3ZIA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1098/rsob.120164
  • Primary Citation of Related Structures:  
    3ZIA

  • 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)-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
A, B, C, K, L
A, B, C, K, L, M
510Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07251 
Go to UniProtKB:  P07251
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07251
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
D, E, F, N, O
D, E, F, N, O, P
478Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for P00830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00830 
Go to UniProtKB:  P00830
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00830
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
G, Q
278Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P38077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38077 
Go to UniProtKB:  P38077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38077
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
H, R
138Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q12165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12165 
Go to UniProtKB:  Q12165
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12165
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
I, S
61Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P21306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P21306 
Go to UniProtKB:  P21306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21306
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATPASE INHIBITOR, MITOCHONDRIAL
J, T
63Saccharomyces cerevisiaeMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P01097 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P01097 
Go to UniProtKB:  P01097
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01097
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
GA [auth K],
U [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth D]
DA [auth E]
EA [auth F]
IA [auth L]
MA [auth M]
BA [auth D],
DA [auth E],
EA [auth F],
IA [auth L],
MA [auth M],
PA [auth N],
RA [auth O],
TA [auth P],
W [auth B],
Y [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
KA [auth L]
LA [auth L]
OA [auth M]
SA [auth O]
AA [auth C],
KA [auth L],
LA [auth L],
OA [auth M],
SA [auth O],
VA [auth P]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth D]
FA [auth F]
HA [auth K]
JA [auth L]
NA [auth M]
CA [auth D],
FA [auth F],
HA [auth K],
JA [auth L],
NA [auth M],
QA [auth N],
UA [auth P],
V [auth A],
X [auth B],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.224α = 90
b = 187.846β = 89.96
c = 181.812γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description