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- EMDB-27911: Cryo-EM of P. calidifontis cytochrome filament -

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Basic information

Entry
Database: EMDB / ID: EMD-27911
TitleCryo-EM of P. calidifontis cytochrome filament
Map datacryo-EM of P. calidifontis cytochrome filament
Sample
  • Complex: extracellular cytochrome filament
    • Protein or peptide: c-type cytochrome
  • Ligand: HEME C
Keywordshelical symmetry / cytochrome filmanet / conductive nanowires / microbial nanowires / ELECTRON TRANSPORT
Function / homologyMultiheme cytochrome superfamily / membrane / Cytochrome c family protein
Function and homology information
Biological speciesPyrobaculum calidifontis (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang F / Cvirkaite-Krupovic V / Krupovic M / Egelman EH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5K99GM138756-02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: 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
DepositionAug 22, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27911.png

Downloads & links

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Map

FileDownload / File: emd_27911.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM of P. calidifontis cytochrome filament
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-0.6748198 - 1.2542143
Average (Standard dev.)0.0020151364 (±0.032388423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_27911_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_27911_half_map_2.map
Annotationhalf 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 : extracellular cytochrome filament

EntireName: extracellular cytochrome filament
Components
  • Complex: extracellular cytochrome filament
    • Protein or peptide: c-type cytochrome
  • Ligand: HEME C

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Supramolecule #1: extracellular cytochrome filament

SupramoleculeName: extracellular cytochrome filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrobaculum calidifontis (archaea)

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Macromolecule #1: c-type cytochrome

MacromoleculeName: c-type cytochrome / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrobaculum calidifontis (archaea)
Molecular weightTheoretical: 40.756312 KDa
SequenceString: MKKFPALITT LLLLAVFVAA TYGPPYSYNH PTNCISCHSN STGTANSQAL SGLTSGPAAG ACDPSQQECV WSHQVLKGTD VWKKCINCH VAIWNSINSG PGNVHSGLLN SYGCACHAVA HVGYGNPTDG YTACIYFYVP RLSTATPGYF GAKPTLDFRN V YICFKGTP ...String:
MKKFPALITT LLLLAVFVAA TYGPPYSYNH PTNCISCHSN STGTANSQAL SGLTSGPAAG ACDPSQQECV WSHQVLKGTD VWKKCINCH VAIWNSINSG PGNVHSGLLN SYGCACHAVA HVGYGNPTDG YTACIYFYVP RLSTATPGYF GAKPTLDFRN V YICFKGTP EGTYTFSGNA PTSLMQLLES KGEVTVKALL VGYDKYANGT VKAKSSAADF LETDFFSALE QAGIFRYEWG TA SGAVLKN PSVRTHPLTE EAPNGETIVM GVFDIHTGDF ILVAPYAPYS RAPYYLPVAV NPGVAACFNC HFVYQGQLGT AKV MEVGGV WKIGIPADVL NSLTDPHKIV MPAAQAAGGG VAPNLSLVAL LATATLLGGA FLALRRRAQ

UniProtKB: Cytochrome c family protein

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Macromolecule #2: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 2 / Number of copies: 4 / 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: 6
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: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 32.38 Å
Applied symmetry - Helical parameters - Δ&Phi: 54.72 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101864

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