[English] 日本語
Yorodumi
- PDB-2krn: High resolution structure of the second SH3 domain of CD2AP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2krn
TitleHigh resolution structure of the second SH3 domain of CD2AP
ComponentsCD2-associated protein
KeywordsSIGNALING PROTEIN / protein / SH3 domain
Function / homology
Function and homology information


neurotrophin signaling pathway / response to glial cell derived neurotrophic factor / regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / slit diaphragm ...neurotrophin signaling pathway / response to glial cell derived neurotrophic factor / regulation of receptor-mediated endocytosis / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / vascular endothelial growth factor receptor binding / slit diaphragm / response to transforming growth factor beta / vesicle organization / podocyte differentiation / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / collateral sprouting / protein heterooligomerization / cell-cell adhesion mediated by cadherin / renal albumin absorption / membrane organization / phosphatidylinositol 3-kinase regulatory subunit binding / glomerulus development / filopodium assembly / cell-cell junction organization / podosome / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / D-glucose import / cell leading edge / filamentous actin / neurotrophin TRK receptor signaling pathway / endocytic vesicle / centriolar satellite / protein secretion / lymph node development / adipose tissue development / stress-activated MAPK cascade / ruffle / actin filament polymerization / ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / liver development / kidney development / trans-Golgi network membrane / actin filament organization / cell periphery / positive regulation of protein secretion / actin filament / regulation of actin cytoskeleton organization / synapse organization / response to insulin / response to virus / neuromuscular junction / protein catabolic process / regulation of synaptic plasticity / lipid metabolic process / beta-catenin binding / fibrillar center / SH3 domain binding / cell-cell adhesion / response to wounding / positive regulation of protein localization to nucleus / male gonad development / neuron projection development / actin filament binding / cell-cell junction / late endosome / protein transport / cell migration / T cell receptor signaling pathway / actin binding / cell cortex / gene expression / growth cone / proteasome-mediated ubiquitin-dependent protein catabolic process / vesicle / negative regulation of neuron apoptotic process / response to oxidative stress / cell population proliferation / cell differentiation / neuron projection / inflammatory response / cadherin binding / cell division / axon / dendrite / protein-containing complex binding / apoptotic process / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily ...CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
CD2-associated protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsOrtega Roldan, J. / Azuaga, A.I. / van Nuland, N.A.J.
CitationJournal: To be Published
Title: Solution Structure, Dynamics and Thermodynamics of the three SH3 domains of CD2AP
Authors: Ortega Roldan, J.L. / Blackledge, M. / van Nuland, N.A.J. / Azuaga, A.I.
History
DepositionDec 21, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD2-associated protein


Theoretical massNumber of molelcules
Total (without water)6,8221
Polymers6,8221
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein CD2-associated protein / Mesenchyme-to-epithelium transition protein with SH3 domains 1 / METS-1


Mass: 6821.562 Da / Num. of mol.: 1 / Fragment: SH3-B domain, UNP residues 111-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd2ap, Mets1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JLQ0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

-
Sample preparation

DetailsContents: 1 mM SH3-B, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: SH3-B
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
RECOORDNederveen et alstructure solution
RECOORDNederveen et alrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichnoe assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 841 / NOE intraresidue total count: 225 / NOE long range total count: 312 / NOE medium range total count: 304
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

+
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