5LQX

Structure of F-ATPase from Pichia angusta, state3

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structure of the mitochondrial ATP synthase fromPichia angustadetermined by electron cryo-microscopy.

Vinothkumar, K.R., Montgomery, M.G., Liu, S., Walker, J.E.

(2016) Proc. Natl. Acad. Sci. U.S.A. 113: 12709-12714

  • DOI: 10.1073/pnas.1615902113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The structure of the intact monomeric ATP synthase from the fungus, Pichia angusta, has been solved by electron cryo-microscopy. The structure provides insights into the mechanical coupling of the transmembrane proton motive force across mitochondria ...

    The structure of the intact monomeric ATP synthase from the fungus, Pichia angusta, has been solved by electron cryo-microscopy. The structure provides insights into the mechanical coupling of the transmembrane proton motive force across mitochondrial membranes in the synthesis of ATP. This mechanism requires a strong and integral stator, consisting of the catalytic α3β3-domain, peripheral stalk, and, in the membrane domain, subunit a and associated supernumerary subunits, kept in contact with the rotor turning at speeds up to 350 Hz. The stator's integrity is ensured by robust attachment of both the oligomycin sensitivity conferral protein (OSCP) to the catalytic domain and the membrane domain of subunit b to subunit a. The ATP8 subunit provides an additional brace between the peripheral stalk and subunit a. At the junction between the OSCP and the apparently stiff, elongated α-helical b-subunit and associated d- and h-subunits, an elbow or joint allows the stator to bend to accommodate lateral movements during the activity of the catalytic domain. The stator may also apply lateral force to help keep the static a-subunit and rotating c10-ring together. The interface between the c10-ring and the a-subunit contains the transmembrane pathway for protons, and their passage across the membrane generates the turning of the rotor. The pathway has two half-channels containing conserved polar residues provided by a bundle of four α-helices inclined at ∼30° to the plane of the membrane, similar to those described in other species. The structure provides more insights into the workings of this amazing machine.

    Organizational Affiliation: 

    The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit f
1
31N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase AAP1 subunit
2
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit a
3
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit b
4
27N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP synthase alpha subunit
A, B, C
510Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for W1Q6W1 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  W1Q6W1
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATP synthase beta subunit
D, E, F
476Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
EC: 7.1.2.2
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for W1QA59 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  W1QA59
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma subunit
G
269Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for W1QGS3 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  W1QGS3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ATP synthase delta subunit
H
138Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for W1QBD1 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  W1QBD1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon subunit
I
63N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ATP synthase inhibitor protein IF1
J
66Bos taurusMutation(s): 0 
Gene Names: ATP5IF1 (ATPI, ATPIF1)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for P01096 (Bos taurus)
Go to UniProtKB:  P01096
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit c
K, L, M, N, O, P, Q, R, S, T
76Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
Gene Names: atp9
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for E7E832 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  E7E832
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ATP synthase OSCP subunit
U
194Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for W1QCI5 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  W1QCI5
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit b
V
204Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for W1Q9V2 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  W1Q9V2
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit d
W
155Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for W1Q731 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  W1Q731
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit h
X
21N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit a
Y
252Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)Mutation(s): 0 
Gene Names: atp6
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
ATP synthase (F-ATPase), State 1
Find proteins for E7E837 (Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1))
Go to UniProtKB:  E7E837
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit a
Z
44N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
A
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
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
1, 2, 3, 4, W, X, Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Data collection, Experimental preparation
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy
  • Version 1.3: 2018-09-12
    Type: Data collection, Database references