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- EMDB-27266: Cryo-EM of the OmcZ nanowires from Geobacter sulfurreducens -

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Basic information

Entry
Database: EMDB / ID: EMD-27266
TitleCryo-EM of the OmcZ nanowires from Geobacter sulfurreducens
Map datacryo-EM of OmcZ filament
Sample
  • Complex: Filament of OmcZ protein
    • Protein or peptide: Cytochrome c
  • Ligand: HEME C
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)
Methodhelical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang F / Chan CH / Mustafa K / Hochbaum AI / Bond DR / Egelman EH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: Elife / Year: 2022
Title: Structure of OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times.
Authors: Fengbin Wang / Chi Ho Chan / Victor Suciu / Khawla Mustafa / Madeline Ammend / Dong Si / Allon I Hochbaum / Edward H Egelman / Daniel R Bond /
Abstract: While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as were composed of type IV pili, it has now been ...While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as were composed of type IV pili, it has now been established that bacterial -type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-electron microscopy (cryo-EM) to determine the structure of a third extracellular filament, formed from the octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE from the same organism, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.
History
DepositionJun 10, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27266.png

Downloads & links

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Map

FileDownload / File: emd_27266.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM of OmcZ filament
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.127
Minimum - Maximum-0.0023573348 - 1.0043259
Average (Standard dev.)0.00046894138 (±0.010238218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_27266_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_27266_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Filament of OmcZ protein

EntireName: Filament of OmcZ protein
Components
  • Complex: Filament of OmcZ protein
    • Protein or peptide: Cytochrome c
  • Ligand: HEME C

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Supramolecule #1: Filament of OmcZ protein

SupramoleculeName: Filament of OmcZ protein / type: complex / Chimera: Yes / 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA
Molecular weightTheoretical: 49.424559 KDa
SequenceString: MKKKVLIGAS LAAVVLTGAA MVGAAVPPPP VNQFLGIYDT KFPNLTKADC LECHVSDTVL VQQHHALINT VTPPASCINT SGTVPPTLA TGCHVMVPDG SGGFTFQDFR NCFNCHTQTP HHTSPAAVAK DCKYCHGNFI DNPLDGHYIP TYSASSVTPM P SGRSVTAT ...String:
MKKKVLIGAS LAAVVLTGAA MVGAAVPPPP VNQFLGIYDT KFPNLTKADC LECHVSDTVL VQQHHALINT VTPPASCINT SGTVPPTLA TGCHVMVPDG SGGFTFQDFR NCFNCHTQTP HHTSPAAVAK DCKYCHGNFI DNPLDGHYIP TYSASSVTPM P SGRSVTAT DGNVVIVQGC EACHQAAPNA IDPKTNTVRP IFSNQDTHHG TGITDCNLCH NTSSNVPIRQ CEVCHGVNSL HN IQKDSPN AANLGTVKPG LEDLGWGHIG NNWDCQGCHW SWFGNSSPYT NATVPAINGQ SSYTVTAGKE AVLTIVGSSF VNV GPDGVT TYQPTVALVS GSTSLTLTPF SVTESEIKVS VPALVEGVYE LRITKANKVS NLAKLTVAPA RIIASATLAT GKTL TITGT GFGPAPSSEY DAGIGVYAGT TQANVISWSD TKVVATSPDF ATNGYVTVKT INGPLSGKIL AAPKKVKR

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Macromolecule #2: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 2 / Number of copies: 8 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 58.1 Å
Applied symmetry - Helical parameters - Δ&Phi: -158.2 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92170

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