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- PDB-3fks: Yeast F1 ATPase in the absence of bound nucleotides -

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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 proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial 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 ...mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial 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 / 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 / Pyruvate Kinase; Chain: A, domain 1 / 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, 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, 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
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

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Components

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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: mitochondriaMitochondrion
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: mitochondriaMitochondrion
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: mitochondriaMitochondrion
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: mitochondriaMitochondrion
References: UniProt: P21306, H+-transporting two-sector ATPase

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Non-polymers , 1 types, 15 molecules

#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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

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Experimental details

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Experiment

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

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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

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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

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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

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