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- PDB-1m3a: Solution structure of a circular form of the truncated N-terminal... -

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Basic information

Entry
Database: PDB / ID: 1m3a
TitleSolution structure of a circular form of the truncated N-terminal SH3 domain from oncogene protein c-Crk.
ComponentsProto-oncogene C-crk
KeywordsPROTEIN BINDING / SH3 / SH3 DOMAIN / CIRCULAR PROTEIN / CYCLIZED PROTEIN / ADAPTOR PROTEIN
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 / regulation of leukocyte migration ...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 / regulation of leukocyte migration / Downstream signal transduction / response to peptide / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / p130Cas linkage to MAPK signaling for integrins / reelin-mediated signaling pathway / regulation of dendrite development / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of natural killer cell mediated cytotoxicity / response to yeast / Regulation of signaling by CBL / Regulation of actin dynamics for phagocytic cup formation / regulation of Rac protein signal transduction / negative regulation of wound healing / negative regulation of cell motility / protein localization to membrane / VEGFA-VEGFR2 Pathway / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / regulation of GTPase activity / enzyme-linked receptor protein signaling pathway / positive regulation of smooth muscle cell migration / dendrite development / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / cellular response to nitric oxide / ephrin receptor signaling pathway / signaling adaptor activity / positive regulation of substrate adhesion-dependent cell spreading / cellular response to transforming growth factor beta stimulus / cytoskeletal protein binding / ephrin receptor binding / phosphotyrosine residue binding / SH2 domain binding / protein tyrosine kinase binding / cell chemotaxis / cellular response to nerve growth factor stimulus / hippocampus development / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / insulin-like growth factor receptor binding / neuron migration / response to hydrogen peroxide / neuromuscular junction / lipid metabolic process / receptor tyrosine kinase binding / cerebral cortex development / SH3 domain binding / : / signaling receptor complex adaptor activity / actin cytoskeleton / cell migration / protein-macromolecule adaptor activity / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / cell population proliferation / protein domain specific binding / ubiquitin protein ligase binding / enzyme binding / 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 / SH3 type barrels. / 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 / SH3 type barrels. / SH2 domain / 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)
MethodSOLUTION NMR / Simulated annealing, torsion angle dynamics
AuthorsSchumann, F.H. / Varadan, R. / Tayakuniyil, P.P. / Hall, J.B. / Camarero, J.A. / Fushman, D.
Citation
Journal: To be Published
Title: Changing protein backbone topology: Structural and dynamic consequences of the backbone cyclization in SH3 domain
Authors: Schumann, F.H. / Varadan, R. / Tayakuniyil, P.P. / Hall, J.B. / Camarero, J.A. / Fushman, D.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Rescuing a destabilized protein fold through backbone cyclization
Authors: Camarero, J.A. / Fushman, D. / Sato, S. / Giriat, I. / Cowburn, D. / Raleigh, D.P. / Muir, T.W.
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene C-crk


Theoretical massNumber of molelcules
Total (without water)6,7751
Polymers6,7751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest target function
RepresentativeModel #1lowest target function

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Components

#1: Protein Proto-oncogene C-crk / P38 / Adapter molecule crk


Mass: 6774.541 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SH3 DOMAIN (residues 135-191) / Mutation: R191G, E135C, deleted A134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CRK / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64010

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
1422D HSQC
1522D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques combined with 2D 1H-15N HSQC data.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM SH3 NA, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN390% H2O/10% D2O
21mM SH3 U-15N, 20mM sodium phosphate, 20 mM DTT-d10, 100 mM NaCl, 0.1% (w/v) NaN390% H2O/10% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 7.2 / Pressure: ambient / Temperature: 307 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6, 3.0Brukercollection
XEASY1.3.1.3Bartels, Xia, Wuethrichdata analysis
DYANA1.6Guentertstructure solution
DYANAGuentert, Wuethrichrefinement
RefinementMethod: Simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures are based on 1090 restraints, 993 are NOE-derived distance contraints, 25 dihedral angle constraints, and 72 distance restraints from hydrogen bonds. Structures were ...Details: The structures are based on 1090 restraints, 993 are NOE-derived distance contraints, 25 dihedral angle constraints, and 72 distance restraints from hydrogen bonds. Structures were calculated using program DYANA. No further refinement was performed.
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: structures with the lowest target function
Conformers calculated total number: 200 / Conformers submitted total number: 20

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