5IK2 | pdb_00005ik2

Caldalaklibacillus thermarum F1-ATPase (epsilon mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1073/pnas.1612035113
  • Primary Citation 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. 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;

Macromolecule Content 

  • Total Structure Weight: 715.81 kDa 
  • Atom Count: 51,018 
  • Modeled Residue Count: 6,445 
  • Deposited Residue Count: 6,484 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C, I, J
A, B, C, I, J, K
479Caldalkalibacillus 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5LA74
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F, L, M
D, E, F, L, M, N
462Caldalkalibacillus 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5LA72
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase gamma chain
G, O
285Caldalkalibacillus 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5LA73
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain
H, P
134Caldalkalibacillus thermarum TA2.A1Mutation(s): 2 
Gene Names: atpCCathTA2_2806
Membrane Entity: Yes 
UniProt
Find proteins for F5LA71 (Caldalkalibacillus thermarum (strain TA2.A1))
Explore F5LA71 
Go to UniProtKB:  F5LA71
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5LA71
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
AB [auth N]
BA [auth E]
GA [auth F]
JA [auth I]
MA [auth J]
AB [auth N],
BA [auth E],
GA [auth F],
JA [auth I],
MA [auth J],
PA [auth K],
Q [auth A],
SA [auth L],
T [auth B],
UA [auth M],
W [auth C],
Z [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
CA [auth E],
VA [auth M]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
CB [auth N]
DA [auth E]
DB [auth N]
EA [auth E]
FA [auth E]
CB [auth N],
DA [auth E],
DB [auth N],
EA [auth E],
FA [auth E],
IA [auth F],
LA [auth I],
OA [auth J],
RA [auth K],
S [auth A],
V [auth B],
WA [auth M],
XA [auth M],
Y [auth C],
YA [auth M],
ZA [auth M]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth D]
BB [auth N]
HA [auth F]
KA [auth I]
NA [auth J]
AA [auth D],
BB [auth N],
HA [auth F],
KA [auth I],
NA [auth J],
QA [auth K],
R [auth A],
TA [auth L],
U [auth B],
X [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.24α = 90
b = 131.29β = 108.2
c = 212.01γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description