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- PDB-1h0a: Epsin ENTH bound to Ins(1,4,5)P3 -

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Basic information

Entry
Database: PDB / ID: 1h0a
TitleEpsin ENTH bound to Ins(1,4,5)P3
ComponentsEPSIN
KeywordsENDOCYTOSIS / EPSIN / ENTH / CLATHRIN / TRISKELION / COATED VESICLES / ALPHA-ALPHA SUPERHELIX / INS(1 / 4 / 5)P3
Function / homology
Function and homology information


positive regulation of clathrin coat assembly / EGFR downregulation / negative regulation of sprouting angiogenesis / clathrin vesicle coat / clathrin coat assembly / molecular sequestering activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / membrane fission ...positive regulation of clathrin coat assembly / EGFR downregulation / negative regulation of sprouting angiogenesis / clathrin vesicle coat / clathrin coat assembly / molecular sequestering activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / membrane fission / clathrin binding / embryonic organ development / clathrin-coated pit / Notch signaling pathway / female pregnancy / phospholipid binding / Schaffer collateral - CA1 synapse / terminal bouton / endocytosis / presynapse / presynaptic membrane / postsynaptic membrane / postsynapse / in utero embryonic development / transmembrane transporter binding / endosome / nucleus / plasma membrane / cytosol
Similarity search - Function
ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Epsin-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFord, M.G.J. / McMahon, H.T. / Evans, P.R.
CitationJournal: Nature / Year: 2002
Title: Curvature of Clathrin-Coated Pits Driven by Epsin
Authors: Ford, M.G.J. / Mills, I. / Peter, B. / Vallis, Y. / Praefcke, G. / Evans, P.R. / Mcmahon, H.T.
History
DepositionJun 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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: EPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2777
Polymers18,4161
Non-polymers8616
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.209, 95.823, 118.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein EPSIN /


Mass: 18416.010 Da / Num. of mol.: 1 / Fragment: ENTH DOMAIN, RESIDUES 1-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS / References: UniProt: O88339
#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.3 Å3/Da / Density % sol: 62.8 %
Crystal growpH: 7.4 / Details: 35-38% DIOXANE, pH 7.40
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135-38 %dioxane1reservoir
21.8 mMIns(a,4,5)P31reservoir
30.600 mMepsinENTH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 / Details: BENT MIRROR
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→74.54 Å / Num. obs: 24504 / % possible obs: 97.6 % / Observed criterion σ(I): 6 / Redundancy: 5.88 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.9798
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.33 / % possible all: 88.5
Reflection
*PLUS
Lowest resolution: 31.87 Å / % possible obs: 98 % / Redundancy: 5.9 %
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 89 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDU

1edu


Resolution: 1.7→74.54 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.725 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS CRYSTALLISATION CONDITIONS CONTAINED A 3-FOLD MOLAR EXCESS OF INS(1,4,5)P3 OVER THE EPSIN ENTH
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2559 10 %RANDOM
Rwork0.185 ---
obs0.189 22928 97.4 %-
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: 28.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2--3.14 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 54 204 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
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_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5931.5801
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.69321311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7163629
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7484.5610
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 162
Rwork0.321 1406
Refinement
*PLUS
Lowest resolution: 31.87 Å / Num. reflection obs: 25487 / % reflection Rfree: 10 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.033
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.3

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