[English] 日本語
Yorodumi
- PDB-1ho8: CRYSTAL STRUCTURE OF THE REGULATORY SUBUNIT H OF THE V-TYPE ATPAS... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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