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- EMDB-10832: Structure of V. alginolyticus PomAB -

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Basic information

Entry
Database: EMDB / ID: EMD-10832
TitleStructure of V. alginolyticus PomAB
Map data
Sample
  • Complex: Stator unit PomAB
    • Protein or peptide: PomA
    • Protein or peptide: PomB
Function / homology
Function and homology information


protein transport / plasma membrane
Similarity search - Function
Putative MotA/TolQ/ExbB family protein / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain
Similarity search - Domain/homology
Flagellar motor protein MotB / MotA/TolQ/ExbB proton channel family protein
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.45 Å
AuthorsSantiveri M / Roa-Eguiara A / Taylor NMI
Funding support Denmark, 2 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Danish Council for Independent Research8123-00002B Denmark
CitationJournal: Cell / Year: 2020
Title: Structure and Function of Stator Units of the Bacterial Flagellar Motor.
Authors: Mònica Santiveri / Aritz Roa-Eguiara / Caroline Kühne / Navish Wadhwa / Haidai Hu / Howard C Berg / Marc Erhardt / Nicholas M I Taylor /
Abstract: Many bacteria use the flagellum for locomotion and chemotaxis. Its bidirectional rotation is driven by a membrane-embedded motor, which uses energy from the transmembrane ion gradient to generate ...Many bacteria use the flagellum for locomotion and chemotaxis. Its bidirectional rotation is driven by a membrane-embedded motor, which uses energy from the transmembrane ion gradient to generate torque at the interface between stator units and rotor. The structural organization of the stator unit (MotAB), its conformational changes upon ion transport, and how these changes power rotation of the flagellum remain unknown. Here, we present ~3 Å-resolution cryoelectron microscopy reconstructions of the stator unit in different functional states. We show that the stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Combining structural data with mutagenesis and functional studies, we identify key residues involved in torque generation and present a detailed mechanistic model for motor function and switching of rotational direction.
History
DepositionApr 6, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10832.png

Downloads & links

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Map

FileDownload / File: emd_10832.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 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: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.3890095 - 0.45341346
Average (Standard dev.)0.00035089525 (±0.014479909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z212.992212.992212.992
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.3890.4530.000

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Supplemental data

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Mask #1

Fileemd_10832_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10832_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10832_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 : Stator unit PomAB

EntireName: Stator unit PomAB
Components
  • Complex: Stator unit PomAB
    • Protein or peptide: PomA
    • Protein or peptide: PomB

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Supramolecule #1: Stator unit PomAB

SupramoleculeName: Stator unit PomAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The stator unit consists of a dimer of PomB surrounded by a pentamer of PomA
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: C43(DE3)

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Macromolecule #1: PomA

MacromoleculeName: PomA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: PomB

MacromoleculeName: PomB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDDEDNKCDC PPPGLPLWMG TFADLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTPI DVIMQQTMDI TQQTLEFHEG ESERAGGTKR DEGKLTGGQS PETSTQNNES AEADMQQQQS KEMSQEMETL MESIKKALER ...String:
MDDEDNKCDC PPPGLPLWMG TFADLMSLLM CFFVLLLSFS EMDVLKFKQI AGSMKFAFGV QNQLEVKDIP KGTSIIAQEF RPGRPEPTPI DVIMQQTMDI TQQTLEFHEG ESERAGGTKR DEGKLTGGQS PETSTQNNES AEADMQQQQS KEMSQEMETL MESIKKALER EIEQGAIEVE NLGQQIVIRM REKGAFPEGS AFLQPKFRPL VRQIAELVKD VPGIVRVSGH TDNRPLDSEL YRSNWDLSSQ RAVSVAQEME KVRGFSHQRL RVRGMADTEP LLPNDSDENR ALNRRVEISI MQGEPLYSEE VPVIQGTLEV LFQGPGGSGS AWSHPQFEKG GGSGGGSGGS AWSHPQFEK

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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

BufferpH: 8
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 91076
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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