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- PDB-1aoj: THE SH3 DOMAIN OF EPS8 EXISTS AS A NOVEL INTERTWINED DIMER -

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Basic information

Entry
Database: PDB / ID: 1aoj
TitleTHE SH3 DOMAIN OF EPS8 EXISTS AS A NOVEL INTERTWINED DIMER
ComponentsEPS8
KeywordsSIGNAL TRANSDUCTION / SH3 DOMAIN / EPS8 / PROLINE RICH PEPTIDE
Function / homology
Function and homology information


regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / stereocilium bundle / behavioral response to ethanol / barbed-end actin filament capping / stereocilium / NMDA selective glutamate receptor complex ...regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / stereocilium bundle / behavioral response to ethanol / barbed-end actin filament capping / stereocilium / NMDA selective glutamate receptor complex / exit from mitosis / Rac protein signal transduction / brush border / actin filament bundle assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / cellular response to leukemia inhibitory factor / adult locomotory behavior / small GTPase binding / ruffle membrane / regulation of cell shape / actin binding / actin cytoskeleton organization / growth cone / cell cortex / postsynaptic density / synapse / glutamatergic synapse / cytosol
Similarity search - Function
Epidermal growth factor receptor kinase substrate, phosphotyrosine-binding domain / Eps8, SH3 domain / Epidermal growth factor receptor kinase substrate 8-like / SAM domain / : / SAM domain (Sterile alpha motif) / EPS8 spectrin-like domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain ...Epidermal growth factor receptor kinase substrate, phosphotyrosine-binding domain / Eps8, SH3 domain / Epidermal growth factor receptor kinase substrate 8-like / SAM domain / : / SAM domain (Sterile alpha motif) / EPS8 spectrin-like domain / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SH3 Domains / Sterile alpha motif/pointed domain superfamily / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Epidermal growth factor receptor kinase substrate 8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKishan, K.V.R. / Newcomer, M.E.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: The SH3 domain of Eps8 exists as a novel intertwined dimer.
Authors: Kishan, K.V. / Scita, G. / Wong, W.T. / Di Fiore, P.P. / Newcomer, M.E.
#1: Journal: Embo J. / Year: 1993
Title: Eps8, a Substrate for the Epidermal Growth Factor Receptor Kinase, Enhances Egf-Dependent Mitogenic Signals
Authors: Fazioli, F. / Minichiello, L. / Matoska, V. / Castagnino, P. / Miki, T. / Wong, W.T. / Di Fiore, P.P.
History
DepositionJul 7, 1997Processing site: BNL
Revision 1.0Jul 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPS8
B: EPS8


Theoretical massNumber of molelcules
Total (without water)14,0902
Polymers14,0902
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-27 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.690, 28.338, 36.825
Angle α, β, γ (deg.)107.53, 96.83, 104.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein EPS8 / SRC HOMOLOGY DOMAIN


Mass: 7044.960 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q08509
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.52 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.4M SODIUM POTASSIUM TARTRATE, PH 7.5. PROTEIN CONC. 6MG/ML. CRYSTALLIZATION TIME 2-3 WEEKS.
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
20.2 Msodium potassium tartrate1drop

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: MSC/YALE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→32 Å / Num. obs: 3406 / % possible obs: 97 % / Observed criterion σ(I): 4 / Redundancy: 6.2 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.3 / % possible all: 92
Reflection
*PLUS
Num. measured all: 21281
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameVersionClassification
ALMNmodel building
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(ALMN)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHF

1shf


Resolution: 2.5→32 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: R-FREE THROUGHOUT / σ(F): 2 / Stereochemistry target values: TNT PROTGEO
Details: REFINEMENT FIRST STARTED WITH X-PLOR SIMULATED ANNEALING PROTOCOL
RfactorNum. reflection% reflectionSelection details
Rfree0.27 140 5 %RANDOM
Rwork0.193 ---
obs-2927 83.4 %-
Solvent computationBsol: 192 Å2 / ksol: 0.679 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 0 35 1019
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00510020.8
X-RAY DIFFRACTIONt_angle_deg1.5413431.3
X-RAY DIFFRACTIONt_dihedral_angle_d22.3526050
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.004292
X-RAY DIFFRACTIONt_gen_planes0.0071405
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.0173710
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.193 / Rfactor Rfree: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg22.3520
X-RAY DIFFRACTIONt_planar_d0.0042
X-RAY DIFFRACTIONt_plane_restr0.0075

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