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- EMDB-23481: Cryo-EM structure of OmcZ nanowire from Geobacter sulfurreducens -

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Basic information

Entry
Database: EMDB / ID: EMD-23481
TitleCryo-EM structure of OmcZ nanowire from Geobacter sulfurreducens
Map datamap of octaheme cytochrome OmcZ nanowire from G. sulfurreducens
Sample
  • Complex: Polymerized cytochrome OmcZ from Geobacter sulfurreducens
    • Protein or peptide: Cytochrome c
  • Ligand: HEME C
Keywordsnanowires / PROTEIN FIBRIL
Function / homologyIPT/TIG domain / Multiheme cytochrome superfamily / IPT domain / Immunoglobulin E-set / Immunoglobulin-like fold / Cytochrome c
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria) / Geobacter sulfurreducens PCA (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGu Y / Srikanth V / Malvankar NS / Samatey FA
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_23481.png

Downloads & links

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Map

FileDownload / File: emd_23481.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of octaheme cytochrome OmcZ nanowire from G. sulfurreducens
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.06084027 - 0.10626797
Average (Standard dev.)0.00007689905 (±0.001351777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 317.952 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_23481_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of octaheme cytochrome OmcZ nanowire from G. sulfurreducens

Fileemd_23481_half_map_1.map
Annotationhalf map of octaheme cytochrome OmcZ nanowire from G. sulfurreducens
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of octaheme cytochrome OmcZ nanowire from G. sulfurreducens

Fileemd_23481_half_map_2.map
Annotationhalf map of octaheme cytochrome OmcZ nanowire from G. sulfurreducens
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polymerized cytochrome OmcZ from Geobacter sulfurreducens

EntireName: Polymerized cytochrome OmcZ from Geobacter sulfurreducens
Components
  • Complex: Polymerized cytochrome OmcZ from Geobacter sulfurreducens
    • Protein or peptide: Cytochrome c
  • Ligand: HEME C

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Supramolecule #1: Polymerized cytochrome OmcZ from Geobacter sulfurreducens

SupramoleculeName: Polymerized cytochrome OmcZ from Geobacter sulfurreducens
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Geobacter sulfurreducens (bacteria)

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Macromolecule #1: Cytochrome c

MacromoleculeName: Cytochrome c / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Geobacter sulfurreducens PCA (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA
Molecular weightTheoretical: 27.686797 KDa
SequenceString: AVPPPPVNQF LGIYDTKFPN LTKADCLECH VSDTVLVQQH HALINTVTPP ASCINTSGTV PPTLATGCHV MVPDGSGGFT FQDFRNCFN CHTQTPHHTS PAAVAKDCKY CHGNFIDNPL DGHYIPTYSA SSVTPMPSGR SVTATDGNVV IVQGCEACHQ A APNAIDPK ...String:
AVPPPPVNQF LGIYDTKFPN LTKADCLECH VSDTVLVQQH HALINTVTPP ASCINTSGTV PPTLATGCHV MVPDGSGGFT FQDFRNCFN CHTQTPHHTS PAAVAKDCKY CHGNFIDNPL DGHYIPTYSA SSVTPMPSGR SVTATDGNVV IVQGCEACHQ A APNAIDPK TNTVRPIFSN QDTHHGTGIT DCNLCHNTSS NVPIRQCEVC HGVNSLHNIQ KDSPNAANLG TVKPGLEDLG WG HIGNNWD CQGCHWSWFG N

UniProtKB: Cytochrome c

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Macromolecule #2: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 2 / Number of copies: 24 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 10.5 / Component - Concentration: 15.0 mM / Component - Formula: C2H7NO / Component - Name: Ethanolamine
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-10 / Number grids imaged: 1 / Number real images: 14508 / Average exposure time: 0.2 sec. / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.08)
Final reconstructionApplied symmetry - Helical parameters - Δz: 57.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -159.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 128409
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsInitial fitting was done with Chimera and refinement was done in Phenix
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient
Output model

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

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