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- PDB-1i0c: EPS8 SH3 CLOSED MONOMER -

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Basic information

Entry
Database: PDB / ID: 1i0c
TitleEPS8 SH3 CLOSED MONOMER
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 / stereocilium bundle / behavioral response to ethanol / barbed-end actin filament capping / exit from mitosis / stereocilium ...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 / exit from mitosis / stereocilium / NMDA selective glutamate receptor complex / 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 / growth cone / actin cytoskeleton organization / 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 / : / EPS8 spectrin-like domain / SAM domain / SAM domain (Sterile alpha motif) / 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 / : / EPS8 spectrin-like domain / 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: 2 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL UNIT IS A MONOMER.

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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
Water1,65792
1
A: EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8


Theoretical massNumber of molelcules
Total (without water)7,0451
Polymers7,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8


Theoretical massNumber of molelcules
Total (without water)7,0451
Polymers7,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.736, 49.736, 36.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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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.: 92 / 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: 1.85 Å3/Da / Density % sol: 33.42 %
Crystal growpH: 4 / Details: pH 4.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
121 %PEG40001reservoir
210 %isopropanol1reservoir
3100 mMsodium citrate1reservoir
414 mg/mlprotein1drop

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→21.54 Å / Num. all: 6799 / Num. obs: 6795 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.1 Å2 / Limit h max: 21 / Limit h min: -20 / Limit k max: 24 / Limit k min: -20 / Limit l max: 18 / Limit l min: 0 / Observed criterion F max: 318300.17 / Observed criterion F min: 0.55 / Rmerge(I) obs: 0.069
Reflection
*PLUS
% possible obs: 99.7 % / Num. measured all: 24299

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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: 2→22 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 713 10.9 %random
Rwork0.189 ---
all-6799 --
obs-6548 96.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 40.1813 Å2 / ksol: 0.342613 e/Å3
Displacement parametersBiso max: 58.2 Å2 / Biso mean: 25.6 Å2 / Biso min: 12.69 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å23.17 Å20 Å2
2--2.53 Å20 Å2
3----5.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 0 92 1055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_improper_angle_d1.01
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 (%)
2-2.090.2328710.40.2356790.02583776691.5
2.09-2.20.287100.2037350.02186782294.8
2.2-2.340.238799.50.2346740.02782775390.9
2.34-2.520.2039410.90.2037530.02186584797.9
2.52-2.770.2119210.70.217460.02285783897.8
2.77-3.170.2069010.80.2057350.02283682598.7
3.17-3.990.1659811.40.167500.01785584899.1
3.99-21.540.1648610.10.1657630.01885384999.5
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: 2 Å / Lowest resolution: 22 Å / σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.232 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.235

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