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- PDB-2j6o: ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 2j6o
TitleATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETEROTRIMER
Components
  • CD2-ASSOCIATED PROTEIN
  • T-CELL SURFACE ANTIGEN CD2
KeywordsPROTEIN BINDING / PHOSPHORYLATION / ADAPTOR PROTEIN / EGFR DOWNREGULATION / CMS / SH3 DOMAIN / SH3-BINDING / COILED COIL / SH3 DOMAIN RECOGNITION / SIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / membrane raft polarization / response to glial cell derived neurotrophic factor / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / slit diaphragm ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / response to glial cell derived neurotrophic factor / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / localization of cell / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / slit diaphragm / podocyte differentiation / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / collateral sprouting / protein heterooligomerization / cell-cell adhesion mediated by cadherin / renal albumin absorption / substrate-dependent cell migration, cell extension / membrane organization / phosphatidylinositol 3-kinase regulatory subunit binding / filopodium assembly / cell-cell junction organization / natural killer cell activation / Nephrin family interactions / heterotypic cell-cell adhesion / podosome / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / clathrin binding / maintenance of blood-brain barrier / nuclear envelope lumen / D-glucose import / cell leading edge / filamentous actin / neurotrophin TRK receptor signaling pathway / centriolar satellite / protein secretion / lymph node development / adipose tissue development / stress-activated MAPK cascade / ruffle / actin filament polymerization / ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / T cell activation / liver development / trans-Golgi network membrane / actin filament organization / positive regulation of interleukin-8 production / positive regulation of protein secretion / Cell surface interactions at the vascular wall / regulation of actin cytoskeleton organization / response to insulin / synapse organization / response to virus / neuromuscular junction / protein catabolic process / regulation of synaptic plasticity / lipid metabolic process / receptor tyrosine kinase binding / structural constituent of cytoskeleton / fibrillar center / response to wounding / cell-cell adhesion / positive regulation of protein localization to nucleus / SH3 domain binding / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / male gonad development / positive regulation of tumor necrosis factor production / actin filament binding / cell-cell junction / cell migration / actin cytoskeleton / late endosome / signaling receptor activity / T cell receptor signaling pathway / growth cone / protein-containing complex assembly / vesicle / negative regulation of neuron apoptotic process / response to oxidative stress / cell population proliferation / cell surface receptor signaling pathway / cadherin binding / inflammatory response / axon / external side of plasma membrane / cell division / signaling receptor binding / dendrite / apoptotic process / Golgi apparatus / cell surface / signal transduction / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm
Similarity search - Function
T-cell surface antigen CD2 / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Variant SH3 domain / SH3 Domains / SH3 domain ...T-cell surface antigen CD2 / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Variant SH3 domain / SH3 Domains / SH3 domain / Immunoglobulin V-set domain / SH3 type barrels. / Immunoglobulin V-set domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
T-cell surface antigen CD2 / CD2-associated protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMoncalian, G. / Cardenes, N. / Deribe, Y.L. / Spinola-Amilibia, M. / Dikic, I. / Bravo, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Atypical Polyproline Recognition by the Cms N-Terminal SH3 Domain.
Authors: Moncalian, G. / Cardenes, N. / Deribe, Y.L. / Spinola-Amilibia, M. / Dikic, I. / Bravo, J.
History
DepositionOct 2, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD2-ASSOCIATED PROTEIN
C: T-CELL SURFACE ANTIGEN CD2


Theoretical massNumber of molelcules
Total (without water)8,5322
Polymers8,5322
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.391, 66.391, 68.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

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Components

#1: Protein CD2-ASSOCIATED PROTEIN / CAS LIGAND WITH MULTIPLE SH3 DOMAINS / ADAPTER PROTEIN CMS / CMS


Mass: 7412.285 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 1-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5K6
#2: Protein/peptide T-CELL SURFACE ANTIGEN CD2 / T-CELL SURFACE ANTIGEN T11/LEU-5 / LFA-2 / LFA-3 RECEPTOR / ERYTHROCYTE RECEPTOR / ROSETTE RECEPTOR / CD2


Mass: 1119.382 Da / Num. of mol.: 1 / Fragment: CMS BINDING SEQUENCE, RESIDUES 324-333 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P06729
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growpH: 5.5 / Details: 20% PEG3000, 0.1M ACETATE PH 5.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 7, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.22→34.36 Å / Num. obs: 3933 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 16.66 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 25.02
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 14.22 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 15.74 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
TRUNCATEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CMSA-CBL-B STRUCTURE

Resolution: 2.23→47.73 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.792 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.361 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICAL UNIT OF THIS STRUCTURE IS A HETEROTRIMER CONSISTING OF TWO CMS SH3A DOMAINS AND ONE CD2 PEPTIDE IN TWO ORIENTATIONS, WITH 0. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICAL UNIT OF THIS STRUCTURE IS A HETEROTRIMER CONSISTING OF TWO CMS SH3A DOMAINS AND ONE CD2 PEPTIDE IN TWO ORIENTATIONS, WITH 0.5 OCCUPANCY EACH. THE SECOND CMS SH3A MOLECULES, AS WELL AS THE SECOND ORIENTATION OF THE PEPTIDE, ARE RELATED TO THAT IN THE ASYMMETRIC UNIT BY A CRYSTALLOGRAPHIC SYMMETRY OPERATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 177 4.52 %RANDOM
Rwork0.241 ---
obs0.243 3932 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 24.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.23→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 0 0 46 580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022562
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.974762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94424.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88315104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.052156
X-RAY DIFFRACTIONr_chiral_restr0.0770.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02432
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2220
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2353
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4823335
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.314534
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0584254
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0076225
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 9.75→47.73 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 3
Rwork0.405 59

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