+Open data
-Basic information
Entry | Database: PDB / ID: 8e5g | |||||||||
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Title | Cryo-EM of A. veneficus cytochrome filament | |||||||||
Components | c-type cytochrome | |||||||||
Keywords | ELECTRON TRANSPORT / helical symmetry / cytochrome filmanet / conductive nanowires / microbial nanowires | |||||||||
Function / homology | Multiheme cytochrome superfamily / HEME C / Uncharacterized protein Function and homology information | |||||||||
Biological species | Archaeoglobus veneficus (archaea) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Wang, F. / Baquero, D.P. / Krupovic, M. / Egelman, E.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2023 Title: Extracellular cytochrome nanowires appear to be ubiquitous in prokaryotes. Authors: Diana P Baquero / Virginija Cvirkaite-Krupovic / Shengen Shawn Hu / Jessie Lynda Fields / Xing Liu / Christopher Rensing / Edward H Egelman / Mart Krupovic / Fengbin Wang / Abstract: Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens, recently identified as extracellular cytochrome nanowires (ECNs), have received wide attention due to ...Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens, recently identified as extracellular cytochrome nanowires (ECNs), have received wide attention due to numerous potential applications. However, whether other organisms employ similar ECNs for electron transfer remains unknown. Here, using cryoelectron microscopy, we describe the atomic structures of two ECNs from two major orders of hyperthermophilic archaea present in deep-sea hydrothermal vents and terrestrial hot springs. Homologs of Archaeoglobus veneficus ECN are widespread among mesophilic methane-oxidizing Methanoperedenaceae, alkane-degrading Syntrophoarchaeales archaea, and in the recently described megaplasmids called Borgs. The ECN protein subunits lack similarities in their folds; however, they share a common heme arrangement, suggesting an evolutionarily optimized heme packing for efficient electron transfer. The detection of ECNs in archaea suggests that filaments containing closely stacked hemes may be a common and widespread mechanism for long-range electron transfer in both prokaryotic domains of life. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e5g.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e5g.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 8e5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e5g_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8e5g_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8e5g_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 8e5g_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/8e5g ftp://data.pdbj.org/pub/pdb/validation_reports/e5/8e5g | HTTPS FTP |
-Related structure data
Related structure data | 27912MC 8e5fC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 27958.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus veneficus (archaea) / References: UniProt: F2KMU8 | ||
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#2: Chemical | ChemComp-HEC / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: extracellular cytochrome filament / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Archaeoglobus veneficus (archaea) |
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 |
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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: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 33.52 ° / Axial rise/subunit: 32.74 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92602 / Symmetry type: HELICAL |