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- EMDB-25881: Cryo-EM structure of PilA-N and PilA-C from Geobacter sulfurreducens -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-25881 | |||||||||
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Title | Cryo-EM structure of PilA-N and PilA-C from Geobacter sulfurreducens | |||||||||
![]() | Cryo-EM structure of PilA-N and PilA-C from Geobacter sulfurreducens | |||||||||
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![]() | helical symmetry / filament / pili / type iv pili / pseudo pili / PROTEIN FIBRIL | |||||||||
Function / homology | ![]() pilus assembly / protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Wang F / Mustafa K | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
Images | ![]() | 129.2 KB | ||
Filedesc metadata | ![]() | 4.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 387.6 KB | Display | ![]() |
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Full document | ![]() | 387.2 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tggMC ![]() 7tfsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of PilA-N and PilA-C from Geobacter sulfurreducens | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Filament of PilA-N and PilA-C proteins
Entire | Name: Filament of PilA-N and PilA-C proteins |
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Components |
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-Supramolecule #1: Filament of PilA-N and PilA-C proteins
Supramolecule | Name: Filament of PilA-N and PilA-C proteins / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Geopilin domain 1 protein
Macromolecule | Name: Geopilin domain 1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.006582 KDa |
Sequence | String: MANYPHTPTQ AAKRRKETLM LQKLRNRKGF TLIELLIVVA IIGILAAIAI PQFSAYRVKA YNSAASSDLR NLKTALESAF ADDQTYPPE S UniProtKB: Geopilin domain 1 protein |
-Macromolecule #2: Geopilin domain 2 protein
Macromolecule | Name: Geopilin domain 2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.087543 KDa |
Sequence | String: MKKIITIVAM LLAMQGIAIA AGKIPTTTMG GKDFTFKPST NVSVSYFTTN GATSTAGTVN TDYAVNTKNS SGNRVFTSTN NTSNIWYIE NDAWKGKAVS DSDVTALGTG DVGKSDFSGT EWKSQ UniProtKB: Geopilin domain 2 protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 reconstruction | Applied 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 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |