[English] 日本語
Yorodumi
- PDB-1iou: SOLUTION STRUCTURE OF YKT6P (1-140) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iou
TitleSOLUTION STRUCTURE OF YKT6P (1-140)
ComponentsYKT6P
KeywordsMEMBRANE PROTEIN / SNARE
Function / homology
Function and homology information


amphisome-lysosome fusion / Golgi cis cisterna membrane / Golgi vesicle fusion to target membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / vacuole fusion, non-autophagic / COPI-mediated anterograde transport / Golgi to endosome transport / COPII-mediated vesicle transport / palmitoyltransferase activity ...amphisome-lysosome fusion / Golgi cis cisterna membrane / Golgi vesicle fusion to target membrane / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / vacuole fusion, non-autophagic / COPI-mediated anterograde transport / Golgi to endosome transport / COPII-mediated vesicle transport / palmitoyltransferase activity / vesicle fusion / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / fungal-type vacuole / vacuolar membrane / autophagosome membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / intracellular protein transport / endosome membrane / endosome / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
YKT6, SNARE motif / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain ...YKT6, SNARE motif / Longin domain / Longin domain profile. / Longin domain / Regulated-SNARE-like domain / Regulated-SNARE-like domain / Synaptobrevin signature. / Synaptobrevin-like / Synaptobrevin / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / Longin-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Synaptobrevin homolog YKT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing with torsion angle dynamics
AuthorsTochio, H. / Tsui, M.M.K. / Banfield, D.K. / Zhang, M.
CitationJournal: SCIENCE / Year: 2001
Title: An autoinhibitory mechanism for nonsyntaxin SNARE proteins revealed by the structure of Ykt6p
Authors: Tochio, H. / Tsui, M.M.K. / Banfield, D.K. / Zhang, M.
History
DepositionApr 9, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YKT6P


Theoretical massNumber of molelcules
Total (without water)15,8551
Polymers15,8551
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 / 200structures with the least restraint violations,structures with the lowest energy
Representative

-
Components

#1: Protein YKT6P / SYNAPTOBREVIN HOMOLOG 1


Mass: 15854.735 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P36015

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1213D 13C-separated NOESY
1323D 15N-separated NOESY
142HNHA
NMR detailsText: na

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM YKT6(1-140) U-15N,13C;50mM phosphate buffer;20mM DTT;2mM EDTA;D2Ophosphate buffer pH 7.0
21.5mM YKT6(1-140) U-15N;50mM phosphate buffer;20mM DTT;2mM EDTA;10% D2Ophosphate buffer pH 7.0
31.5mM YKT6(1-140),13C;50mM phosphate buffer;20mM DTT;2mM EDTA;D2Ophosphate buffer pH 7.0
Sample conditionsIonic strength: 50mM / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS5002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: simulated annealing with torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / 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