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- PDB-2j7i: ATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 2j7i
TitleATYPICAL POLYPROLINE RECOGNITION BY THE CMS N-TERMINAL SH3 DOMAIN. CMS:CD2 HETERODIMER
Components
  • CD2-ASSOCIATED PROTEIN
  • T-CELL SURFACE ANTIGEN CD2
KeywordsPROTEIN BINDING / COILED COIL / POLYMORPHISM / GLYCOPROTEIN / CELL ADHESION / EGFR DOWNREGULATION / IMMUNOGLOBULIN DOMAIN / TRANSMEMBRANE / PHOSPHORYLATION / ADAPTOR PROTEIN / CMS / CD2AD / MEMBRANE / SH3 DOMAIN / SH3-BINDING / SH3 DOMAIN RECOGNITION
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / membrane raft polarization / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / immunological synapse formation / substrate-dependent cell migration, cell extension / protein heterooligomerization / natural killer cell mediated cytotoxicity ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / negative regulation of small GTPase mediated signal transduction / transforming growth factor beta1 production / negative regulation of transforming growth factor beta1 production / response to transforming growth factor beta / immunological synapse formation / substrate-dependent cell migration, cell extension / protein heterooligomerization / natural killer cell mediated cytotoxicity / natural killer cell activation / podosome / Nephrin family interactions / heterotypic cell-cell adhesion / regulation of T cell differentiation / cell leading edge / filamentous actin / centriolar satellite / stress-activated MAPK cascade / ruffle / T cell activation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kidney development / actin filament organization / positive regulation of interleukin-8 production / positive regulation of protein secretion / regulation of actin cytoskeleton organization / Cell surface interactions at the vascular wall / synapse organization / protein catabolic process / neuromuscular junction / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / cell-cell adhesion / receptor tyrosine kinase binding / fibrillar center / SH3 domain binding / positive regulation of protein localization to nucleus / male gonad development / : / cell migration / actin filament binding / cell-cell junction / positive regulation of type II interferon production / actin cytoskeleton / late endosome / positive regulation of tumor necrosis factor production / signaling receptor activity / T cell receptor signaling pathway / protein-containing complex assembly / vesicle / cell surface receptor signaling pathway / cadherin binding / inflammatory response / cell cycle / axon / cell division / external side of plasma membrane / signaling receptor binding / apoptotic process / dendrite / Golgi apparatus / cell surface / signal transduction / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
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 / Immunoglobulin V-set 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: 2.9 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 Src Homology 3 Domain.
Authors: Moncalian, G. / Cardenes, N. / Deribe, Y.L. / Spinola-Amilibia, M. / Dikic, I. / Bravo, J.
History
DepositionOct 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 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
B: CD2-ASSOCIATED PROTEIN
C: T-CELL SURFACE ANTIGEN CD2
D: T-CELL SURFACE ANTIGEN CD2


Theoretical massNumber of molelcules
Total (without water)17,0634
Polymers17,0634
Non-polymers00
Water55831
1
A: CD2-ASSOCIATED PROTEIN
C: T-CELL SURFACE ANTIGEN CD2


Theoretical massNumber of molelcules
Total (without water)8,5322
Polymers8,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CD2-ASSOCIATED PROTEIN
D: T-CELL SURFACE ANTIGEN CD2


Theoretical massNumber of molelcules
Total (without water)8,5322
Polymers8,5322
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.319, 59.719, 70.867
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 CD2-ASSOCIATED PROTEIN / CAS LIGAND WITH MULTIPLE SH3 DOMAINS / ADAPTER PROTEIN CMS / CMS


Mass: 7412.285 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 1-62
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL SH3 DOMAIN FROM CMS (CAS LIGAND WITH MULTIPLE SH3 DOMAINS) OR CD2AP (CD2-ASSOCIATED PROTEIN)
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET 21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSSETTA (DE3) PLYS / 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.: 2 / Fragment: CMS BINDING SEQUENCE, RESIDUES 324-333 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P06729
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growpH: 8 / Details: 30% PEG8000, 0.2M NACL, 0.1M TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179
DetectorType: MARRESERACH / Detector: IMAGE PLATE / Date: Jun 8, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.9→36.29 Å / Num. obs: 3729 / % possible obs: 100 % / Observed criterion σ(I): 2.4 / Redundancy: 8 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 22
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CMSA-CBL-B STRUCTURE

Resolution: 2.9→19.8 Å / Rfactor Rfree error: 0.022 / Data cutoff high absF: 590838.33 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 184 5 %RANDOM
Rwork0.248 ---
obs0.248 3690 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.9924 Å2 / ksol: 0.320003 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.69 Å20 Å20 Å2
2---20.39 Å20 Å2
3---14.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1111 0 0 31 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.36
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.161.5
X-RAY DIFFRACTIONc_mcangle_it7.742
X-RAY DIFFRACTIONc_scbond_it8.212
X-RAY DIFFRACTIONc_scangle_it11.722.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.076 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 17 2.8 %
Rwork0.341 581 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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