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- EMDB-25881: Cryo-EM structure of PilA-N and PilA-C from Geobacter sulfurreducens -

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Basic information

Entry
Database: EMDB / ID: EMD-25881
TitleCryo-EM structure of PilA-N and PilA-C from Geobacter sulfurreducens
Map dataCryo-EM structure of PilA-N and PilA-C from Geobacter sulfurreducens
Sample
  • Complex: Filament of PilA-N and PilA-C proteins
    • Protein or peptide: Geopilin domain 1 protein
    • Protein or peptide: Geopilin domain 2 protein
Keywordshelical symmetry / filament / pili / type iv pili / pseudo pili / PROTEIN FIBRIL
Function / homology
Function and homology information


pilus assembly / protein secretion by the type II secretion system / type II protein secretion system complex / plasma 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 sulfurreducens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang F / Mustafa K
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Nat Microbiol / Year: 2022
Title: Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing.
Authors: Fengbin Wang / Khawla Mustafa / Victor Suciu / Komal Joshi / Chi H Chan / Sol Choi / Zhangli Su / Dong Si / Allon I Hochbaum / Edward H Egelman / Daniel R Bond /
Abstract: Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were ...Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
History
DepositionJan 7, 2022-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7tgg
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7tgg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25881.png

Downloads & links

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Map

FileDownload / File: emd_25881.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of PilA-N and PilA-C from Geobacter sulfurreducens
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21 / Movie #1: 0.21
Minimum - Maximum-0.12977313 - 0.48573798
Average (Standard dev.)0.0030152581 (±0.02348323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.1300.4860.003

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Supplemental data

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Sample components

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Entire : Filament of PilA-N and PilA-C proteins

EntireName: Filament of PilA-N and PilA-C proteins
Components
  • Complex: Filament of PilA-N and PilA-C proteins
    • Protein or peptide: Geopilin domain 1 protein
    • Protein or peptide: Geopilin domain 2 protein

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Supramolecule #1: Filament of PilA-N and PilA-C proteins

SupramoleculeName: Filament of PilA-N and PilA-C proteins / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA

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Macromolecule #1: Geopilin domain 1 protein

MacromoleculeName: Geopilin domain 1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA
Molecular weightTheoretical: 10.006582 KDa
SequenceString:
MANYPHTPTQ AAKRRKETLM LQKLRNRKGF TLIELLIVVA IIGILAAIAI PQFSAYRVKA YNSAASSDLR NLKTALESAF ADDQTYPPE S

UniProtKB: Geopilin domain 1 protein

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Macromolecule #2: Geopilin domain 2 protein

MacromoleculeName: Geopilin domain 2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA
Molecular weightTheoretical: 13.087543 KDa
SequenceString:
MKKIITIVAM LLAMQGIAIA AGKIPTTTMG GKDFTFKPST NVSVSYFTTN GATSTAGTVN TDYAVNTKNS SGNRVFTSTN NTSNIWYIE NDAWKGKAVS DSDVTALGTG DVGKSDFSGT EWKSQ

UniProtKB: Geopilin domain 2 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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 3.0 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: 10.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 89.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112011
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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