4H2D

Crystal structure of NDOR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


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 U S A 110: 7136-7141

  • DOI: 10.1073/pnas.1302378110
  • Primary Citation of Related Structures:  
    4H2D

  • 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 anamorsin--form a stable complex in vivo that was proposed to provide electrons for assembling cytosolic iron-sulfur cluster proteins ...

    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
    • 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
    • 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

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADPH-dependent diflavin oxidoreductase 1A, B165Homo sapiensMutation(s): 0 
Gene Names: NDOR1NR1
EC: 1.6 (PDB Primary Data), 1.18.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHB4 (Homo sapiens)
Explore Q9UHB4 
Go to UniProtKB:  Q9UHB4
PHAROS:  Q9UHB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHB4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.45α = 90
b = 80.45β = 90
c = 101.48γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata 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: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references
  • Version 1.2: 2013-05-15
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary