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- PDB-1i07: EPS8 SH3 DOMAIN INTERTWINED DIMER -

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Basic information

Entry
Database: PDB / ID: 1i07
TitleEPS8 SH3 DOMAIN INTERTWINED DIMER
ComponentsEPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8
KeywordsHORMONE/GROWTH FACTOR / HORMONE-GROWTH FACTOR complex
Function / homology
Function and homology information


regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / behavioral response to ethanol / stereocilium bundle / stereocilium / regulation of Rho protein signal transduction / barbed-end actin filament capping ...regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / behavioral response to ethanol / stereocilium bundle / stereocilium / regulation of Rho protein signal transduction / barbed-end actin filament capping / positive regulation of ruffle assembly / NMDA selective glutamate receptor complex / exit from mitosis / Rac protein signal transduction / regulation of postsynaptic membrane neurotransmitter receptor levels / brush border / actin filament bundle assembly / Rho protein signal transduction / adult locomotory behavior / cellular response to leukemia inhibitory factor / small GTPase binding / ruffle membrane / actin binding / cell cortex / regulation of cell shape / growth cone / actin cytoskeleton organization / vesicle / postsynaptic density / glutamatergic synapse / synapse / plasma membrane / 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) / Tensin/EPS8 phosphotyrosine-binding domain / Phosphotyrosine-binding domain / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / SH3 Domains ...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) / 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 / SH3 type barrels. / Src homology 3 domains / 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: 1.8 Å
AuthorsKishan, K.V.R. / Newcomer, M.E.
Citation
Journal: Protein Sci. / Year: 2001
Title: Effect of pH and salt bridges on structural assembly: molecular structures of the monomer and intertwined dimer of the Eps8 SH3 domain.
Authors: Kishan, K.V. / Newcomer, M.E. / Rhodes, T.H. / Guilliot, S.D.
#1: 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.
History
DepositionJan 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8
B: EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8


Theoretical massNumber of molelcules
Total (without water)14,0902
Polymers14,0902
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-29 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.899, 28.517, 37.188
Angle α, β, γ (deg.)107.39, 96.87, 104.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8


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.: 94 / 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: 1.9 Å3/Da / Density % sol: 35.1 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM1reservoirMgCl2
2100 mMsodium formate1reservoir
3100 mMTris1reservoir
47-10 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDate: Oct 9, 1998 / Details: MSC/YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25.93 Å / Num. all: 9088 / Num. obs: 33871 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4 / Redundancy: 3.7 % / Biso Wilson estimate: 16.4 Å2 / Limit h max: 15 / Limit h min: -15 / Limit k max: 15 / Limit k min: -15 / Limit l max: 20 / Limit l min: 0 / Observed criterion F max: 370952.57 / Observed criterion F min: 0.3 / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 90.2 % / Rmerge(I) obs: 0.353 / % possible all: 90.2
Reflection
*PLUS
Num. obs: 9088 / Num. measured all: 33871

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Processing

Software
NameVersionClassificationNB
CNS0.5refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1AOJ

1aoj


Resolution: 1.8→26 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 517 6.2 %RANDOM
Rwork0.202 ---
all-9590 --
obs-8373 87.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 41.5615 Å2 / ksol: 0.307324 e/Å3
Displacement parametersBiso max: 51.89 Å2 / Biso mean: 22.36 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å21.03 Å21.4 Å2
2--0.98 Å21.19 Å2
3---1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 0 94 1064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_improper_angle_d0.87
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.249554.50.2547790.034121183468.9
1.88-1.980.234514.30.2358900.033118894179.2
1.98-2.110.205534.50.2059450.028118499884.3
2.11-2.270.2116050.219960.0271200105688
2.27-2.50.202635.20.210320.0251204109590.9
2.5-2.860.207161.30.20711020.0521209111892.5
2.86-3.60.2031129.40.20210390.0191191115196.6
3.6-25.930.1841078.90.18410730.0181203118098.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1prot_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramcarbohydrate.top
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 26 Å / σ(F): 2 / % reflection Rfree: 6.2 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.249 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.254

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