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- PDB-1x27: Crystal Structure of Lck SH2-SH3 with SH2 binding site of p130Cas -

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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 / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / 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 / leukocyte migration / cellular response to hepatocyte growth factor stimulus / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / 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 / neurotrophin TRK receptor signaling pathway / phospholipase binding / CD28 dependent PI3K/Akt signaling / platelet-derived growth factor receptor signaling pathway / hemopoiesis / RHOH GTPase cycle / 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 / peptidyl-tyrosine autophosphorylation / positive regulation of intrinsic apoptotic signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / GPVI-mediated activation cascade / release of sequestered calcium ion into cytosol / ruffle / 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 / actin filament organization / integrin-mediated signaling pathway / 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 / positive regulation of T cell activation / cell migration / actin cytoskeleton / Downstream TCR signaling / DAP12 signaling / insulin receptor signaling pathway / lamellipodium / PIP3 activates AKT signaling / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / actin cytoskeleton organization / protein tyrosine kinase activity / protein phosphatase binding / cell adhesion / intracellular signal transduction / positive regulation of cell migration / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / membrane raft / protein phosphorylation / protein domain specific binding / axon / innate immune response / signaling receptor binding / focal adhesion / protein kinase binding / extracellular exosome / ATP binding
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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 %

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