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- EMDB-62924: Cryo-EM structure of Shewanella oneidensis MR-1 MshA pili. -

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Basic information

Entry
Database: EMDB / ID: EMD-62924
TitleCryo-EM structure of Shewanella oneidensis MR-1 MshA pili.
Map data
Sample
  • Cell: Cryo-EM structure of Shewanella oneidensis MR-1 MshA pili.
    • Protein or peptide: MSHA major pilin subunit MshA
KeywordsMSHA major pilin subunit MshA / CELL ADHESION
Function / homologyProkaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / membrane / MSHA major pilin subunit MshA
Function and homology information
Biological speciesShewanella oneidensis MR-1 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi DN / Liu C / Li D / Dai B
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: MSHA major pilin subunit MshA
Authors: Li DN / Liu C
History
DepositionJan 2, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62924.png

Downloads & links

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Map

FileDownload / File: emd_62924.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 199.2 Å		0.83 Å/pix.
x 240 pix.
= 199.2 Å		0.83 Å/pix.
x 240 pix.
= 199.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.016036032 - 0.04644732
Average (Standard dev.)0.00045470876 (±0.0023448952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 199.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62924_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_62924_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 : Cryo-EM structure of Shewanella oneidensis MR-1 MshA pili.

EntireName: Cryo-EM structure of Shewanella oneidensis MR-1 MshA pili.
Components
  • Cell: Cryo-EM structure of Shewanella oneidensis MR-1 MshA pili.
    • Protein or peptide: MSHA major pilin subunit MshA

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Supramolecule #1: Cryo-EM structure of Shewanella oneidensis MR-1 MshA pili.

SupramoleculeName: Cryo-EM structure of Shewanella oneidensis MR-1 MshA pili.
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)

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Macromolecule #1: MSHA major pilin subunit MshA

MacromoleculeName: MSHA major pilin subunit MshA / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 17.670186 KDa
SequenceString:
MKRQQGFTLI ELVVVIIILG ILAVTAAPKF INLQGDARAS ALQGLKGAIQ GANSLVFSKA ALAGKEKGSQ PTFSLGDTGT IAILDGYML ATKASLEAGM DITFDAKADP QPVTADWIID PTAGTPGTAK IYQHGAPANC FLTYTEAKAA NTSTNPATPG E LPKYVITD SGC

UniProtKB: MSHA major pilin subunit MshA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 11.92 Å
Applied symmetry - Helical parameters - Δ&Phi: 81.06 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15544
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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