6GCI

Structure of the bongkrekic acid-inhibited mitochondrial ADP/ATP carrier


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier.

Ruprecht, J.J.King, M.S.Zogg, T.Aleksandrova, A.A.Pardon, E.Crichton, P.G.Steyaert, J.Kunji, E.R.S.

(2019) Cell --: --

  • DOI: 10.1016/j.cell.2018.11.025

  • PubMed Abstract: 
  • Mitochondrial ADP/ATP carriers transport ADP into the mitochondrial matrix for ATP synthesis, and ATP out to fuel the cell, by cycling between cytoplasmic-open and matrix-open states. The structure of the cytoplasmic-open state is known, but it has p ...

    Mitochondrial ADP/ATP carriers transport ADP into the mitochondrial matrix for ATP synthesis, and ATP out to fuel the cell, by cycling between cytoplasmic-open and matrix-open states. The structure of the cytoplasmic-open state is known, but it has proved difficult to understand the transport mechanism in the absence of a structure in the matrix-open state. Here, we describe the structure of the matrix-open state locked by bongkrekic acid bound in the ADP/ATP-binding site at the bottom of the central cavity. The cytoplasmic side of the carrier is closed by conserved hydrophobic residues, and a salt bridge network, braced by tyrosines. Glycine and small amino acid residues allow close-packing of helices on the matrix side. Uniquely, the carrier switches between states by rotation of its three domains about a fulcrum provided by the substrate-binding site. Because these features are highly conserved, this mechanism is likely to apply to the whole mitochondrial carrier family.


    Organizational Affiliation

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK. Electronic address: jjr@mrc-mbu.cam.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ADP/ATP carrier
A
315Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799)Mutation(s): 1 
Find proteins for G2QNH0 (Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Go to UniProtKB:  G2QNH0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody
B
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download SDF File 
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
P6G
Query on P6G

Download SDF File 
Download CCD File 
B
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
BKC
Query on BKC

Download SDF File 
Download CCD File 
A
Bongkrekic acid
Bongkrek acid
C28 H38 O7
SHCXABJSXUACKU-WUTQZGRKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.252 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.650α = 90.00
b = 75.650β = 90.00
c = 295.480γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
AutoPROCdata scaling
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_UU_00015/1
European UnionBelgiumInstruct-ERIC/ESFRI
Other governmentBelgiumResearch Foundation - Flanders (FWO)

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references