Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69351.68 
• Atom Count: 4434 
• Residue Count: 595 
• Unique protein chains: 1

3ZDQ

STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (NUCLEOTIDE-FREE FORM)

• DOI: 10.2210/pdb3ZDQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2012-11-30 Released: 2013-01-23 
• Deposition Author(s): Pike, A.C.W., Shintre, C.A., Krojer, T., von Delft, F., Vollmar, M., Mukhopadhyay, S., Burgess-Brown, N., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Carpenter, E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.244 
• R-Value Work: 0.202 

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

• PubMed: 23716676 
• DOI: 10.1073/pnas.1217042110
• Primary Citation of Related Structures:  
  4AYX, 4AYT, 4AYW


• 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10, MITOCHONDRIAL	A	595	Homo sapiens	Mutation(s): 0  Gene 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GLY	A	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
CDL	A	CARDIOLIPIN DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
LMT	A	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.244 
• R-Value Work: 0.202 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 177.790	α = 90.00
b = 177.790	β = 90.00
c = 50.060	γ = 120.00

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-30 
• Released Date: 2013-01-23 
• Deposition Author(s): Pike, A.C.W., Shintre, C.A., Krojer, T., von Delft, F., Vollmar, M., Mukhopadhyay, S., Burgess-Brown, N., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Carpenter, E.P.

Revision History 

• Version 1.0: 2013-01-23
  Type: Initial release
• Version 1.1: 2013-06-05
  Type: Database references
• 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