5DN6

ATP synthase from Paracoccus denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.297 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 angstrom resolution.

Morales-Rios, E.Montgomery, M.G.Leslie, A.G.Walker, J.E.

(2015) Proc Natl Acad Sci U S A 112: 13231-13236

  • DOI: 10.1073/pnas.1517542112
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of the intact ATP synthase from the α-proteobacterium Paracoccus denitrificans, inhibited by its natural regulatory ζ-protein, has been solved by X-ray crystallography at 4.0 Å resolution. The ζ-protein is bound via its N-terminal α-hel ...

    The structure of the intact ATP synthase from the α-proteobacterium Paracoccus denitrificans, inhibited by its natural regulatory ζ-protein, has been solved by X-ray crystallography at 4.0 Å resolution. The ζ-protein is bound via its N-terminal α-helix in a catalytic interface in the F1 domain. The bacterial F1 domain is attached to the membrane domain by peripheral and central stalks. The δ-subunit component of the peripheral stalk binds to the N-terminal regions of two α-subunits. The stalk extends via two parallel long α-helices, one in each of the related b and b' subunits, down a noncatalytic interface of the F1 domain and interacts in an unspecified way with the a-subunit in the membrane domain. The a-subunit lies close to a ring of 12 c-subunits attached to the central stalk in the F1 domain, and, together, the central stalk and c-ring form the enzyme's rotor. Rotation is driven by the transmembrane proton-motive force, by a mechanism where protons pass through the interface between the a-subunit and c-ring via two half-channels in the a-subunit. These half-channels are probably located in a bundle of four α-helices in the a-subunit that are tilted at ∼30° to the plane of the membrane. Conserved polar residues in the two α-helices closest to the c-ring probably line the proton inlet path to an essential carboxyl group in the c-subunit in the proton uptake site and a proton exit path from the proton release site. The structure has provided deep insights into the workings of this extraordinary molecular machine.


    Organizational Affiliation

    Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom; walker@mrc-mbu.cam.ac.uk andrew@mrc-lmb.cam.ac.uk.



Macromolecules
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chain A
1
20Paracoccus denitrificansMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Chain B
2
15Paracoccus denitrificansMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Chain C
3
19Paracoccus denitrificansMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alpha
A, B, C
511Paracoccus denitrificansMutation(s): 0 
EC: 7.1.2.2
Find proteins for A1B8N8 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B8N8

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit beta
D, E, F
474Paracoccus denitrificansMutation(s): 0 
EC: 7.1.2.2
Find proteins for A1B8P0 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B8P0

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chain
G
290Paracoccus denitrificansMutation(s): 0 
Find proteins for A1B8N9 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B8N9

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit delta
H
188Paracoccus denitrificansMutation(s): 0 
Find proteins for A1B8N7 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B8N7

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon chain
I
148Paracoccus denitrificansMutation(s): 0 
Find proteins for A1B8P1 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B8P1

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ATP synthase F0 subcomplex C subunit
J, K, L, M, N, O, P, Q, R, S, T, U
77Paracoccus denitrificansMutation(s): 0 
Find proteins for A1B618 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B618

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Chain V
V
78Paracoccus denitrificansMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Chain W
W
124Paracoccus denitrificansMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a
X
283Paracoccus denitrificansMutation(s): 0 
Find proteins for A1B619 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B619

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Chain Y
Y
54Paracoccus denitrificansMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Zeta inhibitor protein
Z
104Paracoccus denitrificansMutation(s): 0 
Find proteins for A1B602 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B602
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.98 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.297 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.001α = 90
b = 187.943β = 97.44
c = 164.724γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/M009858/1
Medical Research Council (United Kingdom)United KingdomU105663150
Medical Research Council (United Kingdom)United KingdomU105184325

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Other
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-01-17
    Changes: Experimental preparation
  • Version 2.0: 2018-07-04
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2019-12-04
    Changes: Source and taxonomy, Structure summary