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- PDB-5l23: Crystal structure of the complex between the N-terminal SH3 domai... -

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Basic information

Entry
Database: PDB / ID: 5l23
TitleCrystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand
Components
  • Adapter molecule crk
  • C3G derived peptide
KeywordsPROTEIN BINDING / SH3 / acetylation / amidation / Crkii / C3G
Function / homology
Function and homology information


positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / : / 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 ...positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / : / 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 / Rap protein signal transduction / protein phosphorylated amino acid binding / regulation of T cell migration / negative regulation of neural precursor cell proliferation / p130Cas linkage to MAPK signaling for integrins / reelin-mediated signaling pathway / regulation of dendrite development / regulation of cell junction assembly / 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 / nerve growth factor signaling pathway / negative regulation of wound healing / negative regulation of cell motility / protein localization to membrane / VEGFA-VEGFR2 Pathway / negative regulation of Ras protein signal transduction / establishment of endothelial barrier / positive regulation of Ras protein signal transduction / activation of GTPase activity / MET activates RAP1 and RAC1 / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / Frs2-mediated activation / regulation of GTPase activity / enzyme-linked receptor protein signaling pathway / blood vessel development / positive regulation of smooth muscle cell migration / dendrite development / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / regulation of JNK cascade / platelet-derived growth factor receptor signaling pathway / cellular response to nitric oxide / ephrin receptor signaling pathway / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signaling adaptor activity / Erythropoietin activates RAS / positive regulation of substrate adhesion-dependent cell spreading / cellular response to cAMP / cellular response to transforming growth factor beta stimulus / cell surface receptor protein tyrosine kinase signaling pathway / cytoskeletal protein binding / ephrin receptor binding / phosphotyrosine residue binding / Downstream signal transduction / SH2 domain binding / guanyl-nucleotide exchange factor activity / protein tyrosine kinase binding / cell chemotaxis / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / Regulation of signaling by CBL / hippocampus development / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / insulin-like growth factor receptor binding / neuron migration / negative regulation of canonical Wnt signaling pathway / response to hydrogen peroxide / neuromuscular junction / lipid metabolic process / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / cerebral cortex development / cytokine-mediated signaling pathway / positive regulation of neuron projection development / cell-cell adhesion / SH3 domain binding / phagocytic vesicle membrane / : / signaling receptor complex adaptor activity / cell migration / actin cytoskeleton / protein-macromolecule adaptor activity / nervous system development / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / early endosome
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic 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
DI(HYDROXYETHYL)ETHER / Rap guanine nucleotide exchange factor 1 / Adapter molecule crk
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBhatt, V.S. / Krieger, I. / Sacchettini, J. / Cho, J.-H.
CitationJournal: To Be Published
Title: Crystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand
Authors: Bhatt, V.S. / Krieger, I. / Sacchettini, J. / Cho, J.-H.
History
DepositionJul 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adapter molecule crk
B: C3G derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9094
Polymers8,6972
Non-polymers2122
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-3 kcal/mol
Surface area4920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.600, 41.340, 56.820
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 Adapter molecule crk / Proto-oncogene c-Crk / p38


Mass: 6971.731 Da / Num. of mol.: 1 / Fragment: UNP residues 134-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crk, Crko / Production host: Escherichia coli (E. coli) / References: UniProt: Q64010
#2: Protein/peptide C3G derived peptide


Mass: 1724.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q13905*PLUS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / Details: Lithium sulfate monohydrate, PEG 3350

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→33.43 Å / Num. obs: 6759 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.977 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.7
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.4 / CC1/2: 0.96 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cka

1cka


Resolution: 1.77→33.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21037 264 3.9 %RANDOM
Rwork0.17439 ---
obs0.17587 6462 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.77→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 11 99 726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02662
X-RAY DIFFRACTIONr_bond_other_d00.02616
X-RAY DIFFRACTIONr_angle_refined_deg2.6111.988892
X-RAY DIFFRACTIONr_angle_other_deg3.5563.0071434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.509577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06724.32437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64115113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.588156
X-RAY DIFFRACTIONr_chiral_restr0.1380.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021750
X-RAY DIFFRACTIONr_gen_planes_other0.0280.02148
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.661.035303
X-RAY DIFFRACTIONr_mcbond_other1.5441.03302
X-RAY DIFFRACTIONr_mcangle_it2.561.52378
X-RAY DIFFRACTIONr_mcangle_other2.5641.523379
X-RAY DIFFRACTIONr_scbond_it2.7081.385359
X-RAY DIFFRACTIONr_scbond_other2.7081.385359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2041.934514
X-RAY DIFFRACTIONr_long_range_B_refined6.76910.73839
X-RAY DIFFRACTIONr_long_range_B_other6.78110.723839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.771→1.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 14 -
Rwork0.14 468 -
obs--99.79 %

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