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- PDB-1ckb: STRUCTURAL BASIS FOR THE SPECIFIC INTERACTION OF LYSINE-CONTAININ... -

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Basic information

Entry
Database: PDB / ID: 1ckb
TitleSTRUCTURAL BASIS FOR THE SPECIFIC INTERACTION OF LYSINE-CONTAINING PROLINE-RICH PEPTIDES WITH THE N-TERMINAL SH3 DOMAIN OF C-CRK
Components
  • C-CRK N-TERMINAL SH3 DOMAIN
  • SOS PEPTIDE (PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG-ARG)
KeywordsCOMPLEX (ONCOGENE PROTEIN/PEPTIDE) / COMPLEX (ONCOGENE PROTEIN-PEPTIDE) / COMPLEX (ONCOGENE PROTEIN-PEPTIDE) complex
Function / homology
Function and homology information


PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / Downstream signal transduction ...PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / Downstream signal transduction / regulation of leukocyte migration / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / p130Cas linkage to MAPK signaling for integrins / response to peptide / regulation of dendrite development / Regulation of signaling by CBL / negative regulation of wound healing / Regulation of actin dynamics for phagocytic cup formation / response to yeast / positive regulation of skeletal muscle acetylcholine-gated channel clustering / reelin-mediated signaling pathway / VEGFA-VEGFR2 Pathway / negative regulation of cell motility / negative regulation of natural killer cell mediated cytotoxicity / protein localization to membrane / regulation of GTPase activity / positive regulation of smooth muscle cell migration / enzyme-linked receptor protein signaling pathway / cellular response to insulin-like growth factor stimulus / regulation of cell adhesion mediated by integrin / establishment of cell polarity / dendrite development / positive regulation of Rac protein signal transduction / ephrin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / cytoskeletal protein binding / ephrin receptor binding / insulin-like growth factor receptor binding / signaling adaptor activity / phosphotyrosine residue binding / positive regulation of substrate adhesion-dependent cell spreading / cellular response to nitric oxide / SH2 domain binding / protein tyrosine kinase binding / cell chemotaxis / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / hippocampus development / neuromuscular junction / response to hydrogen peroxide / cellular response to nerve growth factor stimulus / cerebral cortex development / SH3 domain binding / lipid metabolic process / neuron migration / regulation of cell shape / actin cytoskeleton / signaling receptor complex adaptor activity / actin cytoskeleton organization / scaffold protein binding / cell population proliferation / ubiquitin protein ligase binding / protein-containing complex / membrane / plasma membrane / cytoplasm
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 ...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
Adapter molecule crk
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWu, X. / Kuriyan, J.
CitationJournal: Structure / Year: 1995
Title: Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk.
Authors: Wu, X. / Knudsen, B. / Feller, S.M. / Zheng, J. / Sali, A. / Cowburn, D. / Hanafusa, H. / Kuriyan, J.
History
DepositionJan 24, 1995Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-CRK N-TERMINAL SH3 DOMAIN
B: SOS PEPTIDE (PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG-ARG)


Theoretical massNumber of molelcules
Total (without water)8,0462
Polymers8,0462
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-4 kcal/mol
Surface area4220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.400, 47.400, 29.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein C-CRK N-TERMINAL SH3 DOMAIN


Mass: 6814.538 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: PCR PRODUCT / Gene (production host): PCR PRODUCT / Production host: Escherichia coli (E. coli) / References: UniProt: Q64010
#2: Protein/peptide SOS PEPTIDE (PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG-ARG)


Mass: 1231.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.21 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
185 mg/mlprotein1drop
20.1 Msodium acetate1reservoir
30.2 Mammonium acetate1reservoir
49.0 mMSos peptide1drop
528-32 %PEG40001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 18, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5289 / % possible obs: 95.5 % / Redundancy: 4.1 %
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. measured all: 50442 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Mean I/σ(I) obs: 5.4

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.9→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.183 -
obs0.183 4616
Displacement parametersBiso mean: 10.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms537 0 0 204 741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9

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