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- PDB-7lq5: Cryo-EM structure of OmcZ nanowire from Geobacter sulfurreducens -

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Basic information

Entry
Database: PDB / ID: 7lq5
TitleCryo-EM structure of OmcZ nanowire from Geobacter sulfurreducens
ComponentsCytochrome c
KeywordsPROTEIN FIBRIL / nanowires
Function / homologyIPT/TIG domain / Multiheme cytochrome superfamily / IPT domain / Immunoglobulin E-set / Immunoglobulin-like fold / HEME C / Cytochrome c
Function and homology information
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGu, Y. / Srikanth, V. / Malvankar, N.S. / Samatey, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1749662 United States
CitationJournal: 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
DepositionFeb 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,90427
Polymers83,0603
Non-polymers14,84424
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cytochrome c / / OmcZ nanowire


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 / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Polymerized cytochrome OmcZ from Geobacter sulfurreducens
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Geobacter sulfurreducens (bacteria)
Buffer solutionpH: 10.5
Buffer componentConc.: 15 mM / Name: Ethanolamine / Formula: C2H7NO
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 27 / Used frames/image: 2-10

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Processing

SoftwareName: PHENIX / Version: 1.17_3644: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.08CTF correction
7UCSF Chimera1.14model fitting
9RELION3.08initial Euler assignment
10RELION3.08final Euler assignment
12RELION3.083D reconstruction
13PHENIXdev_3689model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -159.1 ° / Axial rise/subunit: 57.8 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128409 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingProtocol: 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
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0137188
ELECTRON MICROSCOPYf_angle_d1.29710191
ELECTRON MICROSCOPYf_dihedral_angle_d21.826987
ELECTRON MICROSCOPYf_chiral_restr0.067915
ELECTRON MICROSCOPYf_plane_restr0.0091179

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