+Open data
-Basic information
Entry | Database: PDB / ID: 7lq5 | ||||||
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Title | Cryo-EM structure of OmcZ nanowire from Geobacter sulfurreducens | ||||||
Components | Cytochrome c | ||||||
Keywords | PROTEIN FIBRIL / nanowires | ||||||
Function / homology | IPT/TIG domain / Multiheme cytochrome superfamily / IPT domain / Immunoglobulin E-set / Immunoglobulin-like fold / HEME C / Cytochrome c Function and homology information | ||||||
Biological species | Geobacter sulfurreducens PCA (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Gu, Y. / Srikanth, V. / Malvankar, N.S. / Samatey, F.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Microbiol / Year: 2023 Title: Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Authors: Yangqi Gu / Matthew J Guberman-Pfeffer / Vishok Srikanth / Cong Shen / Fabian Giska / Kallol Gupta / Yuri Londer / Fadel A Samatey / Victor S Batista / Nikhil S Malvankar / Abstract: OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome ...OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lq5.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lq5.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 7lq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lq5_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 7lq5_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7lq5_validation.xml.gz | 52.2 KB | Display | |
Data in CIF | 7lq5_validation.cif.gz | 67.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/7lq5 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/7lq5 | HTTPS FTP |
-Related structure data
Related structure data | 23481MC 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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1 |
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-Components
#1: Protein | Mass: 27686.797 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Geobacter sulfurreducens PCA (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / References: UniProt: Q74BG5 #2: Chemical | ChemComp-HEC / Has ligand of interest | Y | |
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-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: Polymerized cytochrome OmcZ from Geobacter sulfurreducens Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Geobacter sulfurreducens (bacteria) |
Buffer solution | pH: 10.5 |
Buffer component | Conc.: 15 mM / Name: Ethanolamine / Formula: C2H7NO |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1.2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14508 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 27 / Used frames/image: 2-10 |
-Processing
Software | Name: PHENIX / Version: 1.17_3644: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -159.1 ° / Axial rise/subunit: 57.8 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128409 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient Details: Initial fitting was done with Chimera and refinement was done in Phenix | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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