HEADER TRANSPORT PROTEIN 04-OCT-23 8UFE TITLE MULTIDRUG EFFLUX PUMP EFPA FROM MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRAL MEMBRANE EFFLUX PROTEIN EFPA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 1772; SOURCE 4 GENE: EFPA_1; SOURCE 5 EXPRESSION_SYSTEM: MYCOLICIBACTERIUM SMEGMATIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1772 KEYWDS MULTIDRUG EFFLUX PUMP, EFPA, MYCOBACTERIUM SMEGMATIS, TRANSPORT KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.WANG,M.LIAO REVDAT 1 11-SEP-24 8UFE 0 JRNL AUTH S.WANG,K.WANG,K.SONG,Z.W.LAI,P.LI,D.LI,Y.SUN,Y.MEI,C.XU, JRNL AUTH 2 M.LIAO JRNL TITL STRUCTURES OF THE MYCOBACTERIUM TUBERCULOSIS EFFLUX PUMP JRNL TITL 2 EFPA REVEAL THE MECHANISMS OF TRANSPORT AND INHIBITION. JRNL REF NAT COMMUN V. 15 7710 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 39231991 JRNL DOI 10.1038/S41467-024-51948-9 REMARK 2 REMARK 2 RESOLUTION. 3.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 3.680 REMARK 3 NUMBER OF PARTICLES : 52150 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 8UFE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278003. 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 : 2D ARRAY REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : MULTIDRUG EFFLUX PUMP MSEFPA 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 : 8.00 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 TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5000.00 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) : 200 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 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 THR A 236 CG2 REMARK 470 THR A 300 CG2 REMARK 470 ILE A 372 CD1 REMARK 470 ILE A 384 CD1 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 ARG A 95 -60.02 -101.51 REMARK 500 PHE A 148 73.01 52.83 REMARK 500 SER A 183 143.10 -173.29 REMARK 500 ARG A 211 98.69 -69.98 REMARK 500 LYS A 450 -8.27 72.09 REMARK 500 ALA A 451 -124.57 41.02 REMARK 500 ALA A 493 -56.86 171.19 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 PTY A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8WM5 RELATED DB: PDB REMARK 900 8WM5 CONTAINS THE SAME PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS REMARK 900 RELATED ID: 8UFD RELATED DB: PDB REMARK 900 8UFD CONTAINS THE SAME PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS REMARK 900 RELATED ID: EMD-42205 RELATED DB: EMDB REMARK 900 MULTIDRUG EFFLUX PUMP EFPA FROM MYCOBACTERIUM SMEGMATIS DBREF1 8UFE A 27 496 UNP A0A653FLF0_MYCSM DBREF2 8UFE A A0A653FLF0 27 496 SEQRES 1 A 470 TRP GLY PHE LEU SER ALA VAL ILE ALA ILE GLY GLY MET SEQRES 2 A 470 GLN LEU LEU ALA THR MET ASP SER THR VAL ALA ILE VAL SEQRES 3 A 470 ALA LEU PRO LYS ILE GLN ASP GLU LEU SER LEU SER ASP SEQRES 4 A 470 ALA GLY ARG SER TRP VAL ILE THR ALA TYR VAL LEU THR SEQRES 5 A 470 PHE GLY GLY LEU MET LEU LEU GLY GLY ARG LEU GLY ASP SEQRES 6 A 470 THR ILE GLY ARG LYS ARG THR PHE ILE VAL GLY VAL MET SEQRES 7 A 470 LEU PHE THR ILE ALA SER VAL LEU CYS GLY ILE ALA TRP SEQRES 8 A 470 ASN GLU THR THR LEU VAL THR ALA ARG LEU LEU GLN GLY SEQRES 9 A 470 VAL GLY ALA ALA ILE ALA SER PRO THR GLY LEU ALA LEU SEQRES 10 A 470 VAL ALA THR THR PHE PRO LYS GLY PRO ALA ARG ASN ALA SEQRES 11 A 470 ALA THR ALA VAL PHE GLY ALA MET THR ALA ILE GLY SER SEQRES 12 A 470 VAL MET GLY LEU VAL VAL GLY GLY ALA LEU THR GLU VAL SEQRES 13 A 470 SER TRP ARG TRP ALA PHE LEU VAL ASN VAL PRO ILE GLY SEQRES 14 A 470 LEU VAL MET VAL TYR LEU ALA ARG THR ALA LEU GLN GLU SEQRES 15 A 470 THR ASN ARG GLU ARG MET LYS LEU ASP ALA ALA GLY ALA SEQRES 16 A 470 LEU LEU ALA THR LEU ALA CYS THR ALA ALA VAL PHE ALA SEQRES 17 A 470 PHE THR GLN GLY PRO GLU SER GLY TRP LEU ALA PRO ILE SEQRES 18 A 470 THR LEU ALA SER GLY ALA ALA ALA LEU VAL PHE GLY LEU SEQRES 19 A 470 ALA PHE LEU ILE ALA GLU ARG ASN ALA GLU ASN PRO VAL SEQRES 20 A 470 VAL PRO PHE ALA LEU PHE ARG GLU ARG ASN ARG VAL ALA SEQRES 21 A 470 THR PHE ALA ALA ILE PHE LEU ALA GLY GLY VAL LEU PHE SEQRES 22 A 470 THR LEU THR VAL LEU ILE GLY LEU TYR VAL GLN ASP ILE SEQRES 23 A 470 LEU GLY TYR SER ALA LEU ARG ALA GLY VAL GLY PHE ILE SEQRES 24 A 470 PRO PHE VAL ILE GLY MET GLY ILE GLY LEU GLY ALA ALA SEQRES 25 A 470 SER GLN LEU VAL ARG SER ILE PRO PRO ARG VAL LEU VAL SEQRES 26 A 470 ILE ALA GLY GLY ILE LEU VAL LEU GLY ALA MET ILE TYR SEQRES 27 A 470 GLY SER THR LEU HIS ARG GLY ILE PRO TYR PHE PRO ASN SEQRES 28 A 470 LEU VAL LEU PRO ILE THR ILE GLY GLY ILE GLY ILE GLY SEQRES 29 A 470 THR ILE VAL VAL PRO LEU THR LEU SER ALA ILE ALA GLY SEQRES 30 A 470 VAL ASN LEU ASP ARG ILE GLY PRO ALA SER ALA ILE ALA SEQRES 31 A 470 LEU MET LEU GLN ASN LEU GLY GLY PRO LEU VAL LEU ALA SEQRES 32 A 470 VAL ILE GLN ALA VAL ILE THR SER ARG THR LEU PHE LEU SEQRES 33 A 470 GLY GLY THR THR GLY PRO VAL LYS ALA MET ASN ASP GLU SEQRES 34 A 470 GLN ILE GLY ALA LEU ASP ALA ALA TYR THR TYR GLY LEU SEQRES 35 A 470 LEU TRP VAL ALA ALA VAL ALA VAL LEU VAL GLY ALA ALA SEQRES 36 A 470 ALA LEU PHE ILE GLY TYR THR SER GLN GLN VAL ALA HIS SEQRES 37 A 470 ALA GLN HET PTY A 501 44 HETNAM PTY PHOSPHATIDYLETHANOLAMINE FORMUL 2 PTY C40 H80 N O8 P HELIX 1 AA1 TRP A 27 GLY A 38 1 12 HELIX 2 AA2 GLY A 38 LEU A 61 1 24 HELIX 3 AA3 SER A 64 GLY A 81 1 18 HELIX 4 AA4 LEU A 82 LEU A 89 1 8 HELIX 5 AA5 ARG A 95 ILE A 115 1 21 HELIX 6 AA6 ASN A 118 THR A 147 1 30 HELIX 7 AA7 GLY A 151 LEU A 179 1 29 HELIX 8 AA8 SER A 183 VAL A 190 1 8 HELIX 9 AA9 VAL A 190 ALA A 205 1 16 HELIX 10 AB1 ASP A 217 GLY A 242 1 26 HELIX 11 AB2 ALA A 245 ARG A 267 1 23 HELIX 12 AB3 PHE A 276 ARG A 280 5 5 HELIX 13 AB4 GLU A 281 ILE A 312 1 32 HELIX 14 AB5 SER A 316 VAL A 342 1 27 HELIX 15 AB6 ARG A 343 ILE A 345 5 3 HELIX 16 AB7 PRO A 346 SER A 366 1 21 HELIX 17 AB8 LEU A 378 ILE A 401 1 24 HELIX 18 AB9 ARG A 408 GLY A 443 1 36 HELIX 19 AC1 ASN A 453 GLU A 455 5 3 HELIX 20 AC2 GLN A 456 PHE A 484 1 29 CISPEP 1 PHE A 375 PRO A 376 0 -4.86 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