2HLD

Crystal structure of yeast mitochondrial F1-ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Novel features of the rotary catalytic mechanism revealed in the structure of yeast F(1) ATPase.

Kabaleeswaran, V.Puri, N.Walker, J.E.Leslie, A.G.Mueller, D.M.

(2006) EMBO J 25: 5433-5442

  • DOI: https://doi.org/10.1038/sj.emboj.7601410
  • Primary Citation of Related Structures:  
    2HLD

  • PubMed Abstract: 

    The crystal structure of yeast mitochondrial F(1) ATPase contains three independent copies of the complex, two of which have similar conformations while the third differs in the position of the central stalk relative to the alpha(3)beta(3) sub-assembly. All three copies display very similar asymmetric features to those observed for the bovine enzyme, but the yeast F(1) ATPase structures provide novel information. In particular, the active site that binds ADP in bovine F(1) ATPase has an ATP analog bound and therefore this structure does not represent the ADP-inhibited form. In addition, one of the complexes binds phosphate in the nucleotide-free catalytic site, and comparison with other structures provides a picture of the movement of the phosphate group during initial binding and subsequent catalysis. The shifts in position of the central stalk between two of the three copies of yeast F(1) ATPase and when these structures are compared to those of the bovine enzyme give new insight into the conformational changes that take place during rotational catalysis.


  • Organizational Affiliation

    Department of Biochemistry & Molecular Biology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase alpha chain, mitochondrial
A, B, C, J, K
A, B, C, J, K, L, S, T, U
510Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
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 beta chain, mitochondrial
D, E, F, M, N
D, E, F, M, N, O, V, W, X
478Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ATP2
EC: 3.6.3.14
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 gamma chain, mitochondrial
G, P, Y
278Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
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 delta chain, mitochondrial
H, Q, Z
138Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
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 epsilon chain, mitochondrialAA [auth 1],
I,
R
61Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.3.14
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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
BB [auth U]
CA [auth A]
DB [auth V]
EA [auth B]
FB [auth X]
BB [auth U],
CA [auth A],
DB [auth V],
EA [auth B],
FB [auth X],
GA [auth C],
IA [auth D],
KA [auth F],
MA [auth J],
OA [auth K],
QA [auth L],
SA [auth M],
VA [auth O],
XA [auth S],
ZA [auth T]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
TA [auth N]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth U]
BA [auth A]
CB [auth V]
DA [auth B]
EB [auth X]
AB [auth U],
BA [auth A],
CB [auth V],
DA [auth B],
EB [auth X],
FA [auth C],
HA [auth D],
JA [auth F],
LA [auth J],
NA [auth K],
PA [auth L],
RA [auth M],
UA [auth O],
WA [auth S],
YA [auth T]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.524α = 90
b = 294.132β = 101.67
c = 190.432γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description