+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16215 | ||||||||||||
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Title | VaPomAB MSP1D1 nanodisc | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Flagellar sodium-driven stator unit / MOTOR PROTEIN | ||||||||||||
Function / homology | Function and homology information bacterial-type flagellum-dependent swarming motility / proton transmembrane transport / chemotaxis / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Vibrio alginolyticus (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Haidai H / Nicholas MIT | ||||||||||||
Funding support | Denmark, 3 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit. Authors: Haidai Hu / Philipp F Popp / Mònica Santiveri / Aritz Roa-Eguiara / Yumeng Yan / Freddie J O Martin / Zheyi Liu / Navish Wadhwa / Yong Wang / Marc Erhardt / Nicholas M I Taylor / Abstract: Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively ...Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively driven by sodium-dependent stator units (PomAB). However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the flagellar rotor remained largely unclear. Here, we have determined by cryo-electron microscopy the structure of Vibrio PomAB. The electrostatic potential map uncovers sodium binding sites, which together with functional experiments and molecular dynamics simulations, reveal a mechanism for ion translocation and selectivity. Bulky hydrophobic residues from PomA prime PomA for clockwise rotation. We propose that a dynamic helical motif in PomA regulates the distance between PomA subunit cytoplasmic domains, stator unit activation, and torque transmission. Together, our study provides mechanistic insights for understanding ion selectivity and rotor incorporation of the stator unit of the bacterial flagellum. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16215.map.gz | 230.2 MB | EMDB map data format | |
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Header (meta data) | emd-16215-v30.xml emd-16215.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16215_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_16215.png | 116.6 KB | ||
Filedesc metadata | emd-16215.cif.gz | 5.5 KB | ||
Others | emd_16215_half_map_1.map.gz emd_16215_half_map_2.map.gz | 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16215 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16215 | HTTPS FTP |
-Validation report
Summary document | emd_16215_validation.pdf.gz | 913.2 KB | Display | EMDB validaton report |
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Full document | emd_16215_full_validation.pdf.gz | 912.8 KB | Display | |
Data in XML | emd_16215_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_16215_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16215 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16215 | HTTPS FTP |
-Related structure data
Related structure data | 8briMC 8brdC 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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-Map
File | Download / File: emd_16215.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16215_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16215_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : flagellar sodium-driven stator unit
Entire | Name: flagellar sodium-driven stator unit |
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Components |
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-Supramolecule #1: flagellar sodium-driven stator unit
Supramolecule | Name: flagellar sodium-driven stator unit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio alginolyticus (bacteria) |
-Macromolecule #1: Chemotaxis protein PomA
Macromolecule | Name: Chemotaxis protein PomA / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio alginolyticus (bacteria) |
Molecular weight | Theoretical: 27.283031 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDLATLLGLI GGFAFVIMAM VLGGSIGMFV DVTSILIVVG GSIFVVLMKF TMGQFFGATK IAGKAFMFKA DEPEDLIAKI VEMADAARK GGFLALEEME INNTFMQKGI DLLVDGHDAD VVRAALKKDI ALTDERHTQG TGVFRAFGDV APAMGMIGTL V GLVAMLSN ...String: MDLATLLGLI GGFAFVIMAM VLGGSIGMFV DVTSILIVVG GSIFVVLMKF TMGQFFGATK IAGKAFMFKA DEPEDLIAKI VEMADAARK GGFLALEEME INNTFMQKGI DLLVDGHDAD VVRAALKKDI ALTDERHTQG TGVFRAFGDV APAMGMIGTL V GLVAMLSN MDDPKAIGPA MAVALLTTLY GAILSNMVFF PIADKLSLRR DQETLNRRLI MDGVLAIQDG QNPRVIDSYL KN YLNEGKR ALEIDE UniProtKB: Chemotaxis protein PomA |
-Macromolecule #2: Flagellar motor protein
Macromolecule | Name: Flagellar motor protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio alginolyticus (bacteria) |
Molecular weight | Theoretical: 35.587254 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDDEDNKCDC PPPGLPLWMG TFADLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTP IDVIMQQTMD ITQQTLEFHE GESERAGGTK RDEGKLTGGQ SPETSTQNNE SAEADMQQQQ SKEMSQEMET L MESIKKAL ...String: MDDEDNKCDC PPPGLPLWMG TFADLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTP IDVIMQQTMD ITQQTLEFHE GESERAGGTK RDEGKLTGGQ SPETSTQNNE SAEADMQQQQ SKEMSQEMET L MESIKKAL EREIEQGAIE VENLGQQIVI RMREKGAFPE GSAFLQPKFR PLVRQIAELV KDVPGIVRVS GHTDNRPLDS EL YRSNWDL SSQRAVSVAQ EMEKVRGFSH QRLRVRGMAD TEPLLPNDSD ENRALNRRVE ISIMQGEPLY SEEVPVIQ UniProtKB: Flagellar motor protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 16 mg/mL |
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Buffer | pH: 7.5 / Details: 300mM NaCl, 20mM HEPES 7.5, 0.002%LMNG |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |