[English] 日本語
Yorodumi
- PDB-1yxr: NMR Structure of VPS4A MIT Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yxr
TitleNMR Structure of VPS4A MIT Domain
Componentsvacuolar protein sorting factor 4AVacuole
KeywordsPROTEIN TRAFFICKING / VPS4 / MIT domain
Function / homology
Function and homology information


vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / endosomal vesicle fusion / mitotic cytokinesis checkpoint signaling / positive regulation of viral budding via host ESCRT complex / negative regulation of cytokinesis / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / late endosome to lysosome transport via multivesicular body sorting pathway / intracellular cholesterol transport ...vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / endosomal vesicle fusion / mitotic cytokinesis checkpoint signaling / positive regulation of viral budding via host ESCRT complex / negative regulation of cytokinesis / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / late endosome to lysosome transport via multivesicular body sorting pathway / intracellular cholesterol transport / abscission / ESCRT III complex disassembly / nuclear envelope organization / late endosomal microautophagy / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / ATP-dependent protein disaggregase activity / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / protein targeting to lysosome / multivesicular body sorting pathway / vesicle budding from membrane / vacuole organization / membrane fission / plasma membrane repair / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / vesicle-fusing ATPase / Flemming body / vacuolar membrane / endosomal transport / mitotic metaphase chromosome alignment / ATPase complex / nucleus organization / viral budding via host ESCRT complex / autophagosome maturation / viral release from host cell / regulation of protein localization to plasma membrane / nuclear pore / vesicle-mediated transport / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Budding and maturation of HIV virion / autophagy / spindle pole / regulation of protein localization / late endosome / protein transport / late endosome membrane / midbody / lysosome / early endosome / endosome membrane / endosome / cell division / centrosome / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / automated NOE assignment using CYANA, torsion angle dynamics for structure calculations
AuthorsScott, J.A. / Gaspar, J. / Stuchell, M. / Alam, S. / Skalicky, J. / Sundquist, W.I.
CitationJournal: To be Published
Title: NMR Structure of VPS4A MIT Domain
Authors: Scott, J.A. / Gaspar, J. / Stuchell, M. / Alam, S. / Skalicky, J. / Sundquist, W.I.
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: vacuolar protein sorting factor 4A


Theoretical massNumber of molelcules
Total (without water)9,0561
Polymers9,0561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #18lowest energy

-
Components

#1: Protein vacuolar protein sorting factor 4A / Vacuole / VPS4A / SKD1 protein


Mass: 9056.336 Da / Num. of mol.: 1 / Fragment: MIT Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: pET16b reengineered to contain a TEV cleavage site in place of the normal factor Xa site
Gene: 27183 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UN37

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques

-
Sample preparation

DetailsContents: Uniform labeling with 15N and 13C. / Solvent system: 50 mM NaCl, 20 mM sodium phosphate, 10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Felix97Accelyrs, San Diegoprocessing
Sparky3.11TD Goddard and DG Knellerdata analysis
CYANA2P Guntertstructure solution
CNS1.1AT Brunger, et al.refinement
RefinementMethod: automated NOE assignment using CYANA, torsion angle dynamics for structure calculations
Software ordinal: 1
Details: The structures are based on 1432 NOE derived distance constraints, 150 dihedral angle constraints (generated by TALOS) and 114 distance constraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

+
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