6Q45 | pdb_00006q45

F1-ATPase from Fusobacterium nucleatum

PDB DOI: https://doi.org/10.2210/pdb6Q45/pdb

Classification: HYDROLASE
Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2018-12-05 Released: 2019-07-10
Deposition Author(s): Petri, J., Nakatani, Y., Montgomery, M.G., Ferguson, S.A., Aragao, D., Leslie, A.G.W., Heikal, A., Walker, J.E., Cook, G.M.
Funding Organization(s): Medical Research Council (United Kingdom), Royal Society of New Zealand

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.280 (Depositor), 0.281 (DCC)
R-Value Work:
0.237 (Depositor), 0.238 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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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

PubMed: 31238823 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1098/rsob.190066
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 730.31 kDa
Atom Count: 49,762
Modeled Residue Count: 6,420
Deposited Residue Count: 6,604
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C, I, J A, B, C, I, J, K	500	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: atpA, FN0360 EC: 7.1.2.2 Membrane Entity: Yes
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RGE0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F, L, M D, E, F, L, M, N	462	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: atpD, FN0358 EC: 7.1.2.2 Membrane Entity: Yes
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RGE2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain	G, O	282	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: atpG, FN0359 Membrane Entity: Yes
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RGE1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain	H, P	134	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: atpC, FN0357 Membrane Entity: Yes
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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RGE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth J] SDF format, chain EA [auth K] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C]	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		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain EA [auth K] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain EA [auth K] Focus chain Q [auth A] Focus chain S [auth B] Focus chain U [auth C]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain GA [auth L] SDF format, chain IA [auth N] SDF format, chain W [auth D] SDF format, chain Y [auth F] MOL2 format, chain GA [auth L] MOL2 format, chain IA [auth N] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth F] mmCIF format, chain GA [auth L] mmCIF format, chain IA [auth N] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth F]	GA [auth L], IA [auth N], W [auth D], Y [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain GA [auth L] Focus chain IA [auth N] Focus chain W [auth D] Focus chain Y [auth F] Interactions & Density Focus chain GA [auth L] Focus chain IA [auth N] Focus chain W [auth D] Focus chain Y [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain DA [auth J] SDF format, chain FA [auth K] SDF format, chain HA [auth L] SDF format, chain JA [auth N] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth F] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain HA [auth L] MOL2 format, chain JA [auth N] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain FA [auth K] mmCIF format, chain HA [auth L] mmCIF format, chain JA [auth N] mmCIF format, chain R [auth A] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth F]	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		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain JA [auth N] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain JA [auth N] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.280 (Depositor), 0.281 (DCC)
R-Value Work: 0.237 (Depositor), 0.238 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.94	α = 90
b = 200.209	β = 102.2
c = 201.725	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_U105663150
Medical Research Council (United Kingdom)	United Kingdom	MR/M009858/1
Medical Research Council (United Kingdom)	United Kingdom	MC_U105184325
Royal Society of New Zealand	New Zealand	James 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