[English] 日本語
Yorodumi
- PDB-3fks: Yeast F1 ATPase in the absence of bound nucleotides -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fks
TitleYeast F1 ATPase in the absence of bound nucleotides
Components(ATP synthase subunit ...) x 5
KeywordsHYDROLASE / ATP synthase / ATP phosphatase / F1F0 ATPase / ATP synthesis / ATP-binding / CF(1) / Hydrogen ion transport / Ion transport / Membrane / Mitochondrion / Mitochondrion inner membrane / Nucleotide-binding / Phosphoprotein / Transport
Function / homology
Function and homology information


Mitochondrial protein degradation / proton motive force-driven ATP synthesis / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space ...Mitochondrial protein degradation / proton motive force-driven ATP synthesis / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 ...ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / 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 / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, alpha subunit nucleotide-binding domain / 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 alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / 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. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / 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 / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit delta, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.587 Å
AuthorsKabaleeswaran, V. / Symersky, J. / Shen, H. / Walker, J.E. / Leslie, A.G.W. / Mueller, D.M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Asymmetric structure of the yeast f1 ATPase in the absence of bound nucleotides.
Authors: Kabaleeswaran, V. / Shen, H. / Symersky, J. / Walker, J.E. / Leslie, A.G. / Mueller, D.M.
History
DepositionDec 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
D: ATP synthase subunit beta, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
H: ATP synthase subunit delta, mitochondrial
I: ATP synthase subunit epsilon, mitochondrial
J: ATP synthase subunit alpha, mitochondrial
K: ATP synthase subunit alpha, mitochondrial
L: ATP synthase subunit alpha, mitochondrial
M: ATP synthase subunit beta, mitochondrial
N: ATP synthase subunit beta, mitochondrial
O: ATP synthase subunit beta, mitochondrial
P: ATP synthase subunit gamma, mitochondrial
Q: ATP synthase subunit delta, mitochondrial
R: ATP synthase subunit epsilon, mitochondrial
S: ATP synthase subunit alpha, mitochondrial
T: ATP synthase subunit alpha, mitochondrial
U: ATP synthase subunit alpha, mitochondrial
V: ATP synthase subunit beta, mitochondrial
W: ATP synthase subunit beta, mitochondrial
X: ATP synthase subunit beta, mitochondrial
Y: ATP synthase subunit gamma, mitochondrial
Z: ATP synthase subunit delta, mitochondrial
1: ATP synthase subunit epsilon, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,120,10442
Polymers1,118,67927
Non-polymers1,42515
Water00
1
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
D: ATP synthase subunit beta, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
H: ATP synthase subunit delta, mitochondrial
I: ATP synthase subunit epsilon, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,36814
Polymers372,8939
Non-polymers4755
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38230 Å2
ΔGint-151.1 kcal/mol
Surface area118930 Å2
MethodPISA
2
J: ATP synthase subunit alpha, mitochondrial
K: ATP synthase subunit alpha, mitochondrial
L: ATP synthase subunit alpha, mitochondrial
M: ATP synthase subunit beta, mitochondrial
N: ATP synthase subunit beta, mitochondrial
O: ATP synthase subunit beta, mitochondrial
P: ATP synthase subunit gamma, mitochondrial
Q: ATP synthase subunit delta, mitochondrial
R: ATP synthase subunit epsilon, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,46315
Polymers372,8939
Non-polymers5706
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33710 Å2
ΔGint-126.4 kcal/mol
Surface area110420 Å2
MethodPISA
3
S: ATP synthase subunit alpha, mitochondrial
T: ATP synthase subunit alpha, mitochondrial
U: ATP synthase subunit alpha, mitochondrial
V: ATP synthase subunit beta, mitochondrial
W: ATP synthase subunit beta, mitochondrial
X: ATP synthase subunit beta, mitochondrial
Y: ATP synthase subunit gamma, mitochondrial
Z: ATP synthase subunit delta, mitochondrial
1: ATP synthase subunit epsilon, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,27313
Polymers372,8939
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31620 Å2
ΔGint-110.9 kcal/mol
Surface area112700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.934, 290.487, 188.700
Angle α, β, γ (deg.)90.00, 101.75, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological unit 1: Chains A,B,C,D,E,F,G,H,I. Biological unit 2: Chains J,K,L,M,N,O,P,Q,R. Biological unit 3: Chains S,T,U,V,W,X,Y,Z,1

-
Components

-
ATP synthase subunit ... , 5 types, 27 molecules ABCJKLSTUDEFMNOVWXGPYHQZIR1

#1: Protein
ATP synthase subunit alpha, mitochondrial


Mass: 55007.402 Da / Num. of mol.: 9 / Fragment: UNP residues 36-545 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: mitochondria
References: UniProt: P07251, H+-transporting two-sector ATPase
#2: Protein
ATP synthase subunit beta, mitochondrial


Mass: 52009.965 Da / Num. of mol.: 9 / Fragment: UNP residues 34-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Tissue fraction: mitochondria / Gene: ATP2, J2041, YJR121W / Plasmid: PRS314 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Tissue fraction (production host): mitochondria
References: UniProt: P00830, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit gamma, mitochondrial


Mass: 30657.160 Da / Num. of mol.: 3 / Fragment: UNP residues 34-311 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: mitochondria
References: UniProt: P38077, H+-transporting two-sector ATPase
#4: Protein ATP synthase subunit delta, mitochondrial


Mass: 14565.385 Da / Num. of mol.: 3 / Fragment: UNP residues 23-160 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: mitochondria
References: UniProt: Q12165, H+-transporting two-sector ATPase
#5: Protein ATP synthase subunit epsilon, mitochondrial


Mass: 6618.359 Da / Num. of mol.: 3 / Fragment: UNP residues 2-62 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: mitochondria
References: UniProt: P21306, H+-transporting two-sector ATPase

-
Non-polymers , 1 types, 15 molecules

#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 6.25% PEG 6000, 10% Glycerol, 4% Methanol, 0.05M Sodium acetate, 0.5mM Nickel sulfate, 2 mM Sodium pyrophosphate, 2mM Magnesium chloride, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.587→50 Å / Num. all: 134821 / Num. obs: 134821 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 2.8 % / Biso Wilson estimate: 111.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9
Reflection shellResolution: 3.587→3.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.6 / % possible all: 98

-
Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
PHENIXrefinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1W0J

1w0j


Resolution: 3.587→33.203 Å / SU ML: 0.64 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3062 2727 2.02 %RANDOM
Rwork0.2422 ---
obs0.2435 134790 98.11 %-
all-134821 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.599 Å2 / ksol: 0.28 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.0236 Å20 Å2-4.5563 Å2
2--2.5638 Å20 Å2
3----8.5874 Å2
Refinement stepCycle: LAST / Resolution: 3.587→33.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms71719 0 75 0 71794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.8
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.587-3.65220.42091460.35185711X-RAY DIFFRACTION81
3.6522-3.72230.40581260.33327121X-RAY DIFFRACTION100
3.7223-3.79820.3931360.3147016X-RAY DIFFRACTION100
3.7982-3.88060.35221640.29717047X-RAY DIFFRACTION100
3.8806-3.97080.35591360.28227097X-RAY DIFFRACTION100
3.9708-4.06990.36451420.28727063X-RAY DIFFRACTION100
4.0699-4.17970.34561270.26927070X-RAY DIFFRACTION100
4.1797-4.30250.28681460.25957067X-RAY DIFFRACTION100
4.3025-4.4410.29051580.24057028X-RAY DIFFRACTION100
4.441-4.59940.2991280.23957086X-RAY DIFFRACTION100
4.5994-4.7830.30361360.24177048X-RAY DIFFRACTION100
4.783-50.31861600.2317053X-RAY DIFFRACTION100
5-5.26260.30211540.23557050X-RAY DIFFRACTION100
5.2626-5.59090.31061510.23837057X-RAY DIFFRACTION99
5.5909-6.02020.32591290.23297026X-RAY DIFFRACTION99
6.0202-6.62170.33081570.2337043X-RAY DIFFRACTION99
6.6217-7.570.28691500.2026965X-RAY DIFFRACTION98
7.57-9.50020.22481490.1636953X-RAY DIFFRACTION98
9.5002-33.20460.23151320.19566562X-RAY DIFFRACTION91

+
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