H. halophila dodecin in complex with riboflavin

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Dodecin is the Key Player in Flavin Homeostasis of Archaea.

Grininger, M.Staudtb, H.Johansson, P.Wachtveitl, J.Oesterhelt, D.

(2009) J Biol Chem 284: 13068

  • DOI: https://doi.org/10.1074/jbc.M808063200
  • Primary Citation of Related Structures:  
    2VX9, 2VXA

  • PubMed Abstract: 

    Flavins are employed to transform physical input into biological output signals. In this function, flavins catalyze a variety of light-induced reactions and redox processes. However, nature also provides flavoproteins with the ability to uncouple the mediation of signals. Such proteins are the riboflavin-binding proteins (RfBPs) with their function to store riboflavin for fast delivery of FMN and FAD. Here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin is an RfBP, and we reveal that riboflavin storage is not restricted to eukaryotes. However, the function of the prokaryotic RfBP dodecin seems to be adapted to the requirement of a monocellular organism. While in eukaryotes RfBPs are involved in trafficking riboflavin, and dodecin is responsible for the flavin homeostasis of the cell. Although only 68 amino acids in length, dodecin is of high functional versatility in neutralizing riboflavin to protect the cellular environment from uncontrolled flavin reactivity. Besides the predominant ultrafast quenching of excited states, dodecin prevents light-induced riboflavin reactivity by the selective degradation of riboflavin to lumichrome. Coordinated with the high affinity for lumichrome, the directed degradation reaction is neutral to the cellular environment and provides an alternative pathway for suppressing uncontrolled riboflavin reactivity. Intriguingly, the different structural and functional properties of a homologous bacterial dodecin suggest that dodecin has different roles in different kingdoms of life.

  • Organizational Affiliation

    Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany. grininge@biochem.mpg.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
72Halorhodospira halophilaMutation(s): 0 
Find proteins for A1WUH0 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WUH0 
Go to UniProtKB:  A1WUH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1WUH0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on RBF

Download Ideal Coordinates CCD File 
DA [auth F]
FA [auth G]
KA [auth H]
M [auth A]
MA [auth I]
DA [auth F],
FA [auth G],
KA [auth H],
M [auth A],
MA [auth I],
P [auth B],
PA [auth J],
S [auth C],
SA [auth K],
V [auth D],
VA [auth L],
Z [auth E]
C17 H20 N4 O6
Query on CL

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
EA [auth F]
GA [auth G]
AA [auth E],
BA [auth E],
CA [auth E],
EA [auth F],
GA [auth G],
HA [auth G],
IA [auth G],
JA [auth G],
LA [auth H],
N [auth A],
NA [auth I],
O [auth A],
OA [auth I],
Q [auth B],
QA [auth J],
R [auth B],
RA [auth J],
T [auth C],
TA [auth K],
U [auth C],
UA [auth K],
W [auth D],
X [auth D],
Y [auth D]
Binding Affinity Annotations 
IDSourceBinding Affinity
RBF PDBBind:  2VXA Kd: 2500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.76α = 90
b = 100.51β = 90
c = 100.47γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description