[English] 日本語
Yorodumi
- PDB-1y9j: Solution structure of the rat Sly1 N-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1y9j
TitleSolution structure of the rat Sly1 N-terminal domain
ComponentsSec1 family domain containing protein 1
KeywordsPROTEIN TRANSPORT / membrane traffic / Sly1 / SM proteins / SNAREs / protein NMR
Function / homology
Function and homology information


: / regulation of protein transport / post-Golgi vesicle-mediated transport / regulation of ER to Golgi vesicle-mediated transport / COPII-mediated vesicle transport / : / negative regulation of autophagosome assembly / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / syntaxin binding ...: / regulation of protein transport / post-Golgi vesicle-mediated transport / regulation of ER to Golgi vesicle-mediated transport / COPII-mediated vesicle transport / : / negative regulation of autophagosome assembly / cis-Golgi network / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / syntaxin binding / Golgi-associated vesicle / Golgi cisterna membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / intracellular protein transport / cell morphogenesis / response to toxic substance / response to hypoxia / Golgi membrane / protein-containing complex binding / endoplasmic reticulum membrane / plasma membrane / cytosol
Similarity search - Function
Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sec1 family domain-containing protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsArac, D. / Dulubova, I. / Pei, J. / Huryeva, I. / Grishin, N.V. / Rizo, J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Three-dimensional Structure of the rSly1 N-terminal Domain Reveals a Conformational Change Induced by Binding to Syntaxin 5.
Authors: Arac, D. / Dulubova, I. / Pei, J. / Huryeva, I. / Grishin, N.V. / Rizo, J.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 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: Sec1 family domain containing protein 1


Theoretical massNumber of molelcules
Total (without water)17,6781
Polymers17,6781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1400structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Sec1 family domain containing protein 1 / Syntaxin binding protein 1- like 2 / Vesicle transport-related protein Ra410 / Sly1p


Mass: 17678.289 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Scfd1, Ra410, Sly1, Stxbp1l2 / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 competent cells / References: UniProt: Q62991

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY
NMR detailsText: This structure was determined using standard triple resonance techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM Sly1 N-terminal domain U-15N, 20 mM MES(pH 5.7), 200 mM KCl, 1 mM DTT20 mM MES(pH 5.7), 200 mM KCl, 1 mM DTT
21.2 mM Sly1 N-terminal domain U-15N,13C, 20 mM MES(pH 5.7), 200 mM KCl, 1 mM DTT20 mM MES(pH 5.7), 200 mM KCl, 1 mM DTT
31 mM Sly1 N-terminal domain U-10%13C, 20 mM MES(pH 5.7), 200 mM KCl, 1 mM DTT20 mM MES(pH 5.7), 200 mM KCl, 1 mM DTT
Sample conditionsIonic strength: 200 mM KCl / pH: 5.7 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2.3Delaglioprocessing
NMRView4.1.2Johnsondata analysis
TALOS2003.027.13.05Delagliodata analysis
CNS0.9Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: A total of 2493 restraints were used for the final calculations, including 2133 NOEs (of which 738 were long-range NOEs), 132 hydrogen bond restraints and 228 torsion angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1400 / 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://pdbjlvh1.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