9WTA | pdb_00009wta

Crystal structure of a selenite-soaked multiheme cytochrome c selenoprotein (MccSep)

PDB DOI: https://doi.org/10.2210/pdb9WTA/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Geobacter sulfurreducens PCA
Expression System: Geobacter sulfurreducens PCA
Mutation(s): No

Deposited: 2025-09-16 Released: 2026-07-22
Deposition Author(s): Mihara, H., Yoshizawa, T., Izu, Y., Inoue, M., Aono, R., Zhang, W., Shibamoto, N., Tobe, R., Kurihara, T., Matsumura, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.206 (Depositor), 0.202 (DCC)
R-Value Work:
0.165 (Depositor), 0.161 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Multiheme selenoenzyme essential for elemental sulfur respiration.

Mihara, H., Yoshizawa, T., Izu, Y., Zhang, W., Inoue, M., Shimamoto, N., Tobe, R., Aono, R., Kurihara, T., Matsumura, H.

(2026) Sci Adv 12: eaeg2218-eaeg2218

PubMed: 42647610 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.aeg2218
Primary Citation Related Structures:
9WT8, 9WTA, 9WTB

PubMed Abstract:
Elemental sulfur reduction is a key process in anaerobic ecosystems and the global sulfur cycle. Although elemental sulfur serves as a terminal electron acceptor in microbial respiration, the molecular basis is unclear. Here, we identify a conserved multiheme cytochrome c selenoprotein essential for sulfur reduction in a sulfur-respiring bacterium. Structural and biochemical analyses show that the enzyme forms a tetramer, with each subunit containing five hemes and one selenocysteine residue. The enzyme catalyzes polysulfide reduction at an active site, where a cysteine coordinates the heme iron, while selenocysteine is essential for catalysis. Genetic analyses show that both residues are critical for sulfur respiration in vivo. These findings reveal a selenium-sulfur-dependent catalysis on a heme center for polysulfide reduction, expanding our understanding of microbial energy metabolism.

Organizational Affiliation

College of Life Sciences, Ritsumeikan University; Kusatsu, 525-8577, Japan.

Macromolecule Content

Total Structure Weight: 216.63 kDa
Atom Count: 15,615
Modeled Residue Count: 1,688
Deposited Residue Count: 1,800
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c,Multiheme cytochrome c selenoprotein (MccSep)	A, B, C, D	450	Geobacter sulfurreducens PCA	Mutation(s): 0 Gene Names: GSU2937, GSU2936
UniProt
Find proteins for Q748R4 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q748R4 Go to UniProtKB: Q748R4
Find proteins for Q748R5 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q748R5 Go to UniProtKB: Q748R5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q748R5 Q748R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain BC [auth D] SDF format, chain CC [auth D] SDF format, chain DC [auth D] SDF format, chain E [auth A] SDF format, chain EC [auth D] SDF format, chain F [auth A] SDF format, chain FC [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain HB [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain KB [auth C] MOL2 format, chain BC [auth D] MOL2 format, chain CC [auth D] MOL2 format, chain DC [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EC [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FC [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] mmCIF format, chain BC [auth D] mmCIF format, chain CC [auth D] mmCIF format, chain DC [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EC [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FC [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain HB [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C]	BC [auth D] CC [auth D] DC [auth D] E [auth A] EC [auth D] BC [auth D], CC [auth D], DC [auth D], E [auth A], EC [auth D], F [auth A], FC [auth D], G [auth A], GA [auth B], GB [auth C], H [auth A], HA [auth B], HB [auth C], I [auth A], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C]	HEME C C₃₄ H₃₆ Fe N₄ O₄ YZTICFPLOXKSQO-RGGAHWMASA-L		Interactions Focus chain BC [auth D] Focus chain CC [auth D] Focus chain DC [auth D] Focus chain E [auth A] Focus chain EC [auth D] Focus chain F [auth A] Focus chain FC [auth D] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Interactions & Density Focus chain BC [auth D] Focus chain CC [auth D] Focus chain DC [auth D] Focus chain E [auth A] Focus chain EC [auth D] Focus chain F [auth A] Focus chain FC [auth D] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C]
EPE (Subject of Investigation/LOI) Query on EPE Download:Ideal Coordinates CCD File SDF format, chain NA [auth B] MOL2 format, chain NA [auth B] mmCIF format, chain NA [auth B]	NA [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain NA [auth B] Interactions & Density Focus chain NA [auth B]
BSY (Subject of Investigation/LOI) Query on BSY Download:Ideal Coordinates CCD File SDF format, chain GC [auth D] SDF format, chain J [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth C] MOL2 format, chain GC [auth D] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] mmCIF format, chain GC [auth D] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C]	GC [auth D], J [auth A], LA [auth B], LB [auth C]	BISELENITE ION H O₃ Se MCAHWIHFGHIESP-UHFFFAOYSA-M		Interactions Focus chain GC [auth D] Focus chain J [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Interactions & Density Focus chain GC [auth D] Focus chain J [auth A] Focus chain LA [auth B] Focus chain LB [auth C]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain HC [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth C] MOL2 format, chain HC [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] mmCIF format, chain HC [auth D] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C]	HC [auth D], K [auth A], L [auth A], MA [auth B], MB [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HC [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Interactions & Density Focus chain HC [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth B] Focus chain MB [auth C]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain AC [auth D] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain IC [auth D] SDF format, chain JC [auth D] SDF format, chain KC [auth D] SDF format, chain LC [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NB [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OC [auth D] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth C] SDF format, chain QC [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RB [auth C] SDF format, chain RC [auth D] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain SC [auth D] SDF format, chain TB [auth C] SDF format, chain TC [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain UC [auth D] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth C] SDF format, chain WA [auth B] SDF format, chain WB [auth C] SDF format, chain X [auth A] SDF format, chain XB [auth C] SDF format, chain Y [auth A] SDF format, chain YB [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZB [auth C] SDF format, chain YA [auth B] SDF format, chain XA [auth B] SDF format, chain W [auth A] SDF format, chain TA [auth B] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain PC [auth D] SDF format, chain P [auth A] SDF format, chain OB [auth C] SDF format, chain NC [auth D] SDF format, chain MC [auth D] SDF format, chain BB [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain IC [auth D] MOL2 format, chain JC [auth D] MOL2 format, chain KC [auth D] MOL2 format, chain LC [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OC [auth D] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain RC [auth D] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain SC [auth D] MOL2 format, chain TB [auth C] MOL2 format, chain TC [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain UC [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XB [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YB [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth C] MOL2 format, chain YA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain PC [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth C] MOL2 format, chain NC [auth D] MOL2 format, chain MC [auth D] MOL2 format, chain BB [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain AC [auth D] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain IC [auth D] mmCIF format, chain JC [auth D] mmCIF format, chain KC [auth D] mmCIF format, chain LC [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OC [auth D] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth C] mmCIF format, chain QC [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth C] mmCIF format, chain RC [auth D] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth C] mmCIF format, chain SC [auth D] mmCIF format, chain TB [auth C] mmCIF format, chain TC [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth C] mmCIF format, chain UC [auth D] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain VB [auth C] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XB [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain YB [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain ZB [auth C] mmCIF format, chain YA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain PC [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth C] mmCIF format, chain NC [auth D] mmCIF format, chain MC [auth D] mmCIF format, chain BB [auth B]	AA [auth A] AB [auth B] AC [auth D] BA [auth A] BB [auth B] AA [auth A], AB [auth B], AC [auth D], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth B], FB [auth C], IC [auth D], JC [auth D], KC [auth D], LC [auth D], M [auth A], MC [auth D], N [auth A], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], Q [auth A], QA [auth B], QB [auth C], QC [auth D], R [auth A], RA [auth B], RB [auth C], RC [auth D], S [auth A], SA [auth B], SB [auth C], SC [auth D], T [auth A], TA [auth B], TB [auth C], TC [auth D], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], W [auth A], WA [auth B], WB [auth C], X [auth A], XA [auth B], XB [auth C], Y [auth A], YA [auth B], YB [auth C], Z [auth A], ZA [auth B], ZB [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain IC [auth D] Focus chain JC [auth D] Focus chain KC [auth D] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain IC [auth D] Focus chain JC [auth D] Focus chain KC [auth D] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.206 (Depositor), 0.202 (DCC)
R-Value Work: 0.165 (Depositor), 0.161 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.45	α = 90
b = 123.56	β = 92.15
c = 116.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24K01994
Japan Society for the Promotion of Science (JSPS)	Japan	23K18033
Japan Society for the Promotion of Science (JSPS)	Japan	25H02292

Revision History (Full details and data files)

Version 1.0: 2026-07-22
Type: Initial release
Version 2.0: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2026-09-16
Changes: Database references