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- EMDB-16214: VaPomAB full length Saposin Nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-16214
TitleVaPomAB full length Saposin Nanodisc
Map data
Sample
  • Complex: flagellar sodium-driven stator unit
    • Protein or peptide: VaPomA
    • Protein or peptide: VaPoMB
KeywordsFlagellar sodium-driven stator unit / MOTOR PROTEIN
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsHu H / Taylor NMI
Funding support Denmark, 3 items
OrganizationGrant numberCountry
Novo Nordisk Foundation8123-00002B Denmark
Novo Nordisk FoundationNNF17OC0031006 Denmark
LundbeckfondenR347-2020-2429 Denmark
CitationJournal: 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
DepositionNov 23, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16214.png

Downloads & links

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Map

FileDownload / File: emd_16214.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å		0.83 Å/pix.
x 400 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.3581548 - 2.4286602
Average (Standard dev.)0.00015724996 (±0.046055403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16214_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16214_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : flagellar sodium-driven stator unit

EntireName: flagellar sodium-driven stator unit
Components
  • Complex: flagellar sodium-driven stator unit
    • Protein or peptide: VaPomA
    • Protein or peptide: VaPoMB

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Supramolecule #1: flagellar sodium-driven stator unit

SupramoleculeName: flagellar sodium-driven stator unit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio alginolyticus (bacteria)

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Macromolecule #1: VaPomA

MacromoleculeName: VaPomA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
SequenceString: MDLATLLGLI GGFAFVIMAM VLGGSIGMFV DVTSILIVVG GSIFVVLMKF TMGQFFGATK IAGKAFMFKA DEPEDLIAKI VEMADAARKG GFLALEEMEI NNTFMQKGID LLVDGHDADV VRAALKKDIA LTDERHTQGT GVFRAFGDVA PAMGMIGTLV GLVAMLSNMD ...String:
MDLATLLGLI GGFAFVIMAM VLGGSIGMFV DVTSILIVVG GSIFVVLMKF TMGQFFGATK IAGKAFMFKA DEPEDLIAKI VEMADAARKG GFLALEEMEI NNTFMQKGID LLVDGHDADV VRAALKKDIA LTDERHTQGT GVFRAFGDVA PAMGMIGTLV GLVAMLSNMD DPKAIGPAMA VALLTTLYGA ILSNMVFFPI ADKLSLRRDQ ETLNRRLIMD GVLAIQDGQN PRVIDSYLKN YLNEGKRALE IDE

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Macromolecule #2: VaPoMB

MacromoleculeName: VaPoMB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
SequenceString: MDDEDNKCDC PPPGLPLWMG TFADLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTPI DVIMQENLYF QSQTMDITQQ TLEFHEGESE RAGGTKRDEG KLTGGQSPET STQNNESAEA DMQQQQSKEM SQEMETLMES ...String:
MDDEDNKCDC PPPGLPLWMG TFADLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTPI DVIMQENLYF QSQTMDITQQ TLEFHEGESE RAGGTKRDEG KLTGGQSPET STQNNESAEA DMQQQQSKEM SQEMETLMES IKKALEREIE QGAIEVENLG QQIVIRMREK GAFPEGSAFL QPKFRPLVRQ IAELVKDVPG IVRVSGHTDN RPLDSELYRS NWDLSSQRAV SVAQEMEKVR GFSHQRLRVR GMADTEPLLP NDSDENRALN RRVEISIMQG EPLYSEEVPV IQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration16 mg/mL
BufferpH: 7.5 / Details: 300mM NaCl, 20mM HEPES 7.5, 0.002%LMNG
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Particle selectionNumber selected: 38438
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38438
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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