6GCI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 176: 435-447.e15

  • DOI: 10.1016/j.cell.2018.11.025
  • Primary Citation of Related Structures:  
    6GCI

  • 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 proved difficult to understand the transport mechanism in the absence of a structure in the matrix-open state ...

    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. VIDEO ABSTRACT.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mitochondrial ADP/ATP carrierA315Thermothelomyces thermophilus ATCC 42464Mutation(s): 1 
Gene Names: MYCTH_2316753
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Antiporters
Protein: 
Mitochondrial ADP/ATP carrier, bongkrekic acid-inhibited
Find proteins for G2QNH0 (Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2QNH0 
Go to UniProtKB:  G2QNH0
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NanobodyB131Lama glamaMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
BKC
Query on BKC

Download Ideal Coordinates CCD File 
C [auth A]Bongkrekic acid
C28 H38 O7
SHCXABJSXUACKU-WUTQZGRKSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
I [auth B]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.65α = 90
b = 75.65β = 90
c = 295.48γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references