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- EMDB-47993: Cryo-EM of type IV pilus from Geobacter metallireducens -

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Basic information

Entry
Database: EMDB / ID: EMD-47993
TitleCryo-EM of type IV pilus from Geobacter metallireducens
Map datacryo-EM of T4P in G. metallireducens
Sample
  • Complex: type IV pilus
    • Protein or peptide: Geopilin domain 2 protein
    • Protein or peptide: Geopilin domain 1 protein
Keywordspilus / type iv pilus / helical symmetry / PROTEIN FIBRIL
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / membrane
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Geopilin domain 2 protein / Geopilin domain 1 protein
Similarity search - Component
Biological speciesGeobacter metallireducens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsEgorova M / Petersen HA / Chan CH / Bond DR / Wang F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: To Be Published
Title: Cryo-EM of type IV pilus from Geobacter metallireducens
Authors: Egorova M / Petersen HA / Chan CH / Bond DR / Wang F
History
DepositionNov 21, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47993.png

Downloads & links

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Map

FileDownload / File: emd_47993.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM of T4P in G. metallireducens
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 348.8 Å		1.09 Å/pix.
x 320 pix.
= 348.8 Å		1.09 Å/pix.
x 320 pix.
= 348.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.274
Minimum - Maximum-0.5101422 - 0.9914891
Average (Standard dev.)0.0028356395 (±0.032971438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 348.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half B

Fileemd_47993_half_map_1.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_47993_half_map_2.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : type IV pilus

EntireName: type IV pilus
Components
  • Complex: type IV pilus
    • Protein or peptide: Geopilin domain 2 protein
    • Protein or peptide: Geopilin domain 1 protein

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Supramolecule #1: type IV pilus

SupramoleculeName: type IV pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacter metallireducens (bacteria)

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Macromolecule #1: Geopilin domain 2 protein

MacromoleculeName: Geopilin domain 2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacter metallireducens (bacteria)
Molecular weightTheoretical: 11.607936 KDa
SequenceString:
MKKKIFLTGL CFLSIGSVAF AASKDVTGSG EIGGSNSTPK LAIQTSNQVT LTYDGGTGHT YGIATLHAKG TRKYASTSND TKIYYNDNT ATAAPSAPVG TATIGGSTNW KNAL

UniProtKB: Geopilin domain 2 protein

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Macromolecule #2: Geopilin domain 1 protein

MacromoleculeName: Geopilin domain 1 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacter metallireducens (bacteria)
Molecular weightTheoretical: 7.82807 KDa
SequenceString:
MLQKLRNKKG FTLIELLIVV AIIGILAAIA IPQFAAYRQK AFNSAAESDL KNTKTNLESY YSEHQFYPN

UniProtKB: Geopilin domain 1 protein

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.094 Å
Applied symmetry - Helical parameters - Δ&Phi: 91.753 °
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: 193496
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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