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- PDB-9yuq: A Bundled Antiparallel Cytochrome Nanowire Produced by Desulfurom... -

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Basic information

Entry
Database: PDB / ID: 9yuq
TitleA Bundled Antiparallel Cytochrome Nanowire Produced by Desulfuromonas soudanensis WTL
ComponentsPutative multiheme cytochrome c
KeywordsELECTRON TRANSPORT / multi-heme cytochrome / nanowire / EET / cryo-EM
Function / homologyDoubled CXXCH motif / Doubled CXXCH motif (Paired_CXXCH_1) / Multiheme cytochrome superfamily / HEME C / Putative multiheme cytochrome c
Function and homology information
Biological speciesDesulfuromonas soudanensis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsPetersen, H.A. / Chan, C.H. / Bond, D.R. / Wang, F.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)SC0024303 United States
CitationJournal: Mbio / Year: 2026
Title: A Bundled Antiparallel Cytochrome Nanowire Structure Suggests Roles in Cell-Cell Electron Transfer and Biofilm Formation
Authors: Petersen, H.A. / Chan, C.H. / Carpenter, G.O. / Tabari, M.Z. / Rich-New, S.T. / Zia, A. / Fields, J.L. / Hochbaum, A.I. / Bond, D.R. / Wang, F.
History
DepositionOct 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Putative multiheme cytochrome c
M: Putative multiheme cytochrome c
L: Putative multiheme cytochrome c
K: Putative multiheme cytochrome c
J: Putative multiheme cytochrome c
I: Putative multiheme cytochrome c
C: Putative multiheme cytochrome c
D: Putative multiheme cytochrome c
E: Putative multiheme cytochrome c
F: Putative multiheme cytochrome c
G: Putative multiheme cytochrome c
P: Putative multiheme cytochrome c
Q: Putative multiheme cytochrome c
R: Putative multiheme cytochrome c
S: Putative multiheme cytochrome c
T: Putative multiheme cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,152112
Polymers347,15716
Non-polymers40,99696
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative multiheme cytochrome c


Mass: 21697.295 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Desulfuromonas soudanensis (bacteria) / References: UniProt: A0A0M4DKA8
#2: Chemical...
ChemComp-HEC / HEME C


Mass: 620.519 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
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: Multi-heme cytochrome nanowire / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Desulfuromonas soudanensis (bacteria) / Strain: WTL
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: TFS 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: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 51.44 ° / Axial rise/subunit: 30.75 Å / Axial symmetry: C1
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1241521 / Symmetry type: HELICAL
RefinementHighest resolution: 3.11 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00625392
ELECTRON MICROSCOPYf_angle_d1.39936048
ELECTRON MICROSCOPYf_dihedral_angle_d17.9783774
ELECTRON MICROSCOPYf_chiral_restr0.0463808
ELECTRON MICROSCOPYf_plane_restr0.0054432

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