[English] 日本語
Yorodumi
- PDB-6q45: F1-ATPase from Fusobacterium nucleatum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q45
TitleF1-ATPase from Fusobacterium nucleatum
Components(ATP synthase ...) x 4
KeywordsHYDROLASE / Complex / Fusobacterium / ATPase
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP binding / plasma membrane
Similarity search - Function
ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal ...ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsPetri, J. / Nakatani, Y. / Montgomery, M.G. / Ferguson, S.A. / Aragao, D. / Leslie, A.G.W. / Heikal, A. / Walker, J.E. / Cook, G.M.
Funding support United Kingdom, New Zealand, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105663150 United Kingdom
Medical Research Council (United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (United Kingdom)MC_U105184325 United Kingdom
Royal Society of New ZealandJames Cook Fellowship New Zealand
CitationJournal: Open Biology / Year: 2019
Title: Structure of F1-ATPase from the obligate anaerobe Fusobacterium nucleatum.
Authors: Petri, J. / Nakatani, Y. / Montgomery, M.G. / Ferguson, S.A. / Aragao, D. / Leslie, A.G.W. / Heikal, A. / Walker, J.E. / Cook, G.M.
History
DepositionDec 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
I: ATP synthase subunit alpha
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit beta
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase gamma chain
P: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)730,30936
Polymers725,31416
Non-polymers4,99520
Water61334
1
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,15518
Polymers362,6578
Non-polymers2,49710
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: ATP synthase subunit alpha
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit beta
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase gamma chain
P: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,15518
Polymers362,6578
Non-polymers2,49710
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.940, 200.209, 201.725
Angle α, β, γ (deg.)90.000, 102.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21I
12B
22J
13C
23K
14D
24L
15E
25M
16F
26N
17G
27O

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A25 - 500
2111I25 - 500
1121B26 - 500
2121J26 - 500
1131C27 - 114
2131K27 - 114
1231C140 - 500
2231K140 - 500
1141D1 - 95
2141L1 - 95
1241D125 - 461
2241L125 - 461
1151E1 - 78
2151M1 - 78
1251E109 - 460
2251M109 - 460
1161F1 - 460
2161N1 - 460
1171G3 - 131
2171O3 - 131
1271G151 - 197
2271O151 - 197
1371G221 - 282
2371O221 - 282

NCS ensembles :
ID
1
2
3
4
5
6
7

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.249169, 0.060766, 0.966552), (0.093099, -0.99491, 0.038548), (0.963975, 0.08038, -0.253558)34.279629, -16.012581, 97.568298
3given(1), (1), (1)
4given(0.257499, 0.075214, 0.963347), (0.093264, -0.994246, 0.052697), (0.961767, 0.076277, -0.263032)34.49947, -16.26795, 97.832207
5given(1), (1), (1)
6given(0.271445, 0.071063, 0.959827), (0.093345, -0.994513, 0.047233), (0.957917, 0.076773, -0.276589)34.776161, -16.160179, 97.835121
7given(1), (1), (1)
8given(0.2605, 0.068346, 0.963052), (0.085095, -0.995235, 0.047612), (0.961716, 0.069548, -0.265075)34.513279, -16.32818, 97.793343
9given(1), (1), (1)
10given(0.270455, 0.090436, 0.958476), (0.085863, -0.993877, 0.069548), (0.958896, 0.063488, -0.276564)35.083569, -16.41407, 97.402496
11given(1), (1), (1)
12given(0.274981, 0.077875, 0.958291), (0.09686, -0.993887, 0.052973), (0.956558, 0.078254, -0.280843)34.885609, -16.31321, 97.919167
13given(1), (1), (1)
14given(0.319102, -0.077033, 0.944584), (-0.055367, -0.996504, -0.062563), (0.946102, -0.032334, -0.322252)36.67223, -18.371361, 98.818657

-
Components

-
ATP synthase ... , 4 types, 16 molecules ABCIJKDEFLMNGOHP

#1: Protein
ATP synthase subunit alpha / / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 54834.941 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: atpA, FN0360 / Production host: Escherichia coli (E. coli) / Strain (production host): DK8 / References: UniProt: Q8RGE0
#2: Protein
ATP synthase subunit beta / / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 50274.090 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: atpD, FN0358 / Production host: Escherichia coli (E. coli) / Strain (production host): DK8 / References: UniProt: Q8RGE2
#3: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 32174.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: atpG, FN0359 / Production host: Escherichia coli (E. coli) / Strain (production host): DK8 / References: UniProt: Q8RGE1
#4: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 15155.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: atpC, FN0357 / Production host: Escherichia coli (E. coli) / Strain (production host): DK8 / References: UniProt: Q8RGE3

-
Non-polymers , 4 types, 54 molecules

#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1 ul protein to 0.8ul 100 mM sodium citrate, pH 6.0, 100 mM magnesium acetate and 15.5% [w/v] polyethylene glycol 5000 monomethyl ether and 0.2 ul low melting point agarose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.6→49.29 Å / Num. obs: 97166 / % possible obs: 97 % / Redundancy: 6.1 % / CC1/2: 0.983 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.09 / Rrim(I) all: 0.229 / Net I/σ(I): 6.4 / Num. measured all: 592580 / Scaling rejects: 400
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.6-3.664.41.0552035646460.5510.5551.21.594.6
19.73-49.296.30.10935835700.9830.0430.11715.588.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ik2

5ik2


Resolution: 3.6→49.34 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.861 / WRfactor Rfree: 0.2679 / WRfactor Rwork: 0.2217 / FOM work R set: 0.752 / SU B: 49.839 / SU ML: 0.685 / SU Rfree: 0.76 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.76 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 4871 5 %RANDOM
Rwork0.2374 ---
obs0.2395 92550 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 250.97 Å2 / Biso mean: 110.303 Å2 / Biso min: 48.92 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å2-0 Å23.82 Å2
2---4.7 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 3.6→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49424 0 304 34 49762
Biso mean--84.43 77.93 -
Num. residues----6420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01450524
X-RAY DIFFRACTIONr_bond_other_d0.0010.01747401
X-RAY DIFFRACTIONr_angle_refined_deg0.7591.66568333
X-RAY DIFFRACTIONr_angle_other_deg0.6581.637111069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12956401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45723.0672445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.748159198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.99415300
X-RAY DIFFRACTIONr_chiral_restr0.0290.26840
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0256200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028522
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A712225.97
2B704224.59
3C65678.74
4D643016.8
5E641936.55
6F687410.99
7G370013.82
LS refinement shellResolution: 3.6→3.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 397 -
Rwork0.363 6723 -
all-7120 -
obs--96.29 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more