS LEU GLY SEQRES 6 A 497 ARG ILE GLY ALA LYS THR LEU ILE TYR TYR MET ILE THR SEQRES 7 A 497 THR THR LEU ALA VAL THR ILE GLY LEU ILE LEU ALA ASN SEQRES 8 A 497 ILE PHE LYS PRO GLY LYS GLY LEU SER LEU GLY GLU ILE SEQRES 9 A 497 HIS GLU VAL ALA HIS PRO ASN ALA PRO SER PHE THR GLU SEQRES 10 A 497 THR LEU LEU ASN MET ILE PRO THR ASN PRO PHE GLU ALA SEQRES 11 A 497 MET ALA GLU GLY ASN MET LEU GLN ILE ILE VAL PHE ALA SEQRES 12 A 497 ILE PHE PHE GLY ILE ALA LEU ALA LEU MET GLY GLU LYS SEQRES 13 A 497 ALA GLU PRO VAL LYS LYS PHE PHE ASP SER ALA SER GLU SEQRES 14 A 497 VAL MET PHE LYS ILE THR ASP ILE VAL MET LYS PHE ALA SEQRES 15 A 497 PRO TYR GLY VAL PHE ALA LEU MET ALA TRP THR VAL GLY SEQRES 16 A 497 LYS TYR GLY LEU ASP VAL LEU ALA PRO LEU GLY LYS LEU SEQRES 17 A 497 ILE LEU THR VAL TYR LEU GLY CYS ILE ILE HIS ILE LEU SEQRES 18 A 497 ILE VAL TYR THR LEU LEU LEU ARG PHE LEU CYS LYS ILE SEQRES 19 A 497 ASN PRO LEU ARG PHE PHE LYS LYS ILE LYS GLU ALA MET SEQRES 20 A 497 LEU VAL ALA PHE SER THR CYS SER SER ALA ALA THR LEU SEQRES 21 A 497 PRO VAL THR MET ARG VAL ALA GLU GLU LEU GLY VAL PRO SEQRES 22 A 497 GLU SER ILE ALA SER PHE THR LEU PRO LEU GLY ALA THR SEQRES 23 A 497 ILE ASN MET ASP GLY THR ALA LEU TYR GLN GLY VAL ALA SEQRES 24 A 497 ALA ILE PHE VAL ALA GLN ALA TYR GLY VAL GLU LEU THR SEQRES 25 A 497 LEU GLY GLN GLN LEU THR ILE VAL LEU THR ALA VAL LEU SEQRES 26 A 497 ALA SER ILE GLY THR ALA GLY VAL PRO GLY ALA GLY LEU SEQRES 27 A 497 VAL MET LEU THR MET VAL LEU THR SER VAL GLY LEU PRO SEQRES 28 A 497 LEU GLU GLY ILE ALA LEU ILE ALA GLY ILE ASP ARG ILE SEQRES 29 A 497 LEU ASP MET ALA ARG THR THR VAL ASN VAL THR GLY ASP SEQRES 30 A 497 LEU VAL ALA THR ALA ILE VAL ALA ARG THR GLU ASN GLU SEQRES 31 A 497 LEU ASN ARG GLU MET THR ALA THR PRO LEU GLU VAL LEU SEQRES 32 A 497 GLU SER LYS THR ILE ALA LEU GLY SER SER SER LEU VAL SEQRES 33 A 497 PRO ARG GLY SER GLY GLY GLY SER GLY GLY SER PRO SER SEQRES 34 A 497 ARG LEU GLU GLU GLU LEU ARG ARG ARG LEU THR GLU PRO SEQRES 35 A 497 GLY GLY GLY SER GLY GLY GLY SER ALA TRP SER HIS PRO SEQRES 36 A 497 GLN PHE GLU LYS GLY GLY GLY SER GLY GLY GLY SER GLY SEQRES 37 A 497 GLY SER ALA TRP SER HIS PRO GLN PHE GLU LYS GLY GLY SEQRES 38 A 497 GLY SER GLY GLY GLY SER HIS HIS HIS HIS HIS HIS HIS SEQRES 39 A 497 HIS HIS HIS HELIX 1 AA1 SER A 2 GLY A 22 1 21 HELIX 2 AA2 ASP A 23 PHE A 27 5 5 HELIX 3 AA3 ILE A 28 MET A 41 1 14 HELIX 4 AA4 ILE A 42 GLY A 59 1 18 HELIX 5 AA5 ASP A 60 PHE A 93 1 34 HELIX 6 AA6 SER A 114 ASN A 121 1 8 HELIX 7 AA7 ASN A 126 GLY A 134 1 9 HELIX 8 AA8 ASN A 135 GLY A 154 1 20 HELIX 9 AA9 ALA A 157 LYS A 180 1 24 HELIX 10 AB1 PHE A 181 TYR A 197 1 17 HELIX 11 AB2 GLY A 198 ALA A 203 1 6 HELIX 12 AB3 LEU A 205 LEU A 231 1 27 HELIX 13 AB4 ASN A 235 ILE A 243 1 9 HELIX 14 AB5 ILE A 243 CYS A 254 1 12 HELIX 15 AB6 SER A 255 GLY A 271 1 17 HELIX 16 AB7 PRO A 273 ASN A 288 1 16 HELIX 17 AB8 MET A 289 TYR A 307 1 19 HELIX 18 AB9 THR A 312 LEU A 321 1 10 HELIX 19 AC1 THR A 322 SER A 327 1 6 HELIX 20 AC2 GLY A 329 VAL A 333 5 5 HELIX 21 AC3 GLY A 335 GLY A 349 1 15 HELIX 22 AC4 PRO A 351 ILE A 361 1 11 HELIX 23 AC5 ILE A 361 THR A 387 1 27 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 2917 ASN A 389 MASTER 244 0 0 23 0 0 0 6 2916 1 0 39 END