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Basic information

Entry
Database: PDB / ID: 5ih2
TitleStructure, thermodynamics, and the role of conformational dynamics in the interactions between the N-terminal SH3 domain of CrkII and proline-rich motifs in cAbl
Components
  • Adapter molecule crk
  • Proline rich Peptide
KeywordsSIGNALING PROTEIN / SH3 domain Polyproline II motif
Function / homology
Function and homology information


helper T cell diapedesis / cerebellar neuron development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / response to hepatocyte growth factor / MET receptor recycling / transitional one stage B cell differentiation / Role of ABL in ROBO-SLIT signaling / cerebellum morphogenesis ...helper T cell diapedesis / cerebellar neuron development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / response to hepatocyte growth factor / MET receptor recycling / transitional one stage B cell differentiation / Role of ABL in ROBO-SLIT signaling / cerebellum morphogenesis / DN4 thymocyte differentiation / response to cholecystokinin / Downstream signal transduction / HDR through Single Strand Annealing (SSA) / B cell proliferation involved in immune response / cellular response to endothelin / postsynaptic specialization assembly / regulation of leukocyte migration / RHO GTPases Activate WASPs and WAVEs / regulation of T cell migration / B-1 B cell homeostasis / neuroepithelial cell differentiation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / positive regulation of Wnt signaling pathway, planar cell polarity pathway / protein phosphorylated amino acid binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / alpha-beta T cell differentiation / microspike assembly / p130Cas linkage to MAPK signaling for integrins / Cyclin D associated events in G1 / response to yeast / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / activated T cell proliferation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / regulation of cellular senescence / response to epinephrine / regulation of dendrite development / response to peptide / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / negative regulation of ubiquitin-protein transferase activity / podocyte apoptotic process / regulation of postsynaptic specialization assembly / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of modification of synaptic structure / delta-catenin binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of Rac protein signal transduction / negative regulation of wound healing / Regulation of signaling by CBL / circulatory system development / positive regulation of extracellular matrix organization / regulation of intracellular signal transduction / Regulation of actin dynamics for phagocytic cup formation / neuropilin signaling pathway / neuropilin binding / regulation of extracellular matrix organization / Myogenesis / reelin-mediated signaling pathway / negative regulation of mitotic cell cycle / activation of GTPase activity / bubble DNA binding / positive regulation of establishment of T cell polarity / VEGFA-VEGFR2 Pathway / spleen development / neuromuscular process controlling balance / negative regulation of cell motility / Bergmann glial cell differentiation / positive regulation of blood vessel branching / proline-rich region binding / regulation of cell adhesion mediated by integrin / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of dendrite development / mitogen-activated protein kinase binding / regulation of Cdc42 protein signal transduction / negative regulation of cell-cell adhesion / protein localization to membrane / syntaxin binding / regulation of axon extension / positive regulation of smooth muscle cell migration / regulation of T cell differentiation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor signaling pathway / establishment of cell polarity / enzyme-linked receptor protein signaling pathway / cellular response to insulin-like growth factor stimulus / platelet-derived growth factor receptor-beta signaling pathway / dendrite development / B cell proliferation / negative regulation of cellular senescence / myoblast proliferation / cell leading edge / negative regulation of BMP signaling pathway / cardiac muscle cell proliferation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / associative learning / post-embryonic development
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Variant SH3 domain / SH3 Domains / : ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Variant SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / Src homology 2 domains / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / Tyrosine-protein kinase ABL1 / Adapter molecule crk
Similarity search - Component
Biological speciesMus musculus (house mouse)
Endothia gyrosa (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBhatt, V.S. / Zeng, D. / Krieger, I. / Sacchettini, J.C. / Cho, J.-H.
CitationJournal: Biophys.J. / Year: 2016
Title: Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl.
Authors: Bhatt, V.S. / Zeng, D. / Krieger, I. / Sacchettini, J.C. / Cho, J.H.
History
DepositionFeb 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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_symmetry / _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_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Oct 30, 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: Adapter molecule crk
B: Adapter molecule crk
M: Proline rich Peptide
N: Proline rich Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,03711
Polymers16,5154
Non-polymers5237
Water3,261181
1
A: Adapter molecule crk
M: Proline rich Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4326
Polymers8,2572
Non-polymers1754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-25 kcal/mol
Surface area5540 Å2
MethodPISA
2
B: Adapter molecule crk
N: Proline rich Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6055
Polymers8,2572
Non-polymers3473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-17 kcal/mol
Surface area5220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.222, 29.479, 45.756
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABMN

#1: Protein Adapter molecule crk / Proto-oncogene c-Crk / p38


Mass: 6971.731 Da / Num. of mol.: 2 / 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 Proline rich Peptide


Mass: 1285.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) / References: UniProt: P00520*PLUS

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Non-polymers , 4 types, 188 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.84 Å3/Da / Density % sol: 33.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 11478 / % possible obs: 99.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 38.055
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cka

1cka


Resolution: 1.8→45.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24252 612 5.4 %RANDOM
Rwork0.16964 ---
obs0.17323 10714 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.533 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20.1 Å2
2---0.03 Å20 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 26 181 1353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021238
X-RAY DIFFRACTIONr_bond_other_d00.021168
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.9951656
X-RAY DIFFRACTIONr_angle_other_deg3.4533.0122710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84823.42573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17115221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9731513
X-RAY DIFFRACTIONr_chiral_restr0.1130.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211381
X-RAY DIFFRACTIONr_gen_planes_other0.0240.02280
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_it1.5381.776556
X-RAY DIFFRACTIONr_mcbond_other1.5361.774555
X-RAY DIFFRACTIONr_mcangle_it2.0962.642694
X-RAY DIFFRACTIONr_mcangle_other2.0962.645695
X-RAY DIFFRACTIONr_scbond_it2.7922.144682
X-RAY DIFFRACTIONr_scbond_other2.9272.142683
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2363.09963
X-RAY DIFFRACTIONr_long_range_B_refined6.4516.4111517
X-RAY DIFFRACTIONr_long_range_B_other5.88415.5481437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 48 -
Rwork0.101 762 -
obs--96.09 %

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