9RK4 | pdb_00009rk4

Soluble domain of kuste4569, a Rieske iron-sulfur cluster protein from Kuenenia stuttgartiensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.297 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.265 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9RK4

This is version 1.1 of the entry. See complete history

Literature

Rieske Iron-Sulfur Cluster Proteins From an Anaerobic Ammonium Oxidizer Suggest Unusual Energetics in Their Parent Rieske/Cytochrome b Complexes.

Hauser, D.Sode, M.Andreeva, E.A.Parey, K.Barends, T.R.M.

(2026) Proteins 94: 905-920

  • DOI: https://doi.org/10.1002/prot.70084
  • Primary Citation Related Structures: 
    9RK3, 9RK4

  • PubMed Abstract: 

    Anaerobic ammonium-oxidizing (anammox) bacteria employ a unique, hydrazine-based pathway to obtain energy from nitrite and ammonium. These organisms possess distinct Rieske/cytochrome b complexes whose precise role in anammox metabolism remains unclear, but which have been proposed to include the generation of NAD(P)H. This would require energetics and structural features unusual for such complexes. Here we present crystal structures and electrochemical investigations of the Rieske subunits of two of these complexes from the anammox organism Kuenenia stuttgartiensis, Kuste4569 and Kustd1480. Both proteins display high redox potentials (> + 300 mV), which can be in part explained by their crystal structures and which fit perfectly into the energetic scheme of the proposed NAD(P)H generation mechanism. Moreover, AlphaFold3 models of the parent complexes trace out a path for the electrons required for NAD(P)H production, which includes a proposed, novel b-type heme in the membrane-bound part of the complex.


  • Organizational Affiliation
    • Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 149.3 kDa 
  • Atom Count: 10,368 
  • Modeled Residue Count: 1,320 
  • Deposited Residue Count: 1,320 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Similar to the Rieske Protein II of bc1 complex
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
110Candidatus Kuenenia sp.Mutation(s): 0 
Gene Names: qcrBqcrB_2KsCSTR_29680KSMBR1_3797kuste4569
EC: 1.10.99.1
UniProt
Find proteins for Q1Q5P2 (Kuenenia stuttgartiensis)
Explore Q1Q5P2 
Go to UniProtKB:  Q1Q5P2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1Q5P2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES
(Subject of Investigation/LOI)

Query on FES



Download:Ideal Coordinates CCD File
AA [auth H]
CA [auth I]
EA [auth J]
GA [auth K]
IA [auth L]
AA [auth H],
CA [auth I],
EA [auth J],
GA [auth K],
IA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BA [auth H]
DA [auth I]
FA [auth J]
HA [auth K]
JA [auth L]
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.297 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.265 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.961α = 90
b = 120.73β = 90
c = 209.245γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Database references