[English] 日本語
Yorodumi
- PDB-2ew3: Solution Structure Of The SH3 Domain Of Human SH3GL3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ew3
TitleSolution Structure Of The SH3 Domain Of Human SH3GL3
ComponentsSH3-containing GRB2-like protein 3
KeywordsSIGNALING PROTEIN / SH3 / SH3GL3 / Solution structure
Function / homology
Function and homology information


negative regulation of clathrin-dependent endocytosis / postsynaptic endosome / synaptic vesicle uncoating / NGF-stimulated transcription / postsynaptic density, intracellular component / positive regulation of neuron differentiation / InlB-mediated entry of Listeria monocytogenes into host cell / acrosomal vesicle / central nervous system development / EGFR downregulation ...negative regulation of clathrin-dependent endocytosis / postsynaptic endosome / synaptic vesicle uncoating / NGF-stimulated transcription / postsynaptic density, intracellular component / positive regulation of neuron differentiation / InlB-mediated entry of Listeria monocytogenes into host cell / acrosomal vesicle / central nervous system development / EGFR downregulation / Negative regulation of MET activity / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / early endosome membrane / glutamatergic synapse / lipid binding / signal transduction / identical protein binding / cytoplasm
Similarity search - Function
Endophilin-A3, BAR domain / Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / SH3 Domains / SH3 domain / Src homology 3 domains ...Endophilin-A3, BAR domain / Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / BAR domain / AH/BAR domain superfamily / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGao, Y.G. / Yan, X.Z. / Hu, H.Y.
CitationJournal: To be Published
Title: Structural Basis for the Binding Specificities of Huntingtin Proline-Rich Region with SH3 and WW Domains
Authors: Gao, Y.G. / Yan, X.Z. / Hu, H.Y.
History
DepositionNov 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3-containing GRB2-like protein 3


Theoretical massNumber of molelcules
Total (without water)7,9741
Polymers7,9741
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)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein SH3-containing GRB2-like protein 3 / SH3GL3 / SH3 domain protein 2C / EEN-B2


Mass: 7973.770 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q99963

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D C(CO)NH
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D H(CCO)NH
1623D 15N-TOCSY-HSQC
1713D (H)CCH-TOCSY
1813D 15N-separated NOESY
1913D 13C-separated NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM SH3GL3-SH3 domain U-15N, 13C; 10mM sodium phosphate pH 6.0; 100mM NaCl; 5mM dithiothreitol; 0.05% w/v sodium azide; 92% H2O/8% D2O or 100% D2O92% H2O/8% D2O or 100% D2O
21mM SH3GL3-SH3 domain U-15N; 10mM sodium phosphate pH 6.0; 100mM NaCl; 5mM dithiothreitol; 0.05% w/v sodium azide; 92% H2O/8% D2O92% H2O/8% D2O
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
VNMRcollection
NMRPipeFrank Delagliodata analysis
NMRView5Bruce A. Johnsondata analysis
ARIA2Michael Habeck et al.refinement
CNS1.1A.T.Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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