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- PDB-5loz: STRUCTURE OF YEAST ENT1 ENTH DOMAIN -

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Basic information

Entry
Database: PDB / ID: 5loz
TitleSTRUCTURE OF YEAST ENT1 ENTH DOMAIN
ComponentsEpsin-1
KeywordsUBIQUITIN-BINDING DOMAIN / ALPHA-ALPHA SUPERHELIX / UBIQUITIN RECEPTOR / ENDOCYTOSIS ADAPTOR / UBIQUITIN / CLATHRIN / LIPID / EPS15
Function / homology
Function and homology information


Cargo recognition for clathrin-mediated endocytosis / actin cortical patch assembly / clathrin vesicle coat / cellular bud tip / cellular bud neck / mating projection tip / clathrin binding / ubiquitin binding / actin filament organization / phospholipid binding ...Cargo recognition for clathrin-mediated endocytosis / actin cortical patch assembly / clathrin vesicle coat / cellular bud tip / cellular bud neck / mating projection tip / clathrin binding / ubiquitin binding / actin filament organization / phospholipid binding / endocytosis / early endosome / endosome / plasma membrane / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTanner, N. / Prag, G.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation464/11 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: Acta Crystallogr.,Sect.F / Year: 2012
Title: Purification And Crystallization Of Yeast Ent1 Enth Domain.
Authors: Levin Kravets, O. / Tanner, N. / Shohat, N. / Artzi, S. / Varvak, A. / Reshef, Y. / Attali, I. / Katina, C. / Keren Kaplan, T. / Prag, G.
#2: Journal: Embo J. / Year: 2012
Title: Synthetic Biology Approach To Reconstituting The Ubiquitylation Cascade In Bacteria.
Authors: Keren-Kaplan, T. / Attali, I. / Motamedchaboki, K. / Davis, B.A. / Tanner, N. / Reshef, Y. / Laudon, E. / Kolot, M. / Levin-Kravets, O. / Kleifeld, O. / Glickman, M. / Horazdovsky, B.F. / Wolf, D.A. / Prag, G.
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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epsin-1


Theoretical massNumber of molelcules
Total (without water)15,9811
Polymers15,9811
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.690, 35.460, 110.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Epsin-1


Mass: 15981.050 Da / Num. of mol.: 1 / Fragment: ENTH DOMAIN, RESIDUES 17-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ENT1, YDL161W / Plasmid: MODIFIED PCDFDUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12518
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20%(W/V) PEG 3350, 0.1 M HEPES PH 7.5, 3.5% TACSIMATE PH 7.0, VAPOR DIFFUSION, SITTING DROP
PH range: 7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2010
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→55.42 Å / Num. obs: 9844 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 19.86 Å2 / Rsym value: 0.166 / Net I/σ(I): 6.79
Reflection shellResolution: 1.95→2.06 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.01022 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→55.42 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.353 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 475 4.8 %RANDOM
Rwork0.186 ---
obs0.193 9366 98.7 %-
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: 14.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.95→55.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 0 97 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221178
X-RAY DIFFRACTIONr_bond_other_d0.0080.02831
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9571586
X-RAY DIFFRACTIONr_angle_other_deg0.99732027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5085148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.28924.68864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22515241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1821510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
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_it1.4461.5698
X-RAY DIFFRACTIONr_mcbond_other0.4341.5286
X-RAY DIFFRACTIONr_mcangle_it2.42121128
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8353480
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7674.5451
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 41 -
Rwork0.309 656 -
obs--98.87 %

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