[English] 日本語
Yorodumi
- PDB-2bzy: Homodimer of CrkL-SH3C domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bzy
TitleHomodimer of CrkL-SH3C domain
ComponentsCRK-LIKE PROTEIN
KeywordsSH3 DOMAIN / CRK-LIKE / CRKL / DIMER / NUCLEAR EXPORT
Function / homology
Function and homology information


positive regulation of glial cell migration / chordate pharynx development / extrinsic component of postsynaptic membrane / helper T cell diapedesis / cerebellar neuron development / postsynaptic specialization assembly / urogenital system development / parathyroid gland development / regulation of T cell migration / reelin-mediated signaling pathway ...positive regulation of glial cell migration / chordate pharynx development / extrinsic component of postsynaptic membrane / helper T cell diapedesis / cerebellar neuron development / postsynaptic specialization assembly / urogenital system development / parathyroid gland development / regulation of T cell migration / reelin-mediated signaling pathway / endothelin receptor signaling pathway / regulation of dendrite development / positive regulation of skeletal muscle acetylcholine-gated channel clustering / cranial skeletal system development / B cell apoptotic process / MET receptor recycling / cellular response to interleukin-7 / acetylcholine receptor signaling pathway / MET activates RAP1 and RAC1 / anterior/posterior pattern specification / Frs2-mediated activation / establishment of cell polarity / blood vessel development / dendrite development / outflow tract morphogenesis / positive regulation of Rac protein signal transduction / single fertilization / regulation of cell adhesion mediated by integrin / retinoic acid receptor signaling pathway / fibroblast growth factor receptor signaling pathway / signaling adaptor activity / Erythropoietin activates RAS / positive regulation of substrate adhesion-dependent cell spreading / JNK cascade / cellular response to transforming growth factor beta stimulus / phosphotyrosine residue binding / cell chemotaxis / Downstream signal transduction / thymus development / negative regulation of protein phosphorylation / regulation of cell growth / Regulation of signaling by CBL / hippocampus development / neuron migration / neuromuscular junction / lipid metabolic process / receptor tyrosine kinase binding / cerebral cortex development / male gonad development / cell migration / cellular response to xenobiotic stimulus / T cell receptor signaling pathway / spermatogenesis / Ras protein signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / cadherin binding / positive regulation of protein phosphorylation / negative regulation of gene expression / positive regulation of cell population proliferation / signal transduction / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHarkiolaki, M. / Gilbert, R.J. / Jones, E.Y. / Feller, S.M.
CitationJournal: Structure / Year: 2006
Title: The C-Terminal SH3 Domain of Crkl as a Dynamic Dimerization Module Transiently Exposing a Nuclear Export Signal.
Authors: Harkiolaki, M. / Gilbert, R.J. / Jones, E.Y. / Feller, S.M.
History
DepositionAug 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRK-LIKE PROTEIN
B: CRK-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,1032
Polymers15,1032
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.317, 71.317, 146.428
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.699, -0.533, 0.476), (-0.565, 0.006, -0.825), (0.437, -0.846, -0.306)
Vector: 39.36, 64.339, 50.954)

-
Components

#1: Protein CRK-LIKE PROTEIN / CRKL SH3C


Mass: 7551.613 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 237-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOPP1 / References: UniProt: P46109
Compound detailsPOSSIBLE MEDIATION IN TRANSDUCTION OF INTRACELLULAR SIGNALS

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.42 %
Crystal growpH: 5.6
Details: 0.01 M MGCL2, 5% W/V PEG 8000, 0.2 M KCL2, 0.05 M MES PH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 27, 2003 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 8176 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 28 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 16.74
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 28.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.09 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BZX

2bzx


Resolution: 2.5→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.309 420 5.2 %RANDOM
Rwork0.263 ---
obs0.263 8123 99.6 %-
Solvent computationSolvent model: CNS BULK SOLVENT CORRECTION / Bsol: 60 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.854 Å2-4.963 Å20 Å2
2---3.854 Å20 Å2
3---7.709 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 0 0 982
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.83
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.3963
X-RAY DIFFRACTIONc_mcangle_it3.9244
X-RAY DIFFRACTIONc_scbond_it3.84
X-RAY DIFFRACTIONc_scangle_it5.4435
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4421 48 4.9 %
Rwork0.4297 913 -
obs--100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

+
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