HEADER TRANSPORT PROTEIN 07-JUL-21 7P34 TITLE CRYO-EM STRUCTURE OF THE PROTON-DEPENDENT ANTIBACTERIAL PEPTIDE TITLE 2 TRANSPORTER SBMA-FABS11-1 IN NANODISCS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE ANTIBIOTIC TRANSPORTER SBMA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SLIPT, PROTON TRANSPORT, PEPTIDE TRANSPORT, ANTIBIOTICS, TRANSPORT KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR D.GHILAROV,K.BEIS REVDAT 2 29-SEP-21 7P34 1 TITLE JRNL REVDAT 1 15-SEP-21 7P34 0 JRNL AUTH D.GHILAROV,S.INABA-INOUE,P.STEPIEN,F.QU,E.MICHALCZYK, JRNL AUTH 2 Z.PAKOSZ,N.NOMURA,S.OGASAWARA,G.C.WALKER,S.REBUFFAT,S.IWATA, JRNL AUTH 3 J.G.HEDDLE,K.BEIS JRNL TITL MOLECULAR MECHANISM OF SBMA, A PROMISCUOUS TRANSPORTER JRNL TITL 2 EXPLOITED BY ANTIMICROBIAL PEPTIDES. JRNL REF SCI ADV V. 7 J5363 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 34516884 JRNL DOI 10.1126/SCIADV.ABJ5363 REMARK 2 REMARK 2 RESOLUTION. 3.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, RELION, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE 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 : INITIAL MODEL GENERATED BY BUCCANEER AND REMARK 3 REFINED BY PHENIX 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) : 3.590 REMARK 3 NUMBER OF PARTICLES : 116545 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: THE LOCAL RESOLUTION FOR THE TRANSPORTER IS 3.2A REMARK 4 REMARK 4 7P34 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292116866. 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 PROTON-DRIVEN REMARK 245 PEPTIDE TRANSPORTER SBMA WITH REMARK 245 FAB S11-1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.00 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 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: 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. (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 392 REMARK 465 LEU A 393 REMARK 465 ASP A 394 REMARK 465 GLY A 395 REMARK 465 ASP A 396 REMARK 465 LYS A 397 REMARK 465 ILE A 398 REMARK 465 GLN A 399 REMARK 465 GLU A 400 REMARK 465 VAL A 401 REMARK 465 THR A 402 REMARK 465 HIS A 403 REMARK 465 THR A 404 REMARK 465 LEU A 405 REMARK 465 SER A 406 REMARK 465 GLU B 392 REMARK 465 LEU B 393 REMARK 465 ASP B 394 REMARK 465 GLY B 395 REMARK 465 ASP B 396 REMARK 465 LYS B 397 REMARK 465 ILE B 398 REMARK 465 GLN B 399 REMARK 465 GLU B 400 REMARK 465 VAL B 401 REMARK 465 THR B 402 REMARK 465 HIS B 403 REMARK 465 THR B 404 REMARK 465 LEU B 405 REMARK 465 SER B 406 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 GLN A 120 CG CD OE1 NE2 REMARK 470 GLN B 120 CG CD OE1 NE2 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 PHE A 5 -167.62 -80.00 REMARK 500 PHE A 6 82.24 53.46 REMARK 500 SER A 42 17.47 58.95 REMARK 500 PRO A 46 -176.88 -65.62 REMARK 500 ILE A 88 -60.17 -99.35 REMARK 500 PHE B 6 82.25 53.45 REMARK 500 SER B 42 17.43 59.03 REMARK 500 PRO B 46 -176.90 -65.56 REMARK 500 ILE B 88 -60.22 -99.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13168 RELATED DB: EMDB DBREF 7P34 A 1 406 UNP P0AFY6 SBMA_ECOLI 1 406 DBREF 7P34 B 1 406 UNP P0AFY6 SBMA_ECOLI 1 406 SEQRES 1 A 406 MET PHE LYS SER PHE PHE PRO LYS PRO GLY THR PHE PHE SEQRES 2 A 406 LEU SER ALA PHE VAL TRP ALA LEU ILE ALA VAL ILE PHE SEQRES 3 A 406 TRP GLN ALA GLY GLY GLY ASP TRP VAL ALA ARG ILE THR SEQRES 4 A 406 GLY ALA SER GLY GLN ILE PRO ILE SER ALA ALA ARG PHE SEQRES 5 A 406 TRP SER LEU ASP PHE LEU ILE PHE TYR ALA TYR TYR ILE SEQRES 6 A 406 VAL CYS VAL GLY LEU PHE ALA LEU PHE TRP PHE ILE TYR SEQRES 7 A 406 SER PRO HIS ARG TRP GLN TYR TRP SER ILE LEU GLY THR SEQRES 8 A 406 ALA LEU ILE ILE PHE VAL THR TRP PHE LEU VAL GLU VAL SEQRES 9 A 406 GLY VAL ALA VAL ASN ALA TRP TYR ALA PRO PHE TYR ASP SEQRES 10 A 406 LEU ILE GLN THR ALA LEU SER SER PRO HIS LYS VAL THR SEQRES 11 A 406 ILE GLU GLN PHE TYR ARG GLU VAL GLY VAL PHE LEU GLY SEQRES 12 A 406 ILE ALA LEU ILE ALA VAL VAL ILE SER VAL LEU ASN ASN SEQRES 13 A 406 PHE PHE VAL SER HIS TYR VAL PHE ARG TRP ARG THR ALA SEQRES 14 A 406 MET ASN GLU TYR TYR MET ALA ASN TRP GLN GLN LEU ARG SEQRES 15 A 406 HIS ILE GLU GLY ALA ALA GLN ARG VAL GLN GLU ASP THR SEQRES 16 A 406 MET ARG PHE ALA SER THR LEU GLU ASN MET GLY VAL SER SEQRES 17 A 406 PHE ILE ASN ALA ILE MET THR LEU ILE ALA PHE LEU PRO SEQRES 18 A 406 VAL LEU VAL THR LEU SER ALA HIS VAL PRO GLU LEU PRO SEQRES 19 A 406 ILE ILE GLY HIS ILE PRO TYR GLY LEU VAL ILE ALA ALA SEQRES 20 A 406 ILE VAL TRP SER LEU MET GLY THR GLY LEU LEU ALA VAL SEQRES 21 A 406 VAL GLY ILE LYS LEU PRO GLY LEU GLU PHE LYS ASN GLN SEQRES 22 A 406 ARG VAL GLU ALA ALA TYR ARG LYS GLU LEU VAL TYR GLY SEQRES 23 A 406 GLU ASP ASP ALA THR ARG ALA THR PRO PRO THR VAL ARG SEQRES 24 A 406 GLU LEU PHE SER ALA VAL ARG LYS ASN TYR PHE ARG LEU SEQRES 25 A 406 TYR PHE HIS TYR MET TYR PHE ASN ILE ALA ARG ILE LEU SEQRES 26 A 406 TYR LEU GLN VAL ASP ASN VAL PHE GLY LEU PHE LEU LEU SEQRES 27 A 406 PHE PRO SER ILE VAL ALA GLY THR ILE THR LEU GLY LEU SEQRES 28 A 406 MET THR GLN ILE THR ASN VAL PHE GLY GLN VAL ARG GLY SEQRES 29 A 406 ALA PHE GLN TYR LEU ILE ASN SER TRP THR THR LEU VAL SEQRES 30 A 406 GLU LEU MET SER ILE TYR LYS ARG LEU ARG SER PHE GLU SEQRES 31 A 406 HIS GLU LEU ASP GLY ASP LYS ILE GLN GLU VAL THR HIS SEQRES 32 A 406 THR LEU SER SEQRES 1 B 406 MET PHE LYS SER PHE PHE PRO LYS PRO GLY THR PHE PHE SEQRES 2 B 406 LEU SER ALA PHE VAL TRP ALA LEU ILE ALA VAL ILE PHE SEQRES 3 B 406 TRP GLN ALA GLY GLY GLY ASP TRP VAL ALA ARG ILE THR SEQRES 4 B 406 GLY ALA SER GLY GLN ILE PRO ILE SER ALA ALA ARG PHE SEQRES 5 B 406 TRP SER LEU ASP PHE LEU ILE PHE TYR ALA TYR TYR ILE SEQRES 6 B 406 VAL CYS VAL GLY LEU PHE ALA LEU PHE TRP PHE ILE TYR SEQRES 7 B 406 SER PRO HIS ARG TRP GLN TYR TRP SER ILE LEU GLY THR SEQRES 8 B 406 ALA LEU ILE ILE PHE VAL THR TRP PHE LEU VAL GLU VAL SEQRES 9 B 406 GLY VAL ALA VAL ASN ALA TRP TYR ALA PRO PHE TYR ASP SEQRES 10 B 406 LEU ILE GLN THR ALA LEU SER SER PRO HIS LYS VAL THR SEQRES 11 B 406 ILE GLU GLN PHE TYR ARG GLU VAL GLY VAL PHE LEU GLY SEQRES 12 B 406 ILE ALA LEU ILE ALA VAL VAL ILE SER VAL LEU ASN ASN SEQRES 13 B 406 PHE PHE VAL SER HIS TYR VAL PHE ARG TRP ARG THR ALA SEQRES 14 B 406 MET ASN GLU TYR TYR MET ALA ASN TRP GLN GLN LEU ARG SEQRES 15 B 406 HIS ILE GLU GLY ALA ALA GLN ARG VAL GLN GLU ASP THR SEQRES 16 B 406 MET ARG PHE ALA SER THR LEU GLU ASN MET GLY VAL SER SEQRES 17 B 406 PHE ILE ASN ALA ILE MET THR LEU ILE ALA PHE LEU PRO SEQRES 18 B 406 VAL LEU VAL THR LEU SER ALA HIS VAL PRO GLU LEU PRO SEQRES 19 B 406 ILE ILE GLY HIS ILE PRO TYR GLY LEU VAL ILE ALA ALA SEQRES 20 B 406 ILE VAL TRP SER LEU MET GLY THR GLY LEU LEU ALA VAL SEQRES 21 B 406 VAL GLY ILE LYS LEU PRO GLY LEU GLU PHE LYS ASN GLN SEQRES 22 B 406 ARG VAL GLU ALA ALA TYR ARG LYS GLU LEU VAL TYR GLY SEQRES 23 B 406 GLU ASP ASP ALA THR ARG ALA THR PRO PRO THR VAL ARG SEQRES 24 B 406 GLU LEU PHE SER ALA VAL ARG LYS ASN TYR PHE ARG LEU SEQRES 25 B 406 TYR PHE HIS TYR MET TYR PHE ASN ILE ALA ARG ILE LEU SEQRES 26 B 406 TYR LEU GLN VAL ASP ASN VAL PHE GLY LEU PHE LEU LEU SEQRES 27 B 406 PHE PRO SER ILE VAL ALA GLY THR ILE THR LEU GLY LEU SEQRES 28 B 406 MET THR GLN ILE THR ASN VAL PHE GLY GLN VAL ARG GLY SEQRES 29 B 406 ALA PHE GLN TYR LEU ILE ASN SER TRP THR THR LEU VAL SEQRES 30 B 406 GLU LEU MET SER ILE TYR LYS ARG LEU ARG SER PHE GLU SEQRES 31 B 406 HIS GLU LEU ASP GLY ASP LYS ILE GLN GLU VAL THR HIS SEQRES 32 B 406 THR LEU SER HET PGW A 501 51 HET PGW B 501 51 HETNAM PGW (1R)-2-{[(S)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY) HETNAM 2 PGW PHOSPHORYL]OXY}-1-[(HEXADECANOYLOXY)METHYL]ETHYL (9Z)- HETNAM 3 PGW OCTADEC-9-ENOATE HETSYN PGW 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-(1- HETSYN 2 PGW GLYCEROL)]; PHOSPHATIDYLGLYCEROL FORMUL 3 PGW 2(C40 H77 O10 P) HELIX 1 AA1 LYS A 8 ALA A 29 1 22 HELIX 2 AA2 SER A 48 TRP A 53 5 6 HELIX 3 AA3 SER A 54 SER A 79 1 26 HELIX 4 AA4 TRP A 83 SER A 125 1 43 HELIX 5 AA5 THR A 130 ASN A 177 1 48 HELIX 6 AA6 GLY A 186 SER A 227 1 42 HELIX 7 AA7 TYR A 241 GLY A 262 1 22 HELIX 8 AA8 LEU A 265 GLU A 287 1 23 HELIX 9 AA9 THR A 294 HIS A 315 1 22 HELIX 10 AB1 TYR A 316 ASN A 331 1 16 HELIX 11 AB2 VAL A 332 LEU A 337 1 6 HELIX 12 AB3 LEU A 338 GLY A 345 1 8 HELIX 13 AB4 GLY A 350 SER A 372 1 23 HELIX 14 AB5 TRP A 373 HIS A 391 1 19 HELIX 15 AB6 LYS B 8 ALA B 29 1 22 HELIX 16 AB7 SER B 48 TRP B 53 5 6 HELIX 17 AB8 SER B 54 SER B 79 1 26 HELIX 18 AB9 TRP B 83 SER B 125 1 43 HELIX 19 AC1 THR B 130 ASN B 177 1 48 HELIX 20 AC2 GLY B 186 SER B 227 1 42 HELIX 21 AC3 TYR B 241 GLY B 262 1 22 HELIX 22 AC4 LEU B 265 GLU B 287 1 23 HELIX 23 AC5 THR B 294 HIS B 315 1 22 HELIX 24 AC6 TYR B 316 ASN B 331 1 16 HELIX 25 AC7 VAL B 332 LEU B 337 1 6 HELIX 26 AC8 LEU B 338 GLY B 345 1 8 HELIX 27 AC9 GLY B 350 SER B 372 1 23 HELIX 28 AD1 TRP B 373 HIS B 391 1 19 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