5FL7

Structure of the F1c10 complex from Yarrowia lipolytica ATP synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology.

Hahn, A.Parey, K.Bublitz, M.Mills, D.J.Zickermann, V.Vonck, J.Kuhlbrandt, W.Meier, T.

(2016) Mol Cell 63: 445

  • DOI: https://doi.org/10.1016/j.molcel.2016.05.037
  • Primary Citation of Related Structures:  
    5FL7

  • PubMed Abstract: 

    We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 of the 60 dimer subunits. Horizontal helices of subunit a in Fo wrap around the c-ring rotor, and a total of six vertical helices assigned to subunits a, b, f, i, and 8 span the membrane. Subunit 8 (A6L in human) is an evolutionary derivative of the bacterial b subunit. On the lumenal membrane surface, subunit f establishes direct contact between the two monomers. Comparison with a cryo-EM map of the F1Fo monomer identifies subunits e and g at the lateral dimer interface. They do not form dimer contacts but enable dimer formation by inducing a strong membrane curvature of ∼100°. Our structure explains the structural basis of cristae formation in mitochondria, a landmark signature of eukaryotic cell morphology.


  • Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT ALPHA
A, B, C
536Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6C326 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C326 
Go to UniProtKB:  Q6C326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C326
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT BETA
D, E, F
509Yarrowia lipolyticaMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for Q6CFT7 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6CFT7 
Go to UniProtKB:  Q6CFT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6CFT7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT GAMMA CHAIN, MITOCHONDRIAL293Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6C338 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C338 
Go to UniProtKB:  Q6C338
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C338
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL137Yarrowia lipolyticaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6C877 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C877 
Go to UniProtKB:  Q6C877
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C877
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE EPSILON CHAIN, MITOCHONDRIAL16Yarrowia lipolyticaMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL76Yarrowia lipolyticaMutation(s): 0 
EC: 3.6.3.14
Membrane Entity: Yes 
UniProt
Find proteins for Q37695 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q37695 
Go to UniProtKB:  Q37695
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ37695
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
T [auth A],
V [auth B],
X [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth F],
Z [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D],
CA [auth F],
U [auth A],
W [auth B],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.5α = 90
b = 182.2β = 90
c = 193γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata 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: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2016-08-24
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description