+Open data
-Basic information
Entry | Database: PDB / ID: 7tfs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM of the OmcE nanowires from Geobacter sulfurreducens | |||||||||
Components | Cytochrome c | |||||||||
Keywords | ELECTRON TRANSPORT / PROTEIN FIBRIL / helical symmetry / cytochrome nanowire / filament | |||||||||
Function / homology | Doubled CXXCH motif / Doubled CXXCH motif (Paired_CXXCH_1) / Multiheme cytochrome superfamily / HEME C / Cytochrome c Function and homology information | |||||||||
Biological species | Geobacter sulfurreducens (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Wang, F. / Mustafa, K. / Chan, C.H. / Joshi, K. / Hochbaum, A.I. / Bond, D.R. / Egelman, E.H. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7tfs.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7tfs.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 7tfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tfs_validation.pdf.gz | 911.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7tfs_full_validation.pdf.gz | 920 KB | Display | |
Data in XML | 7tfs_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 7tfs_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/7tfs ftp://data.pdbj.org/pub/pdb/validation_reports/tf/7tfs | HTTPS FTP |
-Related structure data
Related structure data | 25879MC 7tggC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 7
2 |
|
3 |
|
Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 7 / Rise per n subunits: 33.9 Å / Rotation per n subunits: 58.812 °) |
-Components
#1: Protein | Mass: 23839.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / References: UniProt: Q74FJ0 | ||
---|---|---|---|
#2: Chemical | ChemComp-HEC / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Filament of OmcE protein / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
---|---|
Source (natural) | Organism: Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 58.8 ° / Axial rise/subunit: 33.9 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346826 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
|