4H2D

Crystal structure of NDOR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular view of an electron transfer process essential for iron-sulfur protein biogenesis.

Banci, L.Bertini, I.Calderone, V.Ciofi-Baffoni, S.Giachetti, A.Jaiswal, D.Mikolajczyk, M.Piccioli, M.Winkelmann, J.

(2013) Proc.Natl.Acad.Sci.USA 110: 7136-7141

  • DOI: 10.1073/pnas.1302378110

  • PubMed Abstract: 
  • Biogenesis of iron-sulfur cluster proteins is a highly regulated process that requires complex protein machineries. In the cytosolic iron-sulfur protein assembly machinery, two human key proteins--NADPH-dependent diflavin oxidoreductase 1 (Ndor1) and ...

    Biogenesis of iron-sulfur cluster proteins is a highly regulated process that requires complex protein machineries. In the cytosolic iron-sulfur protein assembly machinery, two human key proteins--NADPH-dependent diflavin oxidoreductase 1 (Ndor1) and anamorsin--form a stable complex in vivo that was proposed to provide electrons for assembling cytosolic iron-sulfur cluster proteins. The Ndor1-anamorsin interaction was also suggested to be implicated in the regulation of cell survival/death mechanisms. In the present work we unravel the molecular basis of recognition between Ndor1 and anamorsin and of the electron transfer process. This is based on the structural characterization of the two partner proteins, the investigation of the electron transfer process, and the identification of those protein regions involved in complex formation and those involved in electron transfer. We found that an unstructured region of anamorsin is essential for the formation of a specific and stable protein complex with Ndor1, whereas the C-terminal region of anamorsin, containing the [2Fe-2S] redox center, transiently interacts through complementary charged residues with the FMN-binding site region of Ndor1 to perform electron transfer. Our results propose a molecular model of the electron transfer process that is crucial for understanding the functional role of this interaction in human cells.


    Related Citations: 
    • NADPH-cytochrome P450 oxidoreductase. Structural basis for hydride and electron transfer.
      Hubbard, P.A.,Shen, A.L.,Paschke, R.,Kasper, C.B.,Kim, J.J.
      (2001) J.Biol.Chem. 276: 29163
    • Structure and function of an NADPH-cytochrome P450 oxidoreductase in an open conformation capable of reducing cytochrome P450.
      Hamdane, D.,Xia, C.,Im, S.C.,Zhang, H.,Kim, J.J.,Waskell, L.
      (2009) J.Biol.Chem. 284: 11374
    • Solution structure of the sulfite reductase flavodoxin-like domain from Escherichia coli.
      Sibille, N.,Blackledge, M.,Brutscher, B.,Coves, J.,Bersch, B.
      (2005) Biochemistry 44: 9086


    Organizational Affiliation

    Magnetic Resonance Center and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence, Italy. banci@cerm.unifi.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH-dependent diflavin oxidoreductase 1
A, B
165Homo sapiensMutation(s): 0 
Gene Names: NDOR1 (NR1)
EC: 1.18.1.-
Find proteins for Q9UHB4 (Homo sapiens)
Go to Gene View: NDOR1
Go to UniProtKB:  Q9UHB4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.450α = 90.00
b = 80.450β = 90.00
c = 101.480γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-05-01
    Type: Database references
  • Version 1.2: 2013-05-15
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Structure summary