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- PDB-8d9m: Cryo-EM of the OmcZ nanowires from Geobacter sulfurreducens -

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Basic information

Entry
Database: PDB / ID: 8d9m
TitleCryo-EM of the OmcZ nanowires from Geobacter sulfurreducens
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / PROTEIN FIBRIL / helical symmetry / cytochrome nanowire / filament
Function / homologyIPT/TIG domain / Multiheme cytochrome superfamily / IPT domain / Immunoglobulin E-set / Immunoglobulin-like fold / HEME C / Cytochrome c
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang, F. / Chan, C.H. / Mustafa, 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)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, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.0Sep 14, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Sep 14, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Sep 14, 2022Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Sep 14, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 14, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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)54,3739
Polymers49,4251
Non-polymers4,9488
Water00
1
A: Cytochrome c
hetero molecules
x 7


Theoretical massNumber of molelcules
Total (without water)380,60863
Polymers345,9727
Non-polymers34,63656
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: 58.1 Å / Rotation per n subunits: -158.2 °)

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Components

#1: Protein Cytochrome c / OmcZ


Mass: 49424.559 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: Q74BG5
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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 OmcZ protein / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Geobacter sulfurreducens (bacteria)
Buffer solutionpH: 10.5
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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -158.2 ° / Axial rise/subunit: 58.1 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92170 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616779
ELECTRON MICROSCOPYf_angle_d0.9923779
ELECTRON MICROSCOPYf_dihedral_angle_d18.7552310
ELECTRON MICROSCOPYf_chiral_restr0.0522128
ELECTRON MICROSCOPYf_plane_restr0.0062919

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