[English] 日本語
Yorodumi
- PDB-4tu3: Crystal structure of yeast Sac1/Vps74 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tu3
TitleCrystal structure of yeast Sac1/Vps74 complex
Components
  • Phosphoinositide phosphatase SAC1
  • Vacuolar protein sorting-associated protein 74
KeywordsHYDROLASE/PROTEIN TRANSPORT / Protein Complex / Phosphoric Monoester Hydrolases / Phosphatidylinositol Phosphates / Golgi Apparatus / HYDROLASE-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


phosphatidylinositol-3-phosphatase / Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / regulation of phosphatidylinositol dephosphorylation / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the Golgi membrane / Golgi vesicle budding / serine palmitoyltransferase complex ...phosphatidylinositol-3-phosphatase / Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / regulation of phosphatidylinositol dephosphorylation / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the Golgi membrane / Golgi vesicle budding / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / protein O-linked glycosylation via mannose / Golgi cisterna / protein retention in Golgi apparatus / autophagosome-lysosome fusion / cortical endoplasmic reticulum / phosphatidylinositol dephosphorylation / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / protein N-linked glycosylation / Golgi to plasma membrane protein transport / phosphatidylinositol-4-phosphate binding / Golgi medial cisterna / Golgi cisterna membrane / Golgi organization / endoplasmic reticulum unfolded protein response / trans-Golgi network / mitochondrial outer membrane / Golgi membrane / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / Golgi apparatus / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
yeast vps74-n-term truncation variant fold / yeast vps74-n-term truncation variant domain like / Golgi phosphoprotein 3-like / Golgi phosphoprotein 3-like domain superfamily / Golgi phosphoprotein 3 (GPP34) / SAC domain / SacI homology domain / Sac phosphatase domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol-3-phosphatase SAC1 / Vacuolar protein sorting-associated protein 74
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.187 Å
AuthorsCai, Y. / Horenkamp, F.A. / Reinisch, K.R.
CitationJournal: J.Cell Biol. / Year: 2014
Title: Sac1-Vps74 structure reveals a mechanism to terminate phosphoinositide signaling in the Golgi apparatus.
Authors: Cai, Y. / Deng, Y. / Horenkamp, F. / Reinisch, K.M. / Burd, C.G.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Phosphoinositide phosphatase SAC1
A: Vacuolar protein sorting-associated protein 74


Theoretical massNumber of molelcules
Total (without water)110,5492
Polymers110,5492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.338, 159.338, 143.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Phosphoinositide phosphatase SAC1 / Recessive suppressor of secretory defect


Mass: 71214.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SAC1, RSD1, YKL212W / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P32368, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Protein Vacuolar protein sorting-associated protein 74


Mass: 39334.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VPS74, YDR372C, D9481.15 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q06385

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200mM HEPES at pH 7.0, 35% (v/v) MPD, 0.3M NDSB-195

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.187→29.542 Å / Num. obs: 22586 / % possible obs: 100 % / Redundancy: 9.8 % / Net I/σ(I): 18.8

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZIH, 3LWT

2zih

3lwt


Resolution: 3.187→29.542 Å / Cross valid method: NONE / σ(F): 2.01 / Phase error: 41.04 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2549 2003 8.87 %
Rwork0.226 --
obs0.2289 22586 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.187→29.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5191 0 0 0 5191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025285
X-RAY DIFFRACTIONf_angle_d0.4537174
X-RAY DIFFRACTIONf_dihedral_angle_d9.7471893
X-RAY DIFFRACTIONf_chiral_restr0.031832
X-RAY DIFFRACTIONf_plane_restr0.001923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1884-3.2680.37551390.37211433X-RAY DIFFRACTION88
3.268-3.35620.35511450.36471479X-RAY DIFFRACTION91
3.3562-3.45490.3411450.36161502X-RAY DIFFRACTION91
3.4549-3.56620.39231410.3441451X-RAY DIFFRACTION91
3.5662-3.69340.30251460.3231479X-RAY DIFFRACTION91
3.6934-3.84090.33661410.31531451X-RAY DIFFRACTION91
3.8409-4.01530.32851460.29721492X-RAY DIFFRACTION91
4.0153-4.22640.29061400.28381436X-RAY DIFFRACTION91
4.2264-4.49030.2841460.2551499X-RAY DIFFRACTION91
4.4903-4.83550.23031420.22211462X-RAY DIFFRACTION91
4.8355-5.31940.26311430.22561475X-RAY DIFFRACTION91
5.3194-6.0830.26481440.22681486X-RAY DIFFRACTION91
6.083-7.64050.23181420.20221454X-RAY DIFFRACTION91
7.6405-28.96090.17411430.12811475X-RAY DIFFRACTION91

+
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