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- PDB-2l3p: Structure of the prolyl cis isomer of the Crk Protein -

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Basic information

Entry
Database: PDB / ID: 2l3p
TitleStructure of the prolyl cis isomer of the Crk Protein
ComponentsCis isomer of Crk protein
KeywordsSTRUCTURAL PROTEIN / adapter protein
Function / homology
Function and homology information


ARMS-mediated activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / regulation of intracellular signal transduction / Regulation of actin dynamics for phagocytic cup formation / Downstream signal transduction / negative regulation of wound healing / p130Cas linkage to MAPK signaling for integrins ...ARMS-mediated activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / regulation of intracellular signal transduction / Regulation of actin dynamics for phagocytic cup formation / Downstream signal transduction / negative regulation of wound healing / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / negative regulation of cell motility / regulation of GTPase activity / ephrin receptor signaling pathway / signaling adaptor activity / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / SH2 domain binding / ephrin receptor binding / regulation of actin cytoskeleton organization / receptor tyrosine kinase binding / SH3 domain binding / : / cell migration / regulation of cell shape / actin cytoskeleton organization / signal transduction / 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 / 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
Adapter molecule crk
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKalodimos, C.G. / Sarkar, P. / Saleh, T. / Tzeng, S.R. / Birge, R.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Structural basis for regulation of the Crk signaling protein by a proline switch.
Authors: Sarkar, P. / Saleh, T. / Tzeng, S.R. / Birge, R.B. / Kalodimos, C.G.
History
DepositionSep 21, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Cis isomer of Crk protein


Theoretical massNumber of molelcules
Total (without water)8,7321
Polymers8,7321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cis isomer of Crk protein / Proto-oncogene c-Crk / p38


Mass: 8731.954 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CRK / Production host: Escherichia coli (E. coli) / References: UniProt: Q04929

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D HBHA(CO)NH

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Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N] rckh, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: rckh / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.140 / pH: 5.5 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: ARIA / Version: 1.2 / Developer: Linge, O'Donoghue and Nilges / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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