3ZIA

The structure of F1-ATPase from Saccharomyces cerevisiae inhibited by its regulatory protein IF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure of F1-ATPase from Saccharomyces Cerevisiae Inhibited by its Regulatory Protein If1.

Robinson, G.C.Bason, J.V.Montgomery, M.G.Fearnley, I.M.Mueller, D.M.Leslie, A.G.W.Walker, J.E.

(2013) Open Biol. 3: 164

  • DOI: 10.1098/rsob.120164

  • PubMed Abstract: 
  • The structure of F₁-ATPase from Saccharomyces cerevisiae inhibited by the yeast IF₁ has been determined at 2.5 Å resolution. The inhibitory region of IF₁ from residues 1 to 36 is entrapped between the C-terminal domains of the α(DP)- and β(DP)-subuni ...

    The structure of F₁-ATPase from Saccharomyces cerevisiae inhibited by the yeast IF₁ has been determined at 2.5 Å resolution. The inhibitory region of IF₁ from residues 1 to 36 is entrapped between the C-terminal domains of the α(DP)- and β(DP)-subunits in one of the three catalytic interfaces of the enzyme. Although the structure of the inhibited complex is similar to that of the bovine-inhibited complex, there are significant differences between the structures of the inhibitors and their detailed interactions with F₁-ATPase. However, the most significant difference is in the nucleotide occupancy of the catalytic β(E)-subunits. The nucleotide binding site in β(E)-subunit in the yeast complex contains an ADP molecule without an accompanying magnesium ion, whereas it is unoccupied in the bovine complex. Thus, the structure provides further evidence of sequential product release, with the phosphate and the magnesium ion released before the ADP molecule.


    Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
A, B, C, K, L, M
510Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ATP1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07251
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
D, E, F, N, O, P
478Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ATP2
EC: 3.6.3.14
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00830
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
G, Q
278Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ATP3 (ATP3a, ATP3b)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38077
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
H, R
138Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ATP16
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12165
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
I, S
61Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ATP15
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21306
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATPASE INHIBITOR, MITOCHONDRIAL
J, T
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: INH1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
ATP synthase (F1c10)
Find proteins for P01097 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P01097
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, K
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
B, C, D, E, F, L, M, N, O, P
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
C, L, M, O, P
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, F, K, L, M, N, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 118.224α = 90.00
b = 187.846β = 89.96
c = 181.812γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references