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- PDB-1ho8: CRYSTAL STRUCTURE OF THE REGULATORY SUBUNIT H OF THE V-TYPE ATPAS... -

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Basic information

Entry
Database: PDB / ID: 1ho8
TitleCRYSTAL STRUCTURE OF THE REGULATORY SUBUNIT H OF THE V-TYPE ATPASE OF SACCHAROMYCES CEREVISIAE
ComponentsVACUOLAR ATP SYNTHASE SUBUNIT H
KeywordsHYDROLASE / HEAT repeat
Function / homology
Function and homology information


Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / Golgi membrane
Similarity search - Function
V-type ATPase, subunit H, C-terminal domain / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical ...V-type ATPase, subunit H, C-terminal domain / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
V-type proton ATPase subunit H
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, MAD / Resolution: 2.95 Å
AuthorsSagermann, M. / Stevens, T.H. / Matthews, B.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae.
Authors: Sagermann, M. / Stevens, T.H. / Matthews, B.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Cloning, expression and crystallization of VMA13p, an essential subunit of the vacuolar H+-ATPase of Saccharomyces cerevisiae.
Authors: Sagermann, M. / Matthews, B.W.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: VMA13 encodes a 54-kDa vacuolar H(+)-ATPase subunit required for activity but not assembly of the enzyme complex in Saccharomyces cerevisiae.
Authors: Ho, M.N. / Hirata, R. / Umemoto, N. / Ohya, Y. / Takatsuki, A. / Stevens, T.H. / Anraku, Y.
History
DepositionDec 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 22, 2020Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / pdbx_database_status / software / struct_ref_seq_dif
Item: _diffrn.ambient_pressure / _diffrn.ambient_temp ..._diffrn.ambient_pressure / _diffrn.ambient_temp / _diffrn_radiation.pdbx_wavelength_list / _pdbx_database_status.status_code_sf / _software.name / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 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
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VACUOLAR ATP SYNTHASE SUBUNIT H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7232
Polymers54,6271
Non-polymers961
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.342, 117.342, 119.873
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein VACUOLAR ATP SYNTHASE SUBUNIT H / VMA13 / V-ATPASE H SUBUNIT / VACUOLAR PROTON PUMP H SUBUNIT / V-ATPASE 54 KDA SUBUNIT


Mass: 54626.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41807, EC: 3.6.1.34
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 4.36 Å3/Da / Density % sol: 71.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, Dithiothreitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Sagermann, M., (2000) Acta Crystallogr., Sect.D, 56, 475.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
2100 mM1dropNaCl
31 mMEDTA1drop
41 mMdithiothreitol1drop
510 mg/mlprotein1drop
750 mMTris-HCl1reservoir
85 mMdithiothreitol1reservoir
6ammonium sulfate1reservoir

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Data collection

DiffractionAmbient pressure: 101 kPa / Mean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2000
RadiationMonochromator: Double-Crystal Si 111 crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.979 Å
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→71 Å / Num. all: 20090 / Num. obs: 20090 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.4
Reflection shellResolution: 2.95→3.3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 1.7 / Num. unique all: 5733 / Rsym value: 45.4 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 87426

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Processing

Software
NameVersionClassification
MLPHAREphasing
SHARPphasing
TNTrefinement
MOSFLMdata reduction
SCALA(SCALA)data scaling
RefinementMethod to determine structure: SIR, MAD
Starting model: vma13 poly alanine

Resolution: 2.95→71 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: REFINEMENT AS IMPLEMENTED IN TNT. RESIDUES 54-70 AND 224- 236 WERE NOT MODELED DUE TO DISORDER. RESIDUES 408-415 AND 455-459 WERE PARTIALLY VISIBLE IN THE ELECTRON DENSITY AND REFINED TO HIGH B VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1624 8 %RANDOM
Rwork0.221 ---
all0.223 20130 --
obs0.223 20090 99.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.39 Å27.39 Å20 Å2
2--7.39 Å20 Å2
3----14.78 Å2
Refinement stepCycle: LAST / Resolution: 2.95→71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 5 25 3638
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d22.39
LS refinement shellResolution: 2.95→71 Å
RfactorNum. reflection% reflection
Rfree0.312 1624 -
Rwork0.221 --
obs-20090 99.8 %
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8 % / Rfactor all: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg22.39

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