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- PDB-3a5c: Inter-subunit interaction and quaternary rearrangement defined by... -

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Basic information

Entry
Database: PDB / ID: 3a5c
TitleInter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase
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 / V-ATPase / asymmetric / rotation / vacuolar type / ATP synthesis / ATP-binding / Hydrogen ion transport / Ion transport / Nucleotide-binding / Transport
Function / homology
Function and homology information


plant-type vacuole / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / fungal-type vacuole membrane / 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 ...plant-type vacuole / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / fungal-type vacuole membrane / 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
ATPase, V1 complex, subunit F, bacterial/archaeal / 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 ...ATPase, V1 complex, subunit F, bacterial/archaeal / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
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 / FOURIER SYNTHESIS / Resolution: 4.51 Å
AuthorsNumoto, N. / Hasegawa, Y. / Takeda, K. / Miki, K.
CitationJournal: Embo Rep. / Year: 2009
Title: Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase
Authors: Numoto, N. / Hasegawa, Y. / Takeda, K. / Miki, K.
History
DepositionAug 6, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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

Downloads & links

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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)775,24720
Polymers773,53816
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)387,62310
Polymers386,7698
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)387,62310
Polymers386,7698
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)381.578, 381.578, 147.672
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-type ATPase subunit A


Mass: 63699.980 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56403, H+-transporting two-sector ATPase
#2: Protein
V-type ATP synthase beta chain / V-type ATPase subunit B


Mass: 53219.500 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q56404, H+-transporting two-sector ATPase
#3: Protein V-type ATP synthase subunit D / V-type ATPase subunit D


Mass: 24715.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: O87880, H+-transporting two-sector ATPase
#4: Protein V-type ATP synthase subunit F / V-type ATPase subunit F


Mass: 11294.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
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: 1

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Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6M ammonium sulfate, 0.1M MES-NaOH (pH6.0), 10% dioxane, 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
DetectorDate: Mar 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 70598 / % possible obs: 96.9 % / Redundancy: 5.1 % / Rsym value: 0.087 / Net I/σ(I): 10.3
Reflection shellResolution: 4.5→4.66 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 6683 / Rsym value: 0.417 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3A5D

3a5d


Resolution: 4.51→29.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 11832712.93 / Data cutoff low absF: 0 / Isotropic thermal model: DOMAIN / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED, REFINEMENTS WERE PERFORMED BY THE RIGID BODY AND B-DOMAIN REFINEMENTS. THE DOMAIN DEFINITIONS WERE SET TO FOUR DOMAINS IN THE A SUBUNIT (AI: RESIDUES 1-70; AII: 71- ...Details: BULK SOLVENT MODEL USED, REFINEMENTS WERE PERFORMED BY THE RIGID BODY AND B-DOMAIN REFINEMENTS. THE DOMAIN DEFINITIONS WERE SET TO FOUR DOMAINS IN THE A SUBUNIT (AI: RESIDUES 1-70; AII: 71-198; AIII; 199-429; AIV: 430-577), THREE IN THE B SUBUNIT (BI: 7-80; BII: 81-359; BIII; 360-463), TWO IN THE D SUBUNIT (DI: 1-55 AND DII: 132-205), AND TWO REGIONS OF F (FI: 1-75 AND FII: 76-104), RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.437 3589 5.1 %RANDOM
Rwork0.429 ---
obs-70375 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 160.757 Å2 / ksol: 0.1 e/Å3
Displacement parametersBiso mean: 142.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.094 Å20 Å20 Å2
2---2.094 Å20 Å2
3---4.187 Å2
Refine analyze
FreeObs
Luzzati coordinate error1 Å0.97 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.96 Å
Refinement stepCycle: LAST / Resolution: 4.51→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32080 0 108 0 32188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
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_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.31
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4.5→4.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.494 308 4.8 %
Rwork0.483 6057 -
obs-6365 88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2adp_xplor_paramadp_xplor_top

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