9YUQ | pdb_00009yuq

A Bundled Antiparallel Cytochrome Nanowire Produced by Desulfuromonas soudanensis WTL

PDB DOI: https://doi.org/10.2210/pdb9YUQ/pdb
EM Map EMD-73506: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Desulfuromonas soudanensis
Mutation(s): No

Deposited: 2025-10-22 Released: 2026-08-26
Deposition Author(s): Petersen, H.A., Chan, C.H., Bond, D.R., Wang, F.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.11 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 9YUQ

This is version 1.0 of the entry. See complete history.

Literature

A Bundled Antiparallel Cytochrome Nanowire Structure Suggests Roles in Cell-Cell Electron Transfer and Biofilm Formation

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.

(2026) mBio

Macromolecule Content

Total Structure Weight: 388.15 kDa
Atom Count: 24,832
Modeled Residue Count: 3,168
Deposited Residue Count: 3,488
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative multiheme cytochrome c	A [auth N] B [auth M] C [auth L] D [auth K] E [auth J] A [auth N], B [auth M], C [auth L], D [auth K], E [auth J], F [auth I], G [auth C], H [auth D], I [auth E], J [auth F], K [auth G], L [auth P], M [auth Q], N [auth R], O [auth S], P [auth T]	218	Desulfuromonas soudanensis	Mutation(s): 0
UniProt
Find proteins for A0A0M4DKA8 (Desulfuromonas soudanensis) Explore A0A0M4DKA8 Go to UniProtKB: A0A0M4DKA8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0M4DKA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain AC [auth G] SDF format, chain BA [auth M] SDF format, chain BB [auth C] SDF format, chain CA [auth M] SDF format, chain DA [auth L] SDF format, chain DD [auth S] SDF format, chain EA [auth L] SDF format, chain EC [auth P] SDF format, chain FB [auth C] SDF format, chain FD [auth T] SDF format, chain GB [auth C] SDF format, chain GC [auth P] SDF format, chain IA [auth L] SDF format, chain IB [auth D] SDF format, chain JA [auth K] SDF format, chain JC [auth P] SDF format, chain KA [auth K] SDF format, chain LB [auth D] SDF format, chain MB [auth D] SDF format, chain MC [auth Q] SDF format, chain NA [auth K] SDF format, chain NB [auth E] SDF format, chain OA [auth K] SDF format, chain OB [auth E] SDF format, chain Q [auth N] SDF format, chain QA [auth J] SDF format, chain R [auth N] SDF format, chain RB [auth E] SDF format, chain S [auth N] SDF format, chain SB [auth E] SDF format, chain SC [auth R] SDF format, chain TA [auth J] SDF format, chain UA [auth J] SDF format, chain V [auth N] SDF format, chain VA [auth I] SDF format, chain VC [auth R] SDF format, chain W [auth N] SDF format, chain WA [auth I] SDF format, chain X [auth M] SDF format, chain XA [auth I] SDF format, chain XB [auth F] SDF format, chain XC [auth S] SDF format, chain Y [auth M] SDF format, chain YC [auth S] SDF format, chain ZB [auth G] SDF format, chain YB [auth F] SDF format, chain WC [auth R] SDF format, chain UB [auth F] SDF format, chain TB [auth F] SDF format, chain RC [auth R] SDF format, chain QC [auth Q] SDF format, chain PC [auth Q] SDF format, chain PA [auth J] SDF format, chain LC [auth P] SDF format, chain KC [auth P] SDF format, chain HB [auth C] SDF format, chain HA [auth L] SDF format, chain FC [auth P] SDF format, chain ED [auth T] SDF format, chain CD [auth S] SDF format, chain CB [auth C] SDF format, chain BD [auth S] SDF format, chain BC [auth G] SDF format, chain AB [auth C] MOL2 format, chain AC [auth G] MOL2 format, chain BA [auth M] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth M] MOL2 format, chain DA [auth L] MOL2 format, chain DD [auth S] MOL2 format, chain EA [auth L] MOL2 format, chain EC [auth P] MOL2 format, chain FB [auth C] MOL2 format, chain FD [auth T] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth P] MOL2 format, chain IA [auth L] MOL2 format, chain IB [auth D] MOL2 format, chain JA [auth K] MOL2 format, chain JC [auth P] MOL2 format, chain KA [auth K] MOL2 format, chain LB [auth D] MOL2 format, chain MB [auth D] MOL2 format, chain MC [auth Q] MOL2 format, chain NA [auth K] MOL2 format, chain NB [auth E] MOL2 format, chain OA [auth K] MOL2 format, chain OB [auth E] MOL2 format, chain Q [auth N] MOL2 format, chain QA [auth J] MOL2 format, chain R [auth N] MOL2 format, chain RB [auth E] MOL2 format, chain S [auth N] MOL2 format, chain SB [auth E] MOL2 format, chain SC [auth R] MOL2 format, chain TA [auth J] MOL2 format, chain UA [auth J] MOL2 format, chain V [auth N] MOL2 format, chain VA [auth I] MOL2 format, chain VC [auth R] MOL2 format, chain W [auth N] MOL2 format, chain WA [auth I] MOL2 format, chain X [auth M] MOL2 format, chain XA [auth I] MOL2 format, chain XB [auth F] MOL2 format, chain XC [auth S] MOL2 format, chain Y [auth M] MOL2 format, chain YC [auth S] MOL2 format, chain ZB [auth G] MOL2 format, chain YB [auth F] MOL2 format, chain WC [auth R] MOL2 format, chain UB [auth F] MOL2 format, chain TB [auth F] MOL2 format, chain RC [auth R] MOL2 format, chain QC [auth Q] MOL2 format, chain PC [auth Q] MOL2 format, chain PA [auth J] MOL2 format, chain LC [auth P] MOL2 format, chain KC [auth P] MOL2 format, chain HB [auth C] MOL2 format, chain HA [auth L] MOL2 format, chain FC [auth P] MOL2 format, chain ED [auth T] MOL2 format, chain CD [auth S] MOL2 format, chain CB [auth C] MOL2 format, chain BD [auth S] MOL2 format, chain BC [auth G] MOL2 format, chain AB [auth C] mmCIF format, chain AC [auth G] mmCIF format, chain BA [auth M] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth M] mmCIF format, chain DA [auth L] mmCIF format, chain DD [auth S] mmCIF format, chain EA [auth L] mmCIF format, chain EC [auth P] mmCIF format, chain FB [auth C] mmCIF format, chain FD [auth T] mmCIF format, chain GB [auth C] mmCIF format, chain GC [auth P] mmCIF format, chain IA [auth L] mmCIF format, chain IB [auth D] mmCIF format, chain JA [auth K] mmCIF format, chain JC [auth P] mmCIF format, chain KA [auth K] mmCIF format, chain LB [auth D] mmCIF format, chain MB [auth D] mmCIF format, chain MC [auth Q] mmCIF format, chain NA [auth K] mmCIF format, chain NB [auth E] mmCIF format, chain OA [auth K] mmCIF format, chain OB [auth E] mmCIF format, chain Q [auth N] mmCIF format, chain QA [auth J] mmCIF format, chain R [auth N] mmCIF format, chain RB [auth E] mmCIF format, chain S [auth N] mmCIF format, chain SB [auth E] mmCIF format, chain SC [auth R] mmCIF format, chain TA [auth J] mmCIF format, chain UA [auth J] mmCIF format, chain V [auth N] mmCIF format, chain VA [auth I] mmCIF format, chain VC [auth R] mmCIF format, chain W [auth N] mmCIF format, chain WA [auth I] mmCIF format, chain X [auth M] mmCIF format, chain XA [auth I] mmCIF format, chain XB [auth F] mmCIF format, chain XC [auth S] mmCIF format, chain Y [auth M] mmCIF format, chain YC [auth S] mmCIF format, chain ZB [auth G] mmCIF format, chain YB [auth F] mmCIF format, chain WC [auth R] mmCIF format, chain UB [auth F] mmCIF format, chain TB [auth F] mmCIF format, chain RC [auth R] mmCIF format, chain QC [auth Q] mmCIF format, chain PC [auth Q] mmCIF format, chain PA [auth J] mmCIF format, chain LC [auth P] mmCIF format, chain KC [auth P] mmCIF format, chain HB [auth C] mmCIF format, chain HA [auth L] mmCIF format, chain FC [auth P] mmCIF format, chain ED [auth T] mmCIF format, chain CD [auth S] mmCIF format, chain CB [auth C] mmCIF format, chain BD [auth S] mmCIF format, chain BC [auth G] mmCIF format, chain AB [auth C]	AB [auth C] AC [auth G] BA [auth M] BB [auth C] BC [auth G] AB [auth C], AC [auth G], BA [auth M], BB [auth C], BC [auth G], BD [auth S], CA [auth M], CB [auth C], CD [auth S], DA [auth L], DD [auth S], EA [auth L], EC [auth P], ED [auth T], FB [auth C], FC [auth P], FD [auth T], GB [auth C], GC [auth P], HA [auth L], HB [auth C], IA [auth L], IB [auth D], JA [auth K], JC [auth P], KA [auth K], KC [auth P], LB [auth D], LC [auth P], MB [auth D], MC [auth Q], NA [auth K], NB [auth E], OA [auth K], OB [auth E], PA [auth J], PC [auth Q], Q [auth N], QA [auth J], QC [auth Q], R [auth N], RB [auth E], RC [auth R], S [auth N], SB [auth E], SC [auth R], TA [auth J], TB [auth F], UA [auth J], UB [auth F], V [auth N], VA [auth I], VC [auth R], W [auth N], WA [auth I], WC [auth R], X [auth M], XA [auth I], XB [auth F], XC [auth S], Y [auth M], YB [auth F], YC [auth S], ZB [auth G]	HEME C C₃₄ H₃₆ Fe N₄ O₄ YZTICFPLOXKSQO-RGGAHWMASA-L		Interactions Focus chain AB [auth C] Focus chain AC [auth G] Focus chain BA [auth M] Focus chain BB [auth C] Focus chain BC [auth G] Focus chain BD [auth S] Focus chain CA [auth M] Focus chain CB [auth C] Focus chain CD [auth S] Focus chain DA [auth L] Focus chain DD [auth S] Focus chain EA [auth L] Focus chain EC [auth P] Focus chain ED [auth T] Focus chain FB [auth C] Focus chain FC [auth P] Focus chain FD [auth T] Focus chain GB [auth C] Focus chain GC [auth P] Focus chain HA [auth L] Focus chain HB [auth C] Focus chain IA [auth L] Focus chain IB [auth D] Focus chain JA [auth K] Focus chain JC [auth P] Focus chain KA [auth K] Focus chain KC [auth P] Focus chain LB [auth D] Focus chain LC [auth P] Focus chain MB [auth D] Focus chain MC [auth Q] Focus chain NA [auth K] Focus chain NB [auth E] Focus chain OA [auth K] Focus chain OB [auth E] Focus chain PA [auth J] Focus chain PC [auth Q] Focus chain Q [auth N] Focus chain QA [auth J] Focus chain QC [auth Q] Focus chain R [auth N] Focus chain RB [auth E] Focus chain RC [auth R] Focus chain S [auth N] Focus chain SB [auth E] Focus chain SC [auth R] Focus chain TA [auth J] Focus chain TB [auth F] Focus chain UA [auth J] Focus chain UB [auth F] Focus chain V [auth N] Focus chain VA [auth I] Focus chain VC [auth R] Focus chain W [auth N] Focus chain WA [auth I] Focus chain WC [auth R] Focus chain X [auth M] Focus chain XA [auth I] Focus chain XB [auth F] Focus chain XC [auth S] Focus chain Y [auth M] Focus chain YB [auth F] Focus chain YC [auth S] Focus chain ZB [auth G] Interactions & Density Focus chain AB [auth C] Focus chain AC [auth G] Focus chain BA [auth M] Focus chain BB [auth C] Focus chain BC [auth G] Focus chain BD [auth S] Focus chain CA [auth M] Focus chain CB [auth C] Focus chain CD [auth S] Focus chain DA [auth L] Focus chain DD [auth S] Focus chain EA [auth L] Focus chain EC [auth P] Focus chain ED [auth T] Focus chain FB [auth C] Focus chain FC [auth P] Focus chain FD [auth T] Focus chain GB [auth C] Focus chain GC [auth P] Focus chain HA [auth L] Focus chain HB [auth C] Focus chain IA [auth L] Focus chain IB [auth D] Focus chain JA [auth K] Focus chain JC [auth P] Focus chain KA [auth K] Focus chain KC [auth P] Focus chain LB [auth D] Focus chain LC [auth P] Focus chain MB [auth D] Focus chain MC [auth Q] Focus chain NA [auth K] Focus chain NB [auth E] Focus chain OA [auth K] Focus chain OB [auth E] Focus chain PA [auth J] Focus chain PC [auth Q] Focus chain Q [auth N] Focus chain QA [auth J] Focus chain QC [auth Q] Focus chain R [auth N] Focus chain RB [auth E] Focus chain RC [auth R] Focus chain S [auth N] Focus chain SB [auth E] Focus chain SC [auth R] Focus chain TA [auth J] Focus chain TB [auth F] Focus chain UA [auth J] Focus chain UB [auth F] Focus chain V [auth N] Focus chain VA [auth I] Focus chain VC [auth R] Focus chain W [auth N] Focus chain WA [auth I] Focus chain WC [auth R] Focus chain X [auth M] Focus chain XA [auth I] Focus chain XB [auth F] Focus chain XC [auth S] Focus chain Y [auth M] Focus chain YB [auth F] Focus chain YC [auth S] Focus chain ZB [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain AD [auth S] SDF format, chain CC [auth G] SDF format, chain DB [auth C] SDF format, chain DC [auth G] SDF format, chain EB [auth C] SDF format, chain FA [auth L] SDF format, chain GA [auth L] SDF format, chain GD [auth T] SDF format, chain HC [auth P] SDF format, chain HD [auth T] SDF format, chain IC [auth P] SDF format, chain JB [auth D] SDF format, chain KB [auth D] SDF format, chain LA [auth K] SDF format, chain NC [auth Q] SDF format, chain OC [auth Q] SDF format, chain PB [auth E] SDF format, chain QB [auth E] SDF format, chain SA [auth J] SDF format, chain T [auth N] SDF format, chain TC [auth R] SDF format, chain WB [auth F] SDF format, chain ZC [auth S] SDF format, chain ZA [auth I] SDF format, chain Z [auth M] SDF format, chain YA [auth I] SDF format, chain VB [auth F] SDF format, chain UC [auth R] SDF format, chain U [auth N] SDF format, chain RA [auth J] SDF format, chain MA [auth K] MOL2 format, chain AA [auth M] MOL2 format, chain AD [auth S] MOL2 format, chain CC [auth G] MOL2 format, chain DB [auth C] MOL2 format, chain DC [auth G] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth L] MOL2 format, chain GA [auth L] MOL2 format, chain GD [auth T] MOL2 format, chain HC [auth P] MOL2 format, chain HD [auth T] MOL2 format, chain IC [auth P] MOL2 format, chain JB [auth D] MOL2 format, chain KB [auth D] MOL2 format, chain LA [auth K] MOL2 format, chain NC [auth Q] MOL2 format, chain OC [auth Q] MOL2 format, chain PB [auth E] MOL2 format, chain QB [auth E] MOL2 format, chain SA [auth J] MOL2 format, chain T [auth N] MOL2 format, chain TC [auth R] MOL2 format, chain WB [auth F] MOL2 format, chain ZC [auth S] MOL2 format, chain ZA [auth I] MOL2 format, chain Z [auth M] MOL2 format, chain YA [auth I] MOL2 format, chain VB [auth F] MOL2 format, chain UC [auth R] MOL2 format, chain U [auth N] MOL2 format, chain RA [auth J] MOL2 format, chain MA [auth K] mmCIF format, chain AA [auth M] mmCIF format, chain AD [auth S] mmCIF format, chain CC [auth G] mmCIF format, chain DB [auth C] mmCIF format, chain DC [auth G] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth L] mmCIF format, chain GA [auth L] mmCIF format, chain GD [auth T] mmCIF format, chain HC [auth P] mmCIF format, chain HD [auth T] mmCIF format, chain IC [auth P] mmCIF format, chain JB [auth D] mmCIF format, chain KB [auth D] mmCIF format, chain LA [auth K] mmCIF format, chain NC [auth Q] mmCIF format, chain OC [auth Q] mmCIF format, chain PB [auth E] mmCIF format, chain QB [auth E] mmCIF format, chain SA [auth J] mmCIF format, chain T [auth N] mmCIF format, chain TC [auth R] mmCIF format, chain WB [auth F] mmCIF format, chain ZC [auth S] mmCIF format, chain ZA [auth I] mmCIF format, chain Z [auth M] mmCIF format, chain YA [auth I] mmCIF format, chain VB [auth F] mmCIF format, chain UC [auth R] mmCIF format, chain U [auth N] mmCIF format, chain RA [auth J] mmCIF format, chain MA [auth K]	AA [auth M] AD [auth S] CC [auth G] DB [auth C] DC [auth G] AA [auth M], AD [auth S], CC [auth G], DB [auth C], DC [auth G], EB [auth C], FA [auth L], GA [auth L], GD [auth T], HC [auth P], HD [auth T], IC [auth P], JB [auth D], KB [auth D], LA [auth K], MA [auth K], NC [auth Q], OC [auth Q], PB [auth E], QB [auth E], RA [auth J], SA [auth J], T [auth N], TC [auth R], U [auth N], UC [auth R], VB [auth F], WB [auth F], YA [auth I], Z [auth M], ZA [auth I], ZC [auth S]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain AD [auth S] Focus chain CC [auth G] Focus chain DB [auth C] Focus chain DC [auth G] Focus chain EB [auth C] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain GD [auth T] Focus chain HC [auth P] Focus chain HD [auth T] Focus chain IC [auth P] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain LA [auth K] Focus chain MA [auth K] Focus chain NC [auth Q] Focus chain OC [auth Q] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain RA [auth J] Focus chain SA [auth J] Focus chain T [auth N] Focus chain TC [auth R] Focus chain U [auth N] Focus chain UC [auth R] Focus chain VB [auth F] Focus chain WB [auth F] Focus chain YA [auth I] Focus chain Z [auth M] Focus chain ZA [auth I] Focus chain ZC [auth S] Interactions & Density Focus chain AA [auth M] Focus chain AD [auth S] Focus chain CC [auth G] Focus chain DB [auth C] Focus chain DC [auth G] Focus chain EB [auth C] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain GD [auth T] Focus chain HC [auth P] Focus chain HD [auth T] Focus chain IC [auth P] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain LA [auth K] Focus chain MA [auth K] Focus chain NC [auth Q] Focus chain OC [auth Q] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain RA [auth J] Focus chain SA [auth J] Focus chain T [auth N] Focus chain TC [auth R] Focus chain U [auth N] Focus chain UC [auth R] Focus chain VB [auth F] Focus chain WB [auth F] Focus chain YA [auth I] Focus chain Z [auth M] Focus chain ZA [auth I] Focus chain ZC [auth S]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.11 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	SC0024303

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.