6Q45

F1-ATPase from Fusobacterium nucleatum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of F1-ATPase from the obligate anaerobe Fusobacterium nucleatum.

Petri, J.Nakatani, Y.Montgomery, M.G.Ferguson, S.A.Aragao, D.Leslie, A.G.W.Heikal, A.Walker, J.E.Cook, G.M.

(2019) Open Biol 9: 190066-190066

  • DOI: https://doi.org/10.1098/rsob.190066
  • Primary Citation of Related Structures:  
    6Q45

  • PubMed Abstract: 

    The crystal structure of the F 1 -catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from the pathogenic anaerobic bacterium Fusobacterium nucleatum. The enzyme can hydrolyse ATP but is partially inhibited. The structure is similar to those of the F 1 -ATPases from Caldalkalibacillus thermarum, which is more strongly inhibited in ATP hydrolysis, and in Mycobacterium smegmatis, which has a very low ATP hydrolytic activity. The β E -subunits in all three enzymes are in the conventional 'open' state, and in the case of C. thermarum and M. smegmatis, they are occupied by an ADP and phosphate (or sulfate), but in F. nucleatum, the occupancy by ADP appears to be partial. It is likely that the hydrolytic activity of the F. nucleatum enzyme is regulated by the concentration of ADP, as in mitochondria.


  • Organizational Affiliation

    1 Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago , Dunedin 9054 , New Zealand.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C, I, J
A, B, C, I, J, K
500Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: atpAFN0360
UniProt
Find proteins for Q8RGE0 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355))
Explore Q8RGE0 
Go to UniProtKB:  Q8RGE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RGE0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F, L, M
D, E, F, L, M, N
462Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: atpDFN0358
UniProt
Find proteins for Q8RGE2 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355))
Explore Q8RGE2 
Go to UniProtKB:  Q8RGE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RGE2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chain
G, O
282Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: atpGFN0359
UniProt
Find proteins for Q8RGE1 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355))
Explore Q8RGE1 
Go to UniProtKB:  Q8RGE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RGE1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain
H, P
134Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: atpCFN0357
UniProt
Find proteins for Q8RGE3 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355))
Explore Q8RGE3 
Go to UniProtKB:  Q8RGE3
Entity Groups  
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UniProt GroupQ8RGE3
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth I]
CA [auth J]
EA [auth K]
Q [auth A]
S [auth B]
AA [auth I],
CA [auth J],
EA [auth K],
Q [auth A],
S [auth B],
U [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
GA [auth L],
IA [auth N],
W [auth D],
Y [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth I]
DA [auth J]
FA [auth K]
HA [auth L]
JA [auth N]
BA [auth I],
DA [auth J],
FA [auth K],
HA [auth L],
JA [auth N],
R [auth A],
T [auth B],
V [auth C],
X [auth D],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.94α = 90
b = 200.209β = 102.2
c = 201.725γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105663150
Medical Research Council (United Kingdom)United KingdomMR/M009858/1
Medical Research Council (United Kingdom)United KingdomMC_U105184325
Royal Society of New ZealandNew ZealandJames Cook Fellowship

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description