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- PDB-1edu: CRYSTAL STRUCTURE OF THE ENTH DOMAIN OF RAT EPSIN 1 -

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Basic information

Entry
Database: PDB / ID: 1edu
TitleCRYSTAL STRUCTURE OF THE ENTH DOMAIN OF RAT EPSIN 1
ComponentsEH domain binding protein EPSIN
KeywordsENDOCYTOSIS/EXOCYTOSIS / ALPHA-HELIX / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsHyman, J.H. / Chen, H. / Decamilli, P. / Brunger, A.T.
CitationJournal: J.Cell Biol. / Year: 2000
Title: Epsin 1 undergoes nucleocytosolic shuttling and its eps15 interactor NH(2)-terminal homology (ENTH) domain, structurally similar to Armadillo and HEAT repeats, interacts with the transcription ...Title: Epsin 1 undergoes nucleocytosolic shuttling and its eps15 interactor NH(2)-terminal homology (ENTH) domain, structurally similar to Armadillo and HEAT repeats, interacts with the transcription factor promyelocytic leukemia Zn(2)+ finger protein (PLZF).
Authors: Hyman, J. / Chen, H. / Di Fiore, P.P. / De Camilli, P. / Brunger, A.T.
History
DepositionJan 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EH domain binding protein EPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8085
Polymers17,5601
Non-polymers2484
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.807, 49.807, 99.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein EH domain binding protein EPSIN


Mass: 17559.980 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: NEURON / Organ: BRAIN / Plasmid: PGEX6T-1 / Production host: Bacteria (eubacteria) / References: UniProt: O88339
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Na-HEPES, ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
2100 mMsodium-HEPES1reservoir
310 %PEG10001reservoir
48 %ethylene glycol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11051
21051
31051
41051
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL1-511.06883
SYNCHROTRONSSRL BL1-520.97984
SYNCHROTRONSSRL BL1-530.97961
SYNCHROTRONSSRL BL1-540.92526
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 15, 1999
ADSC QUANTUM 42CCDJun 15, 1999
ADSC QUANTUM 43CCDJun 15, 1999
ADSC QUANTUM 44CCDJun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.068831
20.979841
30.979611
40.925261
ReflectionResolution: 1.8→60 Å / Num. all: 25701 / Num. obs: 24057 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 10.7 % / Biso Wilson estimate: 17.9337 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.26
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Num. unique all: 2560 / % possible all: 68.3
Reflection
*PLUS
Redundancy: 5.44 %
Reflection shell
*PLUS
% possible obs: 68.3 % / Redundancy: 2.03 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.8→500 Å / Stereochemistry target values: huber/engh
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2241 -random
Rwork0.206 ---
all-25723 --
obs-23618 91.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 16 63 1289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.05835
X-RAY DIFFRACTIONc_bond_d0.00507
X-RAY DIFFRACTIONc_torsion_deg17.7785
X-RAY DIFFRACTIONc_torsion_impr_deg0.66397
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 500 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.246 / Rfactor obs: 0.252

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