HEADER MEMBRANE PROTEIN 04-OCT-21 7SFQ TITLE EMRE S64V MUTANT BOUND TO TETRA(4-FLUOROPHENYL)PHOSPHONIUM AT PH 8.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIDRUG TRANSPORTER EMRE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: EFFLUX-MULTIDRUG RESISTANCE PROTEIN EMRE,ETHIDIUM RESISTANCE COMPND 5 PROTEIN,METHYL VIOLOGEN RESISTANCE PROTEIN C; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: EMRE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS MULTIDRUG RESISTANCE PROTEIN, SMR TRANSPORTER, EFFLUX PROTEIN, KEYWDS 2 PROTON-COUPLED, MEMBRANE PROTEIN EXPDTA SOLID-STATE NMR NUMMDL 10 AUTHOR A.A.SHCHERBAKOV,P.J.SPREACKER,A.J.DREGNI,K.A.HENZLER-WILDMAN,M.HONG REVDAT 2 15-MAY-24 7SFQ 1 REMARK REVDAT 1 02-MAR-22 7SFQ 0 JRNL AUTH A.A.SHCHERBAKOV,P.J.SPREACKER,A.J.DREGNI, JRNL AUTH 2 K.A.HENZLER-WILDMAN,M.HONG JRNL TITL HIGH-PH STRUCTURE OF EMRE REVEALS THE MECHANISM OF JRNL TITL 2 PROTON-COUPLED SUBSTRATE TRANSPORT. JRNL REF NAT COMMUN V. 13 991 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35181664 JRNL DOI 10.1038/S41467-022-28556-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS 2019.1 REMARK 3 AUTHORS : UNIVERSITY OF GRONINGEN ROYAL INSTITUTE OF REMARK 3 TECHNOLOGY UPPSALA UNIVERSITY REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE AUTHORS STATE THAT THE STARTING REMARK 3 MODEL FOR STRUCTURE CALCULATION WAS 7JK8. THE LIGAND VCJ WAS REMARK 3 REMOVED FROM THE 7JK8 STRUCTURE AND RE-DOCKED USING HADDOCK, REMARK 3 UNDER NEW CONSTRAINTS MEASURED IN THE PRESENT STUDY. THE DOCKED REMARK 3 STRUCTURES BEST AGREEING WITH EXPERIMENT WERE FURTHER REFINED BY REMARK 3 ALL-ATOM MD SIMULATIONS IN EXPLICIT LIPID BILAYERS TO GENERATE REMARK 3 THE ENSEMBLE DEPOSITED FOR THIS STUDY. REMARK 4 REMARK 4 7SFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000259417. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285 REMARK 210 PH : 8.0 REMARK 210 IONIC STRENGTH : 0.07 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.27 MG/UL [U-13C; U-15N; U-2H] REMARK 210 MULTIDRUG RESISTANCE PROTEIN E (EMRE), COMPLEX WITH TETRA(4- REMARK 210 FLUOROPHENYL)PHOSPHONIUM, 9.5 UG/UL F4TPP, 0.44 MG/UL [U-99% 2H] REMARK 210 D54-DMPC, BILAYERS REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D SOLID-STATE HNH; 3D SOLID REMARK 210 -STATE HCANH; 3D SOLID-STATE REMARK 210 HCONH; 3D SOLID-STATE HCA(CO)NH; REMARK 210 3D SOLID-STATE HCO(CA)NH; 3D REMARK 210 SOLID-STATE H(CA)CB(CACO)NH; 3D REMARK 210 SOLID-STATE HN(CACO)NH; 3D SOLID- REMARK 210 STATE H(NCACO)NH; 3D SOLID-STATE REMARK 210 H(CA)CB(CA)NH; 2D HNH-RESOLVED REMARK 210 1H-19F REDOR; 2D FF EXCHANGE; 2D REMARK 210 WATER-EDITED SOLID-STATE HNH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK WEBSERVER 2.4, TOPSPIN REMARK 210 2.1-4.0, NMRFAM-SPARKY 1.414, REMARK 210 1.470 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 82 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 PRO A 3 REMARK 465 ARG A 106 REMARK 465 SER A 107 REMARK 465 THR A 108 REMARK 465 PRO A 109 REMARK 465 HIS A 110 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 PRO B 3 REMARK 465 ARG B 106 REMARK 465 SER B 107 REMARK 465 THR B 108 REMARK 465 PRO B 109 REMARK 465 HIS B 110 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 1 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 ARG B 29 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 TYR B 60 CB - CG - CD2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 TYR B 60 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 ARG B 82 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 4 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 82 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 5 ARG B 82 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 ARG A 82 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 6 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG B 29 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 6 ARG B 82 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 TYR A 60 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 TYR A 60 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 7 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 ARG A 82 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 7 ARG B 82 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 8 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 8 ARG A 82 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 8 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 8 ARG B 29 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 8 ARG B 82 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 9 ARG A 82 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 9 ARG B 29 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 9 ARG B 82 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 ARG A 29 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 29 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 3.5 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 1 SER A 24 31.86 -86.28 REMARK 500 1 ILE B 5 134.86 -32.51 REMARK 500 1 PRO B 55 126.23 -38.88 REMARK 500 2 ARG A 82 153.60 -34.77 REMARK 500 2 ARG B 29 119.36 -22.08 REMARK 500 2 LEU B 30 13.29 82.58 REMARK 500 2 PRO B 55 138.17 -39.83 REMARK 500 3 PRO A 55 157.16 -48.79 REMARK 500 3 ARG A 82 135.00 -29.12 REMARK 500 4 ILE B 5 130.38 -35.42 REMARK 500 4 PRO B 55 136.15 -39.95 REMARK 500 4 PHE B 78 -68.05 -104.30 REMARK 500 5 PHE A 27 -66.78 -141.96 REMARK 500 5 PRO A 55 131.76 -39.32 REMARK 500 5 TRP A 76 -72.09 -152.27 REMARK 500 5 SER B 24 128.91 -33.18 REMARK 500 5 PHE B 27 160.83 -47.14 REMARK 500 5 LEU B 30 -66.81 76.00 REMARK 500 5 PRO B 55 136.41 -39.51 REMARK 500 6 PRO A 55 121.42 -36.66 REMARK 500 6 TRP A 76 -53.20 -160.38 REMARK 500 6 LEU B 30 -76.25 64.15 REMARK 500 6 SER B 33 36.17 -78.58 REMARK 500 7 PHE A 27 -109.07 -99.48 REMARK 500 7 PRO A 32 -145.33 -92.83 REMARK 500 7 TRP A 76 -46.67 -170.67 REMARK 500 7 PHE A 78 140.95 -35.02 REMARK 500 7 SER B 24 133.23 -33.39 REMARK 500 7 PRO B 32 155.21 -49.64 REMARK 500 7 SER B 33 46.04 -80.84 REMARK 500 8 ARG A 29 151.28 -48.35 REMARK 500 8 PHE A 78 -172.37 -175.44 REMARK 500 8 ARG A 82 140.36 -32.10 REMARK 500 8 LEU B 30 -53.39 79.26 REMARK 500 8 PRO B 55 139.90 -39.16 REMARK 500 9 PHE A 27 -90.38 -134.15 REMARK 500 9 TRP A 76 -50.73 -169.08 REMARK 500 9 LEU A 85 -52.26 -25.35 REMARK 500 9 ILE B 5 106.50 -55.35 REMARK 500 9 LEU B 30 -59.78 78.28 REMARK 500 9 PRO B 32 152.89 -40.85 REMARK 500 9 PRO B 55 137.56 -39.72 REMARK 500 10 PHE A 27 -65.16 -147.78 REMARK 500 10 PRO A 32 141.37 -39.51 REMARK 500 10 TRP A 76 -66.93 -162.63 REMARK 500 10 ARG A 82 70.28 57.61 REMARK 500 10 LEU B 30 -54.49 78.20 REMARK 500 10 PRO B 32 160.58 -46.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 82 0.10 SIDE CHAIN REMARK 500 6 ARG B 29 0.10 SIDE CHAIN REMARK 500 10 TYR A 4 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30957 RELATED DB: BMRB REMARK 900 EMRE S64V MUTANT BOUND TO TETRA(4-FLUOROPHENYL)PHOSPHONIUM AT PH 8.0 DBREF 7SFQ A 1 110 UNP P23895 EMRE_ECOLI 1 110 DBREF 7SFQ B 1 110 UNP P23895 EMRE_ECOLI 1 110 SEQADV 7SFQ VAL A 64 UNP P23895 SER 64 ENGINEERED MUTATION SEQADV 7SFQ VAL B 64 UNP P23895 SER 64 ENGINEERED MUTATION SEQRES 1 A 110 MET ASN PRO TYR ILE TYR LEU GLY GLY ALA ILE LEU ALA SEQRES 2 A 110 GLU VAL ILE GLY THR THR LEU MET LYS PHE SER GLU GLY SEQRES 3 A 110 PHE THR ARG LEU TRP PRO SER VAL GLY THR ILE ILE CYS SEQRES 4 A 110 TYR CYS ALA SER PHE TRP LEU LEU ALA GLN THR LEU ALA SEQRES 5 A 110 TYR ILE PRO THR GLY ILE ALA TYR ALA ILE TRP VAL GLY SEQRES 6 A 110 VAL GLY ILE VAL LEU ILE SER LEU LEU SER TRP GLY PHE SEQRES 7 A 110 PHE GLY GLN ARG LEU ASP LEU PRO ALA ILE ILE GLY MET SEQRES 8 A 110 MET LEU ILE CYS ALA GLY VAL LEU ILE ILE ASN LEU LEU SEQRES 9 A 110 SER ARG SER THR PRO HIS SEQRES 1 B 110 MET ASN PRO TYR ILE TYR LEU GLY GLY ALA ILE LEU ALA SEQRES 2 B 110 GLU VAL ILE GLY THR THR LEU MET LYS PHE SER GLU GLY SEQRES 3 B 110 PHE THR ARG LEU TRP PRO SER VAL GLY THR ILE ILE CYS SEQRES 4 B 110 TYR CYS ALA SER PHE TRP LEU LEU ALA GLN THR LEU ALA SEQRES 5 B 110 TYR ILE PRO THR GLY ILE ALA TYR ALA ILE TRP VAL GLY SEQRES 6 B 110 VAL GLY ILE VAL LEU ILE SER LEU LEU SER TRP GLY PHE SEQRES 7 B 110 PHE GLY GLN ARG LEU ASP LEU PRO ALA ILE ILE GLY MET SEQRES 8 B 110 MET LEU ILE CYS ALA GLY VAL LEU ILE ILE ASN LEU LEU SEQRES 9 B 110 SER ARG SER THR PRO HIS HET VCJ A 201 45 HETNAM VCJ TETRAKIS(4-FLUOROPHENYL)PHOSPHANIUM FORMUL 3 VCJ C24 H16 F4 P 1+ HELIX 1 AA1 ILE A 5 SER A 24 1 20 HELIX 2 AA2 PRO A 32 LEU A 51 1 20 HELIX 3 AA3 PRO A 55 GLY A 77 1 23 HELIX 4 AA4 ASP A 84 LEU A 103 1 20 HELIX 5 AA5 ILE B 5 LYS B 22 1 18 HELIX 6 AA6 VAL B 34 ILE B 54 1 21 HELIX 7 AA7 PRO B 55 GLY B 80 1 26 HELIX 8 AA8 LEU B 85 LEU B 104 1 20 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1