4AYT

STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.5 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.Goubin, S.Shrestha, L.Yang, J.Berridge, G.Ross, J.Stansfeld, P.J.Sansom, M.S.P.Edwards, A.M.Bountra, C.Marsden, B.D.von Delft, F.Bullock, A.N.Gileadi, O.Burgess-Brown, N.A.Carpenter, E.P.

(2013) Proc.Natl.Acad.Sci.USA 110: 9710

  • DOI: 10.1073/pnas.1217042110
  • Primary Citation of Related Structures:  3ZDQ, 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 pote ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10 MITOCHONDRIAL
A
595Homo sapiensGene Names: ABCB10
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
ABCB10 Mitochondrial ABC transporter with bound AMPPC
Find proteins for Q9NRK6 (Homo sapiens)
Go to Gene View: ABCB10
Go to UniProtKB:  Q9NRK6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

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A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
CDL
Query on CDL

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Download CCD File 
A
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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Download CCD File 
A
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
ACP
Query on ACP

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Download CCD File 
A
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ACPKi: 200000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 175.110α = 90.00
b = 175.110β = 90.00
c = 49.550γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references, Structure summary
  • Version 1.2: 2013-06-12
    Type: Database references
  • Version 1.3: 2013-06-26
    Type: Database references
  • Version 1.4: 2015-03-25
    Type: Database references
  • Version 1.5: 2018-01-24
    Type: Database references, Structure summary