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- EMDB-9046: Cryo-EM of the OmcS nanowires from Geobacter sulfurreducens -

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Basic information

Entry
Database: EMDB / ID: EMD-9046
TitleCryo-EM of the OmcS nanowires from Geobacter sulfurreducens
Map dataOmcS nanowire from Geobacter sulfurreducens
Sample
  • Complex: Filament of OmcS protein
    • Protein or peptide: C-type cytochrome OmcS
  • Ligand: HEME C
Keywordshelical symmetry / cytochrome nanowire / cytochrome c3 / filament / ELECTRON TRANSPORT
Function / homology: / Multiheme cytochrome superfamily / anaerobic respiration / cell outer membrane / electron transfer activity / cell surface / metal ion binding / C-type cytochrome OmcS
Function and homology information
Biological speciesGeobacter sulfurreducens PCA (bacteria) / Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang F / Gu Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35GM122510 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1DP2AI138259-01 United States
National Science Foundation (NSF, United States)1749662 United States
CitationJournal: Cell / Year: 2019
Title: Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers.
Authors: Fengbin Wang / Yangqi Gu / J Patrick O'Brien / Sophia M Yi / Sibel Ebru Yalcin / Vishok Srikanth / Cong Shen / Dennis Vu / Nicole L Ing / Allon I Hochbaum / Edward H Egelman / Nikhil S Malvankar /
Abstract: Long-range (>10 μm) transport of electrons along networks of Geobacter sulfurreducens protein filaments, known as microbial nanowires, has been invoked to explain a wide range of globally important ...Long-range (>10 μm) transport of electrons along networks of Geobacter sulfurreducens protein filaments, known as microbial nanowires, has been invoked to explain a wide range of globally important redox phenomena. These nanowires were previously thought to be type IV pili composed of PilA protein. Here, we report a 3.7 Å resolution cryoelectron microscopy structure, which surprisingly reveals that, rather than PilA, G. sulfurreducens nanowires are assembled by micrometer-long polymerization of the hexaheme cytochrome OmcS, with hemes packed within ∼3.5-6 Å of each other. The inter-subunit interfaces show unique structural elements such as inter-subunit parallel-stacked hemes and axial coordination of heme by histidines from neighboring subunits. Wild-type OmcS filaments show 100-fold greater conductivity than other filaments from a ΔomcS strain, highlighting the importance of OmcS to conductivity in these nanowires. This structure explains the remarkable capacity of soil bacteria to transport electrons to remote electron acceptors for respiration and energy sharing.
History
DepositionAug 16, 2018-
Header (metadata) releaseSep 12, 2018-
Map releaseApr 10, 2019-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.61
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.61
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ef8
  • Surface level: 1.61
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ef8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9046.png

Downloads & links

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Map

FileDownload / File: emd_9046.map.gz / Format: CCP4 / Size: 14.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOmcS nanowire from Geobacter sulfurreducens
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 100 pix.
= 105. Å		1.05 Å/pix.
x 100 pix.
= 105. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.61 / Movie #1: 1.61
Minimum - Maximum-2.9128737 - 6.048029
Average (Standard dev.)0.10053164 (±0.5763336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-192
Dimensions100100384
Spacing100100384
CellA: 104.99999 Å / B: 104.99999 Å / C: 403.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z100100384
origin x/y/z0.0000.0000.000
length x/y/z105.000105.000403.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-192
NC/NR/NS100100384
D min/max/mean-2.9136.0480.101

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Supplemental data

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Sample components

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Entire : Filament of OmcS protein

EntireName: Filament of OmcS protein
Components
  • Complex: Filament of OmcS protein
    • Protein or peptide: C-type cytochrome OmcS
  • Ligand: HEME C

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Supramolecule #1: Filament of OmcS protein

SupramoleculeName: Filament of OmcS protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Geobacter sulfurreducens PCA (bacteria)

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Macromolecule #1: C-type cytochrome OmcS

MacromoleculeName: C-type cytochrome OmcS / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Strain: ATCC 51573 / DSM 12127 / PCA
Molecular weightTheoretical: 42.986008 KDa
SequenceString: FHSGGVAECE GCHTMHNSLG GAVMNSATAQ FTTGPMLLQG ATQSSSCLNC HQHAGDTGPS SYHISTAEAD MPAGTAPLQM TPGGDFGWV KKTYTWNVRG LNTSEGERKG HNIVAGDYNY VADTTLTTAP GGTYPANQLH CSSCHDPHGK YRRFVDGSIA T TGLPIKNS ...String:
FHSGGVAECE GCHTMHNSLG GAVMNSATAQ FTTGPMLLQG ATQSSSCLNC HQHAGDTGPS SYHISTAEAD MPAGTAPLQM TPGGDFGWV KKTYTWNVRG LNTSEGERKG HNIVAGDYNY VADTTLTTAP GGTYPANQLH CSSCHDPHGK YRRFVDGSIA T TGLPIKNS GSYQNSNDPT AWGAVGAYRI LGGTGYQPKS LSGSYAFANQ VPAAVAPSTY NRTEATTQTR VAYGQGMSEW CA NCHTDIH NSAYPTNLRH PAGNGAKFGA TIAGLYNSYK KSGDLTGTQA SAYLSLAPFE EGTADYTVLK GHAKIDDTAL TGA DATSNV NCLSCHRAHA SGFDSMTRFN LAYEFTTIAD ASGNSIYGTD PNTSSLQGRS VNEMTAAYYG RTADKFAPYQ RALC NKCHA KD

UniProtKB: C-type cytochrome OmcS

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Macromolecule #2: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 2 / Number of copies: 42 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
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: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1447 / Average electron dose: 2.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 46.7 Å
Applied symmetry - Helical parameters - Δ&Phi: -83.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: OTHER / Software - Name: SPIDER / Details: Model:Map FSC 0.38 cutoff / Number images used: 28293
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6ef8:
Cryo-EM of the OmcS nanowires from Geobacter sulfurreducens

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