[English] 日本語
Yorodumi
- PDB-2fry: Solution structure of the third SH3 domain of human NCK2 adaptor ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fry
TitleSolution structure of the third SH3 domain of human NCK2 adaptor protein
ComponentsCytoplasmic protein NCK2
KeywordsPROTEIN BINDING / SH3
Function / homology
Function and homology information


Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / : / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / cytoskeletal anchor activity / signal complex assembly / Activation of RAC1 ...Regulation of cortical dendrite branching / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / : / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / immunological synapse formation / dendritic spine development / cytoskeletal anchor activity / signal complex assembly / Activation of RAC1 / Nephrin family interactions / vesicle membrane / Ephrin signaling / lamellipodium assembly / positive regulation of actin filament polymerization / RHOV GTPase cycle / negative regulation of PERK-mediated unfolded protein response / RHOU GTPase cycle / ephrin receptor signaling pathway / positive regulation of T cell proliferation / signaling adaptor activity / phosphotyrosine residue binding / Downstream signal transduction / T cell activation / actin filament organization / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / VEGFA-VEGFR2 Pathway / cell migration / signaling receptor complex adaptor activity / scaffold protein binding / postsynaptic density / negative regulation of cell population proliferation / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / cytosol / cytoplasm
Similarity search - Function
Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / Cytoplasmic protein NCK / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain ...Nck2, SH3 domain 1 / Nck2, SH3 domain 2 / Nck2, SH3 domain 3 / Nck2, SH2 domain / Cytoplasmic protein NCK / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Cytoplasmic protein NCK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLiu, J.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Insight into the Binding Diversity between the Human Nck2 SH3 Domains and Proline-Rich Proteins
Authors: Liu, J. / Li, M. / Ran, X. / Fan, J.S. / Song, J.
History
DepositionJan 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytoplasmic protein NCK2


Theoretical massNumber of molelcules
Total (without water)6,9741
Polymers6,9741
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Cytoplasmic protein NCK2 / NCK adaptor protein 2 / SH2/SH3 adaptor protein NCK-beta / Nck-2


Mass: 6973.820 Da / Num. of mol.: 1 / Fragment: SH3_3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32-a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O43639

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

-
Sample preparation

DetailsContents: 50mM phosphate buffer, 90% H2O, 10% D2O, 0.01% NaN3, 10mM DTT
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerrefinement
NMRPipe2004Frank Delaglioprocessing
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 812 restraints, 722 are NOE-derived distance constraints, 90 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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