5HKK

Caldalaklibacillus thermarum F1-ATPase (wild type)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum.

Ferguson, S.A.Cook, G.M.Montgomery, M.G.Leslie, A.G.Walker, J.E.

(2016) Proc Natl Acad Sci U S A 113: 10860-10865

  • DOI: 10.1073/pnas.1612035113
  • Primary Citation of Related Structures:  
    5HKK, 5IK2

  • PubMed Abstract: 
  • The crystal structure has been determined of the F1-catalytic domain of the F-ATPase from Caldalkalibacillus thermarum, which hydrolyzes adenosine triphosphate (ATP) poorly. It is very similar to those of active mitochondrial and bacterial F1-ATPases. In the F-ATPase from Geobacillus stearothermophilus, conformational changes in the ε-subunit are influenced by intracellular ATP concentration and membrane potential ...

    The crystal structure has been determined of the F1-catalytic domain of the F-ATPase from Caldalkalibacillus thermarum, which hydrolyzes adenosine triphosphate (ATP) poorly. It is very similar to those of active mitochondrial and bacterial F1-ATPases. In the F-ATPase from Geobacillus stearothermophilus, conformational changes in the ε-subunit are influenced by intracellular ATP concentration and membrane potential. When ATP is plentiful, the ε-subunit assumes a "down" state, with an ATP molecule bound to its two C-terminal α-helices; when ATP is scarce, the α-helices are proposed to inhibit ATP hydrolysis by assuming an "up" state, where the α-helices, devoid of ATP, enter the α3β3-catalytic region. However, in the Escherichia coli enzyme, there is no evidence that such ATP binding to the ε-subunit is mechanistically important for modulating the enzyme's hydrolytic activity. In the structure of the F1-ATPase from C. thermarum, ATP and a magnesium ion are bound to the α-helices in the down state. In a form with a mutated ε-subunit unable to bind ATP, the enzyme remains inactive and the ε-subunit is down. Therefore, neither the γ-subunit nor the regulatory ATP bound to the ε-subunit is involved in the inhibitory mechanism of this particular enzyme. The structure of the α3β3-catalytic domain is likewise closely similar to those of active F1-ATPases. However, although the βE-catalytic site is in the usual "open" conformation, it is occupied by the unique combination of an ADP molecule with no magnesium ion and a phosphate ion. These bound hydrolytic products are likely to be the basis of inhibition of ATP hydrolysis.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alphaA, B, C, I, J, K502Caldalkalibacillus thermarum TA2.A1Mutation(s): 0 
Gene Names: atpACathTA2_2809
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for F5LA74 (Caldalkalibacillus thermarum (strain TA2.A1))
Explore F5LA74 
Go to UniProtKB:  F5LA74
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit betaD, E, F, L, M, N462Caldalkalibacillus thermarum TA2.A1Mutation(s): 0 
Gene Names: atpDCathTA2_2807
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for F5LA72 (Caldalkalibacillus thermarum (strain TA2.A1))
Explore F5LA72 
Go to UniProtKB:  F5LA72
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase gamma chainG, O286Caldalkalibacillus thermarum TA2.A1Mutation(s): 0 
Gene Names: atpGCathTA2_2808
Membrane Entity: Yes 
UniProt
Find proteins for F5LA73 (Caldalkalibacillus thermarum (strain TA2.A1))
Explore F5LA73 
Go to UniProtKB:  F5LA73
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase epsilon chainH, P135Caldalkalibacillus thermarum TA2.A1Mutation(s): 0 
Gene Names: atpCCathTA2_2806
Membrane Entity: Yes 
UniProt
Find proteins for F5LA71 (Caldalkalibacillus thermarum (strain TA2.A1))
Explore F5LA71 
Go to UniProtKB:  F5LA71
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
EA [auth H], SA [auth P]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth F] , FA [auth I] , HA [auth J] , JA [auth K] , LA [auth L] , NA [auth M] , PA [auth N] , Q [auth A] , 
BA [auth F], FA [auth I], HA [auth J], JA [auth K], LA [auth L], NA [auth M], PA [auth N], Q [auth A], T [auth B], V [auth C], X [auth D], Z [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth E], OA [auth M]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
S [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth F] , DA [auth G] , GA [auth I] , IA [auth J] , KA [auth K] , MA [auth L] , QA [auth N] , R [auth A] , 
CA [auth F], DA [auth G], GA [auth I], IA [auth J], KA [auth K], MA [auth L], QA [auth N], R [auth A], RA [auth O], U [auth B], W [auth C], Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.82α = 90
b = 130.79β = 107.97
c = 210.39γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU1065663150
Medical Research Council (United Kingdom)United KingdomU105184325
Medical Research Council (United Kingdom)United KingdomMR/M009858/1
James Cook FellowshipNew Zealand--
Health Research CouncilNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-09-28
    Changes: Database references
  • Version 1.2: 2016-10-12
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence