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- PDB-5lp0: CRYSTAL STRUCTURE OF THE ZEBRA FISH ENTH DOMAIN FROM EPSIN1 IN 1.... -

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Basic information

Entry
Database: PDB / ID: 5lp0
TitleCRYSTAL STRUCTURE OF THE ZEBRA FISH ENTH DOMAIN FROM EPSIN1 IN 1.41 ANGSTROM RESOLUTION
ComponentsEpsin 1
KeywordsSIGNALING PROTEIN / ALPHA-HELIX / INTRACELLULAR MEMBRANE TRAFFICKING / ENDOCYTOSIS MEMBRANE ASSEMBLY / UBIQUITIN-BINDING PROTEIN
Function / homology
Function and homology information


lipid binding / cytoplasm
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
PHOSPHATE ION / : / Epsin 1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsLevin-Kravets, O. / Prag, G.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation464/11 Israel
Israel Science Foundation1695/08 Israel
Citation
Journal: Nat.Methods / Year: 2016
Title: A bacterial genetic selection system for ubiquitylation cascade discovery.
Authors: Levin-Kravets, O. / Tanner, N. / Shohat, N. / Attali, I. / Keren-Kaplan, T. / Shusterman, A. / Artzi, S. / Varvak, A. / Reshef, Y. / Shi, X. / Zucker, O. / Baram, T. / Katina, C. / Pilzer, I. ...Authors: Levin-Kravets, O. / Tanner, N. / Shohat, N. / Attali, I. / Keren-Kaplan, T. / Shusterman, A. / Artzi, S. / Varvak, A. / Reshef, Y. / Shi, X. / Zucker, O. / Baram, T. / Katina, C. / Pilzer, I. / Ben-Aroya, S. / Prag, G.
#1: Journal: 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.
#2: Journal: Nature / Year: 2002
Title: Curvature Of Clathrin-Coated Pits Driven By Epsin.
Authors: Ford, M.G. / Mills, I.G. / Peter, B.J. / Vallis, Y. / Praefcke, G.J. / Evans, P.R. / Mcmahon, H.T.
History
DepositionAug 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Dec 13, 2017Group: Advisory / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity.pdbx_description / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epsin 1
B: Epsin 1
C: Epsin 1
D: Epsin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2586
Polymers67,0684
Non-polymers1902
Water14,826823
1
A: Epsin 1


Theoretical massNumber of molelcules
Total (without water)16,7671
Polymers16,7671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epsin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8622
Polymers16,7671
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Epsin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8622
Polymers16,7671
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Epsin 1


Theoretical massNumber of molelcules
Total (without water)16,7671
Polymers16,7671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.364, 51.724, 64.639
Angle α, β, γ (deg.)89.33, 76.37, 79.74
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Epsin 1


Mass: 16767.115 Da / Num. of mol.: 4 / Fragment: ENTH DOMAIN RESIDUES 18-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: epn1 / Plasmid: PGST P.2 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: F1Q523, UniProt: F1Q5Z9*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 19% (W/V) PEG 3350, 0.1M POTASSIUM PHOSPHATE MONOBASIC MONOHYDRATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97881 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97881 Å / Relative weight: 1
ReflectionResolution: 1.41→62.788 Å / Num. obs: 95136 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 15.35 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.6
Reflection shellResolution: 1.41→1.46 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.8_1069refinement
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H0A

1h0a


Resolution: 1.41→40.49 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.202 4738 4.98 %
Rwork0.154 --
obs0.157 95053 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.52 Å2
Refinement stepCycle: LAST / Resolution: 1.41→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 10 823 5309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094842
X-RAY DIFFRACTIONf_angle_d1.1346563
X-RAY DIFFRACTIONf_dihedral_angle_d14.3741966
X-RAY DIFFRACTIONf_chiral_restr0.065714
X-RAY DIFFRACTIONf_plane_restr0.006844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4091-1.42510.29071540.18682796X-RAY DIFFRACTION87
1.4251-1.44190.26871430.17122931X-RAY DIFFRACTION91
1.4419-1.45950.25591590.15872943X-RAY DIFFRACTION92
1.4595-1.47790.25461400.15392966X-RAY DIFFRACTION92
1.4779-1.49740.22021410.15272955X-RAY DIFFRACTION93
1.4974-1.51790.2621800.15652990X-RAY DIFFRACTION91
1.5179-1.53960.24331330.15732954X-RAY DIFFRACTION93
1.5396-1.56260.22181220.14672967X-RAY DIFFRACTION91
1.5626-1.5870.23051540.13462866X-RAY DIFFRACTION90
1.587-1.6130.20661650.13592929X-RAY DIFFRACTION91
1.613-1.64080.23871590.13742988X-RAY DIFFRACTION93
1.6408-1.67070.2111460.13513083X-RAY DIFFRACTION95
1.6707-1.70280.23061650.1372990X-RAY DIFFRACTION94
1.7028-1.73750.1971590.13453045X-RAY DIFFRACTION94
1.7375-1.77530.20761720.14343036X-RAY DIFFRACTION95
1.7753-1.81660.20381340.14743025X-RAY DIFFRACTION95
1.8166-1.86210.22821530.15123014X-RAY DIFFRACTION93
1.8621-1.91240.22421550.15482982X-RAY DIFFRACTION92
1.9124-1.96870.20231600.15473024X-RAY DIFFRACTION96
1.9687-2.03220.2241590.15043087X-RAY DIFFRACTION95
2.0322-2.10480.2121440.14263052X-RAY DIFFRACTION95
2.1048-2.18910.2061680.14293094X-RAY DIFFRACTION96
2.1891-2.28870.17131530.13573053X-RAY DIFFRACTION96
2.2887-2.40940.19121860.1443014X-RAY DIFFRACTION94
2.4094-2.56030.18611740.14623091X-RAY DIFFRACTION97
2.5603-2.7580.18571830.15133092X-RAY DIFFRACTION97
2.758-3.03540.2011690.16043131X-RAY DIFFRACTION97
3.0354-3.47450.19711700.16113054X-RAY DIFFRACTION96
3.4745-4.37660.17431820.1513085X-RAY DIFFRACTION97
4.3766-40.51180.20111560.19833078X-RAY DIFFRACTION96

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