4AYW

STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (PLATE FORM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

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Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history


Literature

Structures of Abcb10, a Human ATP-Binding Cassette Transporter in Apo- and Nucleotide-Bound States

Shintre, C.A.Pike, A.C.W.Li, Q.Kim, J.Barr, A.J.von Delft, F.Goub, S.Shrestha, L.Yang, J.Berridge, G.Ross, J.Stansfeld, P.J.Sansoa, M.S.P.Edwards, M.Bountra, C.Marsden, B.D.von Delft, F.Bullock, A.N.Gileadi, O.Burgess-Brown, N.Carpenter, E.P.

(2013) Proc Natl Acad Sci U S A 110: 9710

  • DOI: https://doi.org/10.1073/pnas.1217042110
  • Primary Citation of Related Structures:  
    3ZDQ, 4AYT, 4AYW, 4AYX

  • PubMed Abstract: 

    ABCB10 is one of the three ATP-binding cassette (ABC) transporters found in the inner membrane of mitochondria. In mammals ABCB10 is essential for erythropoiesis, and for protection of mitochondria against oxidative stress. ABCB10 is therefore a potential therapeutic target for diseases in which increased mitochondrial reactive oxygen species production and oxidative stress play a major role. The crystal structure of apo-ABCB10 shows a classic exporter fold ABC transporter structure, in an open-inwards conformation, ready to bind the substrate or nucleotide from the inner mitochondrial matrix or membrane. Unexpectedly, however, ABCB10 adopts an open-inwards conformation when complexed with nonhydrolysable ATP analogs, in contrast to other transporter structures which adopt an open-outwards conformation in complex with ATP. The three complexes of ABCB10/ATP analogs reported here showed varying degrees of opening of the transport substrate binding site, indicating that in this conformation there is some flexibility between the two halves of the protein. These structures suggest that the observed plasticity, together with a portal between two helices in the transmembrane region of ABCB10, assist transport substrate entry into the substrate binding cavity. These structures indicate that ABC transporters may exist in an open-inwards conformation when nucleotide is bound. We discuss ways in which this observation can be aligned with the current views on mechanisms of ABC transporters.


  • Organizational Affiliation

    Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10619Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRK6 (Homo sapiens)
Explore Q9NRK6 
Go to UniProtKB:  Q9NRK6
PHAROS:  Q9NRK6
GTEx:  ENSG00000135776 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRK6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ANP PDBBind:  4AYW Ki: 1.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.7α = 90
b = 101.7β = 90
c = 294.73γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2013-06-05
    Changes: Database references, Structure summary
  • Version 1.3: 2013-06-12
    Changes: Database references
  • Version 1.4: 2013-08-07
    Changes: Database references
  • Version 1.5: 2015-03-25
    Changes: Database references
  • Version 1.6: 2018-01-24
    Changes: Database references, Structure summary
  • Version 1.7: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other