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

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Entry
Database: PDB / ID: 6ef8
TitleCryo-EM of the OmcS nanowires from Geobacter sulfurreducens
ComponentsC-type cytochrome OmcS
KeywordsELECTRON TRANSPORT / helical symmetry / cytochrome nanowire / cytochrome c3 / filament
Function / homologyMultiheme cytochrome superfamily / cell outer membrane / oxidoreductase activity / cell surface / metal ion binding / HEME C / C-type cytochrome OmcS
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, F. / Gu, Y. / Egelman, E.H. / Malvankar, N.S.
Funding support United States, 3items
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, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: C-type cytochrome OmcS
B: C-type cytochrome OmcS
C: C-type cytochrome OmcS
D: C-type cytochrome OmcS
E: C-type cytochrome OmcS
F: C-type cytochrome OmcS
G: C-type cytochrome OmcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,87949
Polymers300,9027
Non-polymers25,97742
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area67310 Å2
ΔGint-1047 kcal/mol
Surface area92910 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 7 / Rise per n subunits: 46.7 Å / Rotation per n subunits: -83.1 °)

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Components

#1: Protein
C-type cytochrome OmcS / Outer membrane cytochrome S


Mass: 42986.008 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Source: (natural) Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Strain: ATCC 51573 / DSM 12127 / PCA / References: UniProt: Q74A86
#2: Chemical...
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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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: Filament of OmcS protein / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Geobacter sulfurreducens PCA (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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
Image recordingElectron dose: 2.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1447
Image scansMovie frames/image: 30

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Processing

EM software
IDNameCategory
1EMAN2particle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
12SPIDER3D reconstruction
13Rosettamodel refinement
14PHENIXmodel refinement
15Cootmodel refinement
16UCSF Chimeramodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -83.1 ° / Axial rise/subunit: 46.7 Å / Axial symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: OTHER / Num. of particles: 28293 / Algorithm: BACK PROJECTION / Details: Model:Map FSC 0.38 cutoff / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL

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