4XD7

Structure of thermophilic F1-ATPase inhibited by epsilon subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a thermophilic F1 -ATPase inhibited by an epsilon-subunit: deeper insight into the epsilon-inhibition mechanism.

Shirakihara, Y.Shiratori, A.Tanikawa, H.Nakasako, M.Yoshida, M.Suzuki, T.

(2015) Febs J. 282: 2895-2913

  • DOI: 10.1111/febs.13329

  • PubMed Abstract: 
  • F1-ATPase (F1) is the catalytic sector in F(o)F1-ATP synthase that is responsible for ATP production in living cells. In catalysis, its three catalytic β-subunits undergo nucleotide occupancy-dependent and concerted open-close conformational changes ...

    F1-ATPase (F1) is the catalytic sector in F(o)F1-ATP synthase that is responsible for ATP production in living cells. In catalysis, its three catalytic β-subunits undergo nucleotide occupancy-dependent and concerted open-close conformational changes that are accompanied by rotation of the γ-subunit. Bacterial and chloroplast F1 are inhibited by their own ε-subunit. In the ε-inhibited Escherichia coli F1 structure, the ε-subunit stabilizes the overall conformation (half-closed, closed, open) of the β-subunits by inserting its C-terminal helix into the α3β3 cavity. The structure of ε-inhibited thermophilic F1 is similar to that of E. coli F1, showing a similar conformation of the ε-subunit, but the thermophilic ε-subunit stabilizes another unique overall conformation (open, closed, open) of the β-subunits. The ε-C-terminal helix 2 and hook are conserved between the two structures in interactions with target residues and in their positions. Rest of the ε-C-terminal domains are in quite different conformations and positions, and have different modes of interaction with targets. This region is thought to serve ε-inhibition differently. For inhibition, the ε-subunit contacts the second catches of some of the β- and α-subunits, the N- and C-terminal helices, and some of the Rossmann fold segments. Those contacts, as a whole, lead to positioning of those β- and α- second catches in ε-inhibition-specific positions, and prevent rotation of the γ-subunit. Some of the structural features are observed even in IF1 inhibition in mitochondrial F1.


    Organizational Affiliation

    National Institute of Genetics, Mishima, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alpha
A, B, C
502Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: atpA
EC: 7.1.2.2
Find proteins for P09219 (Bacillus sp. (strain PS3))
Go to UniProtKB:  P09219
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit beta
D, E, F
483Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: atpD
EC: 7.1.2.2
Find proteins for P07677 (Bacillus sp. (strain PS3))
Go to UniProtKB:  P07677
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chain
G
285Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: atpG
Find proteins for P09222 (Bacillus sp. (strain PS3))
Go to UniProtKB:  P09222
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon chain
H
133Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: atpC
Find proteins for P07678 (Bacillus sp. (strain PS3))
Go to UniProtKB:  P07678
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.250 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 233.395α = 90.00
b = 233.395β = 90.00
c = 303.964γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Source and taxonomy
  • Version 1.2: 2017-04-19
    Type: Structure summary