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- PDB-3w3a: Crystal structure of V1-ATPase at 3.9 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3w3a
TitleCrystal structure of V1-ATPase at 3.9 angstrom resolution
Components
  • V-type ATP synthase alpha chain
  • V-type ATP synthase beta chain
  • V-type ATP synthase subunit D
  • V-type ATP synthase subunit F
KeywordsHYDROLASE / ATP SYNTHESIS / HYDROGEN ION TRANSPORT / NUCLEOTIDE-BINDING / Catalytic Domain / Molecular Motor Proteins / Quaternary / Proton-Translocating ATPases / Thermus thermophilus / Vacuolar Proton-Translocating ATPases / Hydrolysis
Function / homology
Function and homology information


vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lysosomal membrane / ATP binding
Similarity search - Function
Helix Hairpins - #3240 / ATPase, V1 complex, subunit F / Rossmann fold - #12240 / ATPase, V1 complex, subunit F, bacterial/archaeal / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D ...Helix Hairpins - #3240 / ATPase, V1 complex, subunit F / Rossmann fold - #12240 / ATPase, V1 complex, subunit F, bacterial/archaeal / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / 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 / V-type ATP synthase subunit D / V-type ATP synthase subunit F / V-type ATP synthase alpha chain / V-type ATP synthase beta chain
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.9 Å
AuthorsNagamatsu, Y. / Takeda, K. / Kuranaga, T. / Numoto, N. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Origin of Asymmetry at the Intersubunit Interfaces of V1-ATPase from Thermusthermophilus
Authors: Nagamatsu, Y. / Takeda, K. / Kuranaga, T. / Numoto, N. / Miki, K.
History
DepositionDec 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: V-type ATP synthase alpha chain
B: V-type ATP synthase alpha chain
C: V-type ATP synthase alpha chain
D: V-type ATP synthase beta chain
E: V-type ATP synthase beta chain
F: V-type ATP synthase beta chain
G: V-type ATP synthase subunit D
H: V-type ATP synthase subunit F
I: V-type ATP synthase alpha chain
J: V-type ATP synthase alpha chain
K: V-type ATP synthase alpha chain
L: V-type ATP synthase beta chain
M: V-type ATP synthase beta chain
N: V-type ATP synthase beta chain
O: V-type ATP synthase subunit D
P: V-type ATP synthase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)756,93720
Polymers755,22816
Non-polymers1,7094
Water00
1
A: V-type ATP synthase alpha chain
B: V-type ATP synthase alpha chain
C: V-type ATP synthase alpha chain
D: V-type ATP synthase beta chain
E: V-type ATP synthase beta chain
F: V-type ATP synthase beta chain
G: V-type ATP synthase subunit D
H: V-type ATP synthase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,46910
Polymers377,6148
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: V-type ATP synthase alpha chain
J: V-type ATP synthase alpha chain
K: V-type ATP synthase alpha chain
L: V-type ATP synthase beta chain
M: V-type ATP synthase beta chain
N: V-type ATP synthase beta chain
O: V-type ATP synthase subunit D
P: V-type ATP synthase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,46910
Polymers377,6148
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: V-type ATP synthase alpha chain
B: V-type ATP synthase alpha chain
C: V-type ATP synthase alpha chain
D: V-type ATP synthase beta chain
E: V-type ATP synthase beta chain
F: V-type ATP synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,2938
Polymers343,4396
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29960 Å2
ΔGint-71 kcal/mol
Surface area115650 Å2
MethodPISA
4
G: V-type ATP synthase subunit D
H: V-type ATP synthase subunit F


Theoretical massNumber of molelcules
Total (without water)34,1752
Polymers34,1752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-23 kcal/mol
Surface area19720 Å2
MethodPISA
5
I: V-type ATP synthase alpha chain
J: V-type ATP synthase alpha chain
K: V-type ATP synthase alpha chain
L: V-type ATP synthase beta chain
M: V-type ATP synthase beta chain
N: V-type ATP synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,2938
Polymers343,4396
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30070 Å2
ΔGint-75 kcal/mol
Surface area115660 Å2
MethodPISA
6
O: V-type ATP synthase subunit D
P: V-type ATP synthase subunit F


Theoretical massNumber of molelcules
Total (without water)34,1752
Polymers34,1752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-23 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)382.144, 382.144, 148.248
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
V-type ATP synthase alpha chain / V-ATPase subunit A


Mass: 63628.902 Da / Num. of mol.: 6 / Fragment: SUBUNIT A / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
References: UniProt: Q56403, H+-transporting two-sector ATPase
#2: Protein
V-type ATP synthase beta chain / V-ATPase subunit B


Mass: 50850.738 Da / Num. of mol.: 6 / Fragment: SUBUNIT B / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
References: UniProt: Q56404, H+-transporting two-sector ATPase
#3: Protein V-type ATP synthase subunit D / V-ATPase subunit D


Mass: 23350.973 Da / Num. of mol.: 2 / Fragment: SUBUNIT D / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
References: UniProt: O87880, H+-transporting two-sector ATPase
#4: Protein V-type ATP synthase subunit F / V-ATPase subunit F


Mass: 10824.321 Da / Num. of mol.: 2 / Fragment: SUBUNIT F / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579
References: UniProt: P74903, H+-transporting two-sector ATPase
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6M ammonium sulfate, 10%(v/v) dioxane, 100mM MES(pH 6.0), 10mM ADP, 10mM magnesium chloride, 1.0mM alminum nitrate, 1.0mM potassium fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. all: 101564 / Num. obs: 101564 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.097 / Net I/σ(I): 12.4
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 12.4 / Num. unique all: 101564 / Rsym value: 0.097 / % possible all: 90.3

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.9→49.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 160446.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.381 5124 5 %RANDOM
Rwork0.328 ---
obs0.328 101522 90.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 1213.96 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.68 Å20 Å20 Å2
2--9.68 Å20 Å2
3----19.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.95 Å0.83 Å
Luzzati d res low-5 Å
Luzzati sigma a1.21 Å1.05 Å
Refinement stepCycle: LAST / Resolution: 3.9→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53116 0 108 0 53224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.47
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it10.581.5
X-RAY DIFFRACTIONc_mcangle_it17.972
X-RAY DIFFRACTIONc_scbond_it220.352
X-RAY DIFFRACTIONc_scangle_it245.142.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.9→4.04 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.476 770 5.1 %
Rwork0.451 14295 -
obs--81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6new_toadp

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