[English] 日本語
Yorodumi
- PDB-1x27: Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x27
TitleCrystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas
Components
  • CRK-associated substrate
  • Proto-oncogene tyrosine-protein kinase LCK
KeywordsSIGNALING PROTEIN / Lck-Cas complex / LCK phospho-peptide complex / High affinity LCK-Cas complex
Function / homology
Function and homology information


p130Cas linkage to MAPK signaling for integrins / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / VEGFA-VEGFR2 Pathway / Downstream signal transduction / antigen receptor-mediated signaling pathway / cellular response to endothelin / regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / negative regulation of substrate adhesion-dependent cell spreading / endothelin receptor signaling pathway ...p130Cas linkage to MAPK signaling for integrins / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / VEGFA-VEGFR2 Pathway / Downstream signal transduction / antigen receptor-mediated signaling pathway / cellular response to endothelin / regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / negative regulation of substrate adhesion-dependent cell spreading / endothelin receptor signaling pathway / Fc-gamma receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / CD28 co-stimulation / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / Regulation of KIT signaling / cellular response to hepatocyte growth factor stimulus / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / leukocyte migration / phospholipase activator activity / CD8 receptor binding / pericentriolar material / positive regulation of T cell receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / neurotrophin TRK receptor signaling pathway / RHOH GTPase cycle / platelet-derived growth factor receptor signaling pathway / hemopoiesis / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / cellular response to nitric oxide / vascular endothelial growth factor receptor signaling pathway / phosphatidylinositol 3-kinase binding / T cell receptor binding / positive regulation of intrinsic apoptotic signaling pathway / peptidyl-tyrosine autophosphorylation / release of sequestered calcium ion into cytosol / extrinsic component of cytoplasmic side of plasma membrane / GPVI-mediated activation cascade / ruffle / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / phosphotyrosine residue binding / positive regulation of endothelial cell migration / SH2 domain binding / cell chemotaxis / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / integrin-mediated signaling pathway / actin filament organization / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / Signaling by SCF-KIT / platelet activation / SH3 domain binding / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / activation of cysteine-type endopeptidase activity involved in apoptotic process / cell migration / actin cytoskeleton / Downstream TCR signaling / positive regulation of T cell activation / insulin receptor signaling pathway / PIP3 activates AKT signaling / DAP12 signaling / lamellipodium / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / actin cytoskeleton organization / protein phosphatase binding / protein tyrosine kinase activity / cell adhesion / intracellular signal transduction / positive regulation of cell migration / response to xenobiotic stimulus / membrane raft / G protein-coupled receptor signaling pathway / protein domain specific binding / axon / protein phosphorylation / innate immune response / focal adhesion / signaling receptor binding / protein kinase binding / extracellular exosome
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 / Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 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 / Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Lck / Breast cancer anti-estrogen resistance protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNasertorabi, F. / Tars, K. / Becherer, K. / Kodandapani, R. / Liljas, L. / Vuori, K. / Ely, K.R.
CitationJournal: J.MOL.RECOG. / Year: 2006
Title: Molecular basis for regulation of Src by the docking protein p130Cas
Authors: Nasertorabi, F. / Tars, K. / Becherer, K. / Kodandapani, R. / Liljas, L. / Vuori, K. / Ely, K.R.
History
DepositionApr 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase LCK
B: Proto-oncogene tyrosine-protein kinase LCK
C: Proto-oncogene tyrosine-protein kinase LCK
D: Proto-oncogene tyrosine-protein kinase LCK
E: Proto-oncogene tyrosine-protein kinase LCK
F: Proto-oncogene tyrosine-protein kinase LCK
I: CRK-associated substrate
J: CRK-associated substrate
K: CRK-associated substrate
L: CRK-associated substrate
M: CRK-associated substrate
N: CRK-associated substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,00318
Polymers120,86512
Non-polymers1386
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-112 kcal/mol
Surface area42840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.415, 107.289, 166.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Proto-oncogene tyrosine-protein kinase LCK / P56-LCK / LSK / T cell-specific protein-tyrosine kinase


Mass: 18878.982 Da / Num. of mol.: 6 / Fragment: SH2-SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCK / Plasmid: pET 28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21-DE3 / References: UniProt: P06239, EC: 2.7.1.112
#2: Protein/peptide
CRK-associated substrate / p130cas / Breast cancer anti-estrogen resistance 1 protein


Mass: 1265.262 Da / Num. of mol.: 6 / Fragment: residues 759-767 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. Identical to naturally accured sequence in p130Cas
References: UniProt: Q63767
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: N-tris[hydroxymethyl]methyl-3-aminopropane-sulfonic acid, di_potasium hydrogen phosphate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 37482 / Num. obs: 37482 / % possible obs: 96.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 79 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 5316 / Rsym value: 0.482 / % possible all: 96

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCK

1lck


Resolution: 2.7→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.317 1850 random
Rwork0.247 --
all0.25 37399 -
obs0.247 35549 -
Displacement parametersBiso mean: 60.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8192 0 6 47 8245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.38 311 -
Rwork0.33 --
obs-5784 95.5 %

+
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