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 9WTB | pdb_00009wtb

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.210 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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

  • 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: 216.08 kDa 
  • Atom Count: 15,586 
  • Modeled Residue Count: 1,688 
  • Deposited Residue Count: 1,800 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c,Multiheme cytochrome c selenoprotein (MccSep)
A, B, C, D
450Geobacter sulfurreducens PCAMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ748R4Q748R5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
(Subject of Investigation/LOI)

Query on HEC


Download:Ideal Coordinates CCD File
AB [auth C]
BB [auth C]
CA [auth B]
CB [auth C]
DA [auth B]
AB [auth C],
BB [auth C],
CA [auth B],
CB [auth C],
DA [auth B],
DB [auth C],
E [auth A],
EA [auth B],
EB [auth C],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
I [auth A],
VB [auth D],
WB [auth D],
XB [auth D],
YB [auth D],
ZB [auth D]
HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
EPE
(Subject of Investigation/LOI)

Query on EPE


Download:Ideal Coordinates CCD File
IA [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SE4
(Subject of Investigation/LOI)

Query on SE4


Download:Ideal Coordinates CCD File
AC [auth D],
FB [auth C],
HA [auth B],
J [auth A]		SELENATE ION
O4 Se
QYHFIVBSNOWOCQ-UHFFFAOYSA-L
EDO
(Subject of Investigation/LOI)

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
BC [auth D]
CC [auth D]
DC [auth D]
AA [auth A],
BA [auth A],
BC [auth D],
CC [auth D],
DC [auth D],
EC [auth D],
FC [auth D],
GB [auth C],
GC [auth D],
HB [auth C],
HC [auth D],
IB [auth C],
IC [auth D],
JA [auth B],
JB [auth C],
JC [auth D],
K [auth A],
KA [auth B],
KB [auth C],
KC [auth D],
L [auth A],
LA [auth B],
LB [auth C],
LC [auth D],
M [auth A],
MA [auth B],
MB [auth C],
MC [auth D],
N [auth A],
NA [auth B],
NB [auth C],
NC [auth D],
O [auth A],
OA [auth B],
OB [auth C],
P [auth A],
PA [auth B],
PB [auth C],
Q [auth A],
QA [auth B],
QB [auth C],
R [auth A],
RA [auth B],
RB [auth C],
S [auth A],
SA [auth B],
SB [auth C],
T [auth A],
TA [auth B],
TB [auth D],
U [auth A],
UA [auth B],
UB [auth D],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
X [auth A],
XA [auth B],
Y [auth A],
YA [auth B],
Z [auth A],
ZA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.210 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.64α = 90
b = 123.83β = 91.94
c = 116.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan24K01994
Japan Society for the Promotion of Science (JSPS)Japan23K18033
Japan Society for the Promotion of Science (JSPS)Japan25H02292

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