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Yorodumi- EMDB-29087: Heterodimeric ABC transporter BmrCD in the occluded conformation ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29087 | |||||||||
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Title | Heterodimeric ABC transporter BmrCD in the occluded conformation bound to ATP: BmrCD_OC-ATP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | transporter / complex / lipids / MEMBRANE PROTEIN / TRANSLOCASE | |||||||||
Function / homology | Function and homology information ATPase-coupled lipid transmembrane transporter activity / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Tang Q / Mchaourab H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Authors: Qingyu Tang / Matt Sinclair / Hale S Hasdemir / Richard A Stein / Erkan Karakas / Emad Tajkhorshid / Hassane S Mchaourab / Abstract: Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound ...Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29087.map.gz | 388.9 MB | EMDB map data format | |
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Header (meta data) | emd-29087-v30.xml emd-29087.xml | 23.2 KB 23.2 KB | Display Display | EMDB header |
Images | emd_29087.png | 61.8 KB | ||
Filedesc metadata | emd-29087.cif.gz | 6.6 KB | ||
Others | emd_29087_additional_1.map.gz emd_29087_additional_2.map.gz emd_29087_additional_3.map.gz emd_29087_additional_4.map.gz emd_29087_additional_5.map.gz | 398.1 MB 397.9 MB 398.2 MB 397.9 MB 383.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29087 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29087 | HTTPS FTP |
-Validation report
Summary document | emd_29087_validation.pdf.gz | 525 KB | Display | EMDB validaton report |
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Full document | emd_29087_full_validation.pdf.gz | 524.6 KB | Display | |
Data in XML | emd_29087_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_29087_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29087 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29087 | HTTPS FTP |
-Related structure data
Related structure data | 8fhkMC 8fmvC 8fpfC 8szcC 8t1pC 8t3kC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29087.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.647 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #5
File | emd_29087_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #4
File | emd_29087_additional_2.map | ||||||||||||
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Density Histograms |
-Additional map: #3
File | emd_29087_additional_3.map | ||||||||||||
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Density Histograms |
-Additional map: #2
File | emd_29087_additional_4.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_29087_additional_5.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Heterodimeric BmrCD with ligands ATP and lipids
Entire | Name: Heterodimeric BmrCD with ligands ATP and lipids |
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Components |
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-Supramolecule #1: Heterodimeric BmrCD with ligands ATP and lipids
Supramolecule | Name: Heterodimeric BmrCD with ligands ATP and lipids / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
-Macromolecule #1: Probable multidrug resistance ABC transporter ATP-binding/permeas...
Macromolecule | Name: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
Molecular weight | Theoretical: 77.369898 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKIGKTLWRY ALLYRKLLIT AVLLLTVAVG AELTGPFIGK KMIDDHILGI EKTWYEAAEK DKNAVQFHGV SYVREDRLQE PVSKAKEAH IYQVGMAFYF VDQAVSFDGN RTVSDGKLTI TNGDKSRAYA AEKLTKQELF QFYQPEIKGM VLLIALYGGL L VFSVFFQY ...String: MKIGKTLWRY ALLYRKLLIT AVLLLTVAVG AELTGPFIGK KMIDDHILGI EKTWYEAAEK DKNAVQFHGV SYVREDRLQE PVSKAKEAH IYQVGMAFYF VDQAVSFDGN RTVSDGKLTI TNGDKSRAYA AEKLTKQELF QFYQPEIKGM VLLIALYGGL L VFSVFFQY GQHYLLQMSA NRIIQKMRQD VFSHIQKMPI RYFDNLPAGK VVARITNDTE AIRDLYVTVL STFVTSGIYM FG IFTALFL LDVKLAFVAL AIVPIIWLWS VIYRRYASYY NQKIRSINSD INAKMNESIQ GMTIIQAFRH QKETMREFEE LNE SHFYFQ NRMLNLNSLM SHNLVNVIRN LAFVALIWHF GGASLNAAGI VSIGVLYAFV DYLNRLFQPI TGIVNQFSKL ELAR VSAGR VFELLEEKNT EEAGEPAKER ALGRVEFRDV SFAYQEGEEV LKHISFTAQK GETVALVGHT GSGKSSILNL LFRFY DAQK GDVLIDGKSI YNMSRQELRS HMGIVLQDPY LFSGTIGSNV SLDDERMTEE EIKNALRQVG AEPLLKKLPK GINEPV IEK GSTLSSGERQ LISFARALAF DPAILILDQA TAHIDTETEA VIQKALDVVK QGRTTFVIAH RLSTIRNADQ ILVLDKG EI VERGNHEELM ALEGQYYQMY ELQKGQKHSI ALEHHHHHH UniProtKB: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheH |
-Macromolecule #2: Probable multidrug resistance ABC transporter ATP-binding/permeas...
Macromolecule | Name: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate |
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) |
Molecular weight | Theoretical: 67.602961 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MLEFSVLKKL GWFFKAYWLR YTIAIVLLLA VNVIEMFPPK LLGNAIDDMK AGAFTAEGLL FYIGIFFVL TAAVYIMSYF WMHQLFGGAN LMEKILRTKL MGHLLTMSPP FYEKNRTGDL MARGTNDLQA VSLTTGFGIL T LVDSTMFM ...String: MGSSHHHHHH SSGLVPRGSH MLEFSVLKKL GWFFKAYWLR YTIAIVLLLA VNVIEMFPPK LLGNAIDDMK AGAFTAEGLL FYIGIFFVL TAAVYIMSYF WMHQLFGGAN LMEKILRTKL MGHLLTMSPP FYEKNRTGDL MARGTNDLQA VSLTTGFGIL T LVDSTMFM MTIFLTMGFL ISWKLTFAAI IPLPVMAIAI SLYGSKIHER FTEAQNAFGA LNDRVLESVS GVRVIRAYVQ ET NDVRRFN EMTADVYQKN MKVAFIDSLF EPTVKLLVGA SYLIGLGYGA FLVFRNELTL GELVSFNVYL GMMIWPMFAI GEL INVMQR GNASLDRVNE TLSYETDVTD PKQPADLKEP GDIVFSHVSF TYPSSTSDNL QDISFTVRKG QTVGIAGKTG SGKT TIIKQ LLRQYPPGEG SITFSGVPIQ QIPLDRLRGW IGYVPQDHLL FSRTVKENIL YGKQDATDKE VQQAIAEAHF EKDLH MLPS GLETMVGEKG VALSGGQKQR ISIARALMAN PEILILDQSL SAVDAKTEAA IIKNIRENRK GKTTFILTHR LSAVEH ADL ILVMDGGVIA ERGTHQELLA NNGWYREQYE RQQLFTAEEG GAGA UniProtKB: Probable multidrug resistance ABC transporter ATP-binding/permease protein YheI |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #4: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 4 / Number of copies: 16 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 15.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.4 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91128 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |