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- EMDB-73506: A Bundled Antiparallel Cytochrome Nanowire Produced by Desulfurom... -

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Basic information

Entry
Database: EMDB / ID: EMD-73506
TitleA Bundled Antiparallel Cytochrome Nanowire Produced by Desulfuromonas soudanensis WTL
Map data
Sample
  • Complex: Multi-heme cytochrome nanowire
    • Protein or peptide: Putative multiheme cytochrome c
  • Ligand: HEME C
  • Ligand: CALCIUM ION
Keywordsmulti-heme cytochrome / nanowire / EET / cryo-EM / ELECTRON TRANSPORT
Function / homologyDoubled CXXCH motif / Doubled CXXCH motif (Paired_CXXCH_1) / Multiheme cytochrome superfamily / Putative multiheme cytochrome c
Function and homology information
Biological speciesDesulfuromonas soudanensis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsPetersen HA / Chan CH / Bond DR / Wang F
Funding support United States, 1 items
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 HA / Chan CH / Carpenter GO / Tabari MZ / Rich-New ST / Zia A / Fields JL / Hochbaum AI / Bond DR / Wang F
History
DepositionOct 22, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73506.png

Downloads & links

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Map

FileDownload / File: emd_73506.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0486
Minimum - Maximum-0.0018049523 - 2.195223
Average (Standard dev.)0.0029335597 (±0.037971966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73506_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73506_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Multi-heme cytochrome nanowire

EntireName: Multi-heme cytochrome nanowire
Components
  • Complex: Multi-heme cytochrome nanowire
    • Protein or peptide: Putative multiheme cytochrome c
  • Ligand: HEME C
  • Ligand: CALCIUM ION

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Supramolecule #1: Multi-heme cytochrome nanowire

SupramoleculeName: Multi-heme cytochrome nanowire / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Desulfuromonas soudanensis (bacteria) / Strain: WTL

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Macromolecule #1: Putative multiheme cytochrome c

MacromoleculeName: Putative multiheme cytochrome c / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Desulfuromonas soudanensis (bacteria)
Molecular weightTheoretical: 21.697295 KDa
SequenceString: MKKVLVLAAA LVLAAAPAMA VIKDTKHDLS SGNVNGSGSN TDETCVFCHT PHGASASGTA PLWNRTNDTT PTGTYGNPTG TMNAVPLAA DVALTDAVLC LSCHDGSIGN TLTNPPNSLG ATALAVTATL SAGANLGADM SNDHPIGMSY GDAITGGDTE L VAAAGGLP ...String:
MKKVLVLAAA LVLAAAPAMA VIKDTKHDLS SGNVNGSGSN TDETCVFCHT PHGASASGTA PLWNRTNDTT PTGTYGNPTG TMNAVPLAA DVALTDAVLC LSCHDGSIGN TLTNPPNSLG ATALAVTATL SAGANLGADM SNDHPIGMSY GDAITGGDTE L VAAAGGLP LFSQTLSVAG AKTDVVWCSS CHDVHGKVGV STFLQVTNAA SALCTTCHSK

UniProtKB: Putative multiheme cytochrome c

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Macromolecule #2: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 2 / Number of copies: 64 / Formula: HEC
Molecular weightTheoretical: 620.519 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 32 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 10.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 30.75 Å
Applied symmetry - Helical parameters - Δ&Phi: 51.44 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1241521
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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