[English] 日本語
Yorodumi
- PDB-1wyx: The Crystal Structure of the p130Cas SH3 Domain at 1.1 A Resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wyx
TitleThe Crystal Structure of the p130Cas SH3 Domain at 1.1 A Resolution
ComponentsCRK-associated substrate
KeywordsCELL ADHESION / Beta sheets
Function / homology
Function and homology information


antigen receptor-mediated signaling pathway / endothelin receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / cellular response to hepatocyte growth factor stimulus / p130Cas linkage to MAPK signaling for integrins / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ruffle ...antigen receptor-mediated signaling pathway / endothelin receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / cellular response to hepatocyte growth factor stimulus / p130Cas linkage to MAPK signaling for integrins / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ruffle / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of endothelial cell migration / Downstream signal transduction / cell chemotaxis / integrin-mediated signaling pathway / regulation of cell growth / actin filament organization / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / VEGFA-VEGFR2 Pathway / SH3 domain binding / actin cytoskeleton / cell migration / insulin receptor signaling pathway / lamellipodium / T cell receptor signaling pathway / regulation of apoptotic process / cell adhesion / positive regulation of cell migration / G protein-coupled receptor signaling pathway / cell division / axon / focal adhesion / protein kinase binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / BCAR1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / SH3 Domains / SH3 domain ...: / BCAR1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal 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
Breast cancer anti-estrogen resistance protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsWisniewska, M. / Bossenmaier, B. / Georges, G. / Hesse, F. / Dangl, M. / Kuenkele, K.P. / Ioannidis, I. / Huber, R. / Engh, R.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The 1.1 A resolution crystal structure of the p130cas SH3 domain and ramifications for ligand selectivity
Authors: Wisniewska, M. / Bossenmaier, B. / Georges, G. / Hesse, F. / Dangl, M. / Kunkele, K.P. / Ioannidis, I. / Huber, R. / Engh, R.A.
History
DepositionFeb 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRK-associated substrate
B: CRK-associated substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6104
Polymers15,5242
Non-polymers862
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.071, 56.193, 37.924
Angle α, β, γ (deg.)90.00, 116.22, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CRK-associated substrate / Crk-associated tyrosine kinase substrate p130cas / CAS / p130Cas / Breast cancer anti-estrogen ...Crk-associated tyrosine kinase substrate p130cas / CAS / p130Cas / Breast cancer anti-estrogen resistance 1 protein


Mass: 7761.914 Da / Num. of mol.: 2 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P56945
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: acetate, magnesium chloride, PEG 8000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2003
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.1→34.1 Å / % possible obs: 93 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shellResolution: 1.1→1.15 Å

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→34.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.499 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19109 2441 5 %RANDOM
Rwork0.17571 ---
all0.177 ---
obs0.17651 46200 93.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.02 Å2
2--0.19 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.14→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 5 165 1248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211102
X-RAY DIFFRACTIONr_bond_other_d0.0020.021014
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9731487
X-RAY DIFFRACTIONr_angle_other_deg0.69132368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675135
X-RAY DIFFRACTIONr_chiral_restr0.0830.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021205
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02205
X-RAY DIFFRACTIONr_nbd_refined0.2170.2152
X-RAY DIFFRACTIONr_nbd_other0.2420.21117
X-RAY DIFFRACTIONr_nbtor_other0.0810.2691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3640.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.218
X-RAY DIFFRACTIONr_mcbond_it1.0931.5675
X-RAY DIFFRACTIONr_mcangle_it1.79321080
X-RAY DIFFRACTIONr_scbond_it2.1733427
X-RAY DIFFRACTIONr_scangle_it3.444.5407
X-RAY DIFFRACTIONr_rigid_bond_restr1.11921102
X-RAY DIFFRACTIONr_sphericity_free2.82166
X-RAY DIFFRACTIONr_sphericity_bonded2.46721082
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 206
Rwork0.255 3265

+
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