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- PDB-5j08: Crystal structure of yeast Ent5 N-terminal domain-native P21 -

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Basic information

Entry
Database: PDB / ID: 5j08
TitleCrystal structure of yeast Ent5 N-terminal domain-native P21
ComponentsEpsin-5
KeywordsPROTEIN TRANSPORT / Vesicular transport / ENT5 / N-terminal domain / inositol phosphate
Function / homology
Function and homology information


clathrin vesicle coat / early endosome to Golgi transport / Golgi to endosome transport / late endosome to vacuole transport via multivesicular body sorting pathway / phosphatidylinositol-3,5-bisphosphate binding / clathrin binding / phospholipid binding / endocytosis / protein transport / endosome ...clathrin vesicle coat / early endosome to Golgi transport / Golgi to endosome transport / late endosome to vacuole transport via multivesicular body sorting pathway / phosphatidylinositol-3,5-bisphosphate binding / clathrin binding / phospholipid binding / endocytosis / protein transport / endosome / endosome membrane / plasma membrane / cytosol / 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 / 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: 1.8 Å
AuthorsZhang, F. / Song, Y. / Li, X. / Teng, M.K.
Funding support China, 2items
OrganizationGrant numberCountry
the Chinese Ministry of Science and Technology2012CB917200 and 2009CB825500 China
the Chinese National Natural Science Foundation31270014, 31130018, 30900224 and 10979039 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Structural and functional insight into the N-terminal domain of the clathrin adaptor Ent5 from Saccharomyces cerevisiae
Authors: Zhang, F. / Song, Y. / Ebrahimi, M. / Niu, L. / Teng, M.K. / Li, X.
History
DepositionMar 28, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epsin-5


Theoretical massNumber of molelcules
Total (without water)20,2771
Polymers20,2771
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.345, 51.758, 59.452
Angle α, β, γ (deg.)90.00, 103.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Epsin-5


Mass: 20277.492 Da / Num. of mol.: 1 / Fragment: UNP residues 31-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ENT5, YDR153C / Production host: Escherichia coli (E. coli) / References: UniProt: Q03769
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.5M Potassium thiocyanate,0.1M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 13631 / % possible obs: 84.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 35.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 12.8 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CMW

5cmw


Resolution: 1.8→28.96 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.559 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22002 676 5 %RANDOM
Rwork0.19984 ---
obs0.20086 12944 84.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.518 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å22.34 Å2
2---2.58 Å2-0 Å2
3---2.34 Å2
Refinement stepCycle: 1 / Resolution: 1.8→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 73 1367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191324
X-RAY DIFFRACTIONr_bond_other_d0.0040.021301
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9641789
X-RAY DIFFRACTIONr_angle_other_deg0.82332965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6665162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65122.98257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82315240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7031511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
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_it1.5192.715651
X-RAY DIFFRACTIONr_mcbond_other1.5112.712650
X-RAY DIFFRACTIONr_mcangle_it2.454.064812
X-RAY DIFFRACTIONr_mcangle_other2.4494.065813
X-RAY DIFFRACTIONr_scbond_it1.9062.92673
X-RAY DIFFRACTIONr_scbond_other1.9052.921674
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1684.286978
X-RAY DIFFRACTIONr_long_range_B_refined4.49921.971554
X-RAY DIFFRACTIONr_long_range_B_other4.43121.8821539
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 57 -
Rwork0.196 1094 -
obs--97.13 %

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