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- PDB-1uj0: Crystal Structure of STAM2 SH3 domain in complex with a UBPY-deri... -

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Basic information

Entry
Database: PDB / ID: 1uj0
TitleCrystal Structure of STAM2 SH3 domain in complex with a UBPY-derived peptide
Components
  • deubiquitinating enzyme UBPY
  • signal transducing adaptor molecule (SH3 domain and ITAM motif) 2
KeywordsSIGNALING PROTEIN/SIGNALING PROTEIN / STAM / SH3 / deubiquitinating enzyme / Grb2 / Gads / PXXP / Hrs / endocytosis / early endosome / SIGNALING PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


Downregulation of ERBB2:ERBB3 signaling / RHOU GTPase cycle / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of MET activity / EGFR downregulation / Regulation of FZD by ubiquitination / negative regulation of lysosomal protein catabolic process / acrosomal membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis ...Downregulation of ERBB2:ERBB3 signaling / RHOU GTPase cycle / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of MET activity / EGFR downregulation / Regulation of FZD by ubiquitination / negative regulation of lysosomal protein catabolic process / acrosomal membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / protein K48-linked deubiquitination / endosome organization / Ub-specific processing proteases / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / mitotic cytokinesis / protein deubiquitination / cellular response to dexamethasone stimulus / phosphatidylinositol binding / ubiquitin binding / cellular response to nerve growth factor stimulus / regulation of protein stability / SH3 domain binding / positive regulation of canonical Wnt signaling pathway / protein transport / regulation of protein localization / midbody / early endosome membrane / Ras protein signal transduction / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / early endosome / endosome membrane / postsynaptic density / glutamatergic synapse / proteolysis / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
STAM2, SH3 domain / : / : / USP8 WW domain / : / USP8 dimerisation domain / USP8 dimerisation domain / VHS domain / VHS domain / VHS domain profile. ...STAM2, SH3 domain / : / : / USP8 WW domain / : / USP8 dimerisation domain / USP8 dimerisation domain / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / : / Rhodanese Homology Domain / ENTH/VHS / Rhodanese-like domain / Ubiquitin interaction motif / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ubiquitin-interacting motif. / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / SH3 Domains / SH3 domain / Papain-like cysteine peptidase superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / : / Signal transducing adapter molecule 2 / Ubiquitin carboxyl-terminal hydrolase 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKaneko, T. / Kumasaka, T. / Ganbe, T. / Sato, T. / Miyazawa, K. / Kitamura, N. / Tanaka, N.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain.
Authors: Kaneko, T. / Kumasaka, T. / Ganbe, T. / Sato, T. / Miyazawa, K. / Kitamura, N. / Tanaka, N.
History
DepositionJul 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: signal transducing adaptor molecule (SH3 domain and ITAM motif) 2
B: deubiquitinating enzyme UBPY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4393
Polymers8,3442
Non-polymers951
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-8 kcal/mol
Surface area4240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.454, 48.454, 58.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 / STAM2 SH3 domain


Mass: 7059.673 Da / Num. of mol.: 1 / Fragment: RESIDUES 200-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: O88811
#2: Protein/peptide deubiquitinating enzyme UBPY / UBPY-derived peptide


Mass: 1284.483 Da / Num. of mol.: 1 / Fragment: RESIDUES 699-709 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse).
References: GenBank: 11414862, UniProt: Q80U87*PLUS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.29 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.08M Sodium Phosphate monobasic, 1.92M Potassium phosphate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.6 mg/mlprotein1drop
20.08 Msodium phosphate1reservoir
31.92 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 2, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→34.1 Å / Num. obs: 8501 / % possible obs: 97.9 % / Observed criterion σ(I): 6
Reflection shellResolution: 1.7→1.79 Å / % possible all: 96.8
Reflection
*PLUS
Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.11 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.525 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22966 898 10.6 %RANDOM
Rwork0.21458 ---
all0.2163 8500 --
obs0.2163 7602 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.802 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å20 Å2
2--0.58 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 5 64 617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021565
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.924764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.23565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02445
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2245
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4581.5333
X-RAY DIFFRACTIONr_mcangle_it2.582534
X-RAY DIFFRACTIONr_scbond_it3.3833232
X-RAY DIFFRACTIONr_scangle_it5.3524.5230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 57
Rwork0.301 561
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.673

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