4XD7

Structure of thermophilic F1-ATPase inhibited by epsilon subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 

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
  • Primary Citation of Related Structures:  
    4XD7

  • 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

    ERATO, Japan Science and Technology Corporation (JST), Yokohama, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alphaABC502Bacillus sp. PS3Mutation(s): 0 
Gene Names: atpA
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Find proteins for P09219 (Bacillus sp. (strain PS3))
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Go to UniProtKB:  P09219
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit betaDEF483Bacillus sp. PS3Mutation(s): 0 
Gene Names: atpD
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Find proteins for P07677 (Bacillus sp. (strain PS3))
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Go to UniProtKB:  P07677
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase gamma chainG285Bacillus sp. PS3Mutation(s): 0 
Gene Names: atpG
Find proteins for P09222 (Bacillus sp. (strain PS3))
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Go to UniProtKB:  P09222
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase epsilon chainH133Bacillus sp. PS3Mutation(s): 0 
Gene Names: atpC
Find proteins for P07678 (Bacillus sp. (strain PS3))
Explore P07678 
Go to UniProtKB:  P07678
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 233.395α = 90
b = 233.395β = 90
c = 303.964γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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