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- PDB-7tfs: Cryo-EM of the OmcE nanowires from Geobacter sulfurreducens -

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Basic information

Entry
Database: PDB / ID: 7tfs
TitleCryo-EM of the OmcE nanowires from Geobacter sulfurreducens
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / PROTEIN FIBRIL / helical symmetry / cytochrome nanowire / filament
Function / homologyDoubled CXXCH motif / Doubled CXXCH motif (Paired_CXXCH_1) / Multiheme cytochrome superfamily / HEME C / Cytochrome c
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang, F. / Mustafa, K. / Chan, C.H. / Joshi, K. / Hochbaum, A.I. / Bond, D.R. / Egelman, E.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Nat Microbiol / Year: 2022
Title: Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing.
Authors: Fengbin Wang / Khawla Mustafa / Victor Suciu / Komal Joshi / Chi H Chan / Sol Choi / Zhangli Su / Dong Si / Allon I Hochbaum / Edward H Egelman / Daniel R Bond /
Abstract: Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were ...Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
History
DepositionJan 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3145
Polymers23,8401
Non-polymers2,4744
Water00
1
A: Cytochrome c
hetero molecules
x 7


Theoretical massNumber of molelcules
Total (without water)184,19635
Polymers166,8787
Non-polymers17,31828
Water0
TypeNameSymmetry operationNumber
helical symmetry operation6
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 7 / Rise per n subunits: 33.9 Å / Rotation per n subunits: 58.812 °)

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Components

#1: Protein Cytochrome c


Mass: 23839.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / References: UniProt: Q74FJ0
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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 OmcE protein / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 58.8 ° / Axial rise/subunit: 33.9 Å / Axial symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346826 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045052
ELECTRON MICROSCOPYf_angle_d0.9317047
ELECTRON MICROSCOPYf_dihedral_angle_d16.553711
ELECTRON MICROSCOPYf_chiral_restr0.043699
ELECTRON MICROSCOPYf_plane_restr0.009885

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