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- PDB-3onl: yeast Ent3_ENTH-Vti1p_Habc complex structure -

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Basic information

Entry
Database: PDB / ID: 3onl
Titleyeast Ent3_ENTH-Vti1p_Habc complex structure
Components
  • Epsin-3
  • t-SNARE VTI1
KeywordsPROTEIN TRANSPORT / HELIX / ENTH / HABC / recognition between SNARE and adaptor
Function / homology
Function and homology information


vacuolar calcium ion homeostasis / amphisome-lysosome fusion / Retrograde transport at the Trans-Golgi-Network / vesicle fusion with Golgi apparatus / Golgi vesicle fusion to target membrane / clathrin vesicle coat / early endosome to Golgi transport / Golgi to vacuole transport / vacuole fusion, non-autophagic / Golgi to endosome transport ...vacuolar calcium ion homeostasis / amphisome-lysosome fusion / Retrograde transport at the Trans-Golgi-Network / vesicle fusion with Golgi apparatus / Golgi vesicle fusion to target membrane / clathrin vesicle coat / early endosome to Golgi transport / Golgi to vacuole transport / vacuole fusion, non-autophagic / Golgi to endosome transport / Platelet degranulation / late endosome to vacuole transport via multivesicular body sorting pathway / SNAP receptor activity / SNARE complex / vesicle fusion / intra-Golgi vesicle-mediated transport / multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / fungal-type vacuole membrane / retrograde transport, endosome to Golgi / phosphatidylinositol-3,5-bisphosphate binding / vacuolar membrane / clathrin binding / autophagosome membrane / SNARE binding / intracellular protein transport / macroautophagy / ER to Golgi transport vesicle membrane / phospholipid binding / endocytosis / late endosome membrane / protein transport / actin cytoskeleton organization / endosome / endosome membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
t-snare proteins / GOSR2/Membrin/Bos1 / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE protein N-terminus / Vesicle transport v-SNARE, N-terminal domain superfamily / Snare region anchored in the vesicle membrane C-terminus / ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain ...t-snare proteins / GOSR2/Membrin/Bos1 / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE protein N-terminus / Vesicle transport v-SNARE, N-terminal domain superfamily / Snare region anchored in the vesicle membrane C-terminus / ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / ENTH/VHS / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Epsin-3 / t-SNARE VTI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, J. / Fang, P. / Niu, L. / Teng, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Epsin N-terminal homology domains bind on opposite sides of two SNAREs
Authors: Wang, J. / Gossing, M. / Fang, P. / Zimmermann, J. / Li, X. / von Mollard, G.F. / Niu, L. / Teng, M.
History
DepositionAug 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Apr 2, 2014Group: Derived calculations
Revision 1.3Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epsin-3
B: Epsin-3
C: t-SNARE VTI1


Theoretical massNumber of molelcules
Total (without water)46,2393
Polymers46,2393
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.683, 82.351, 95.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHERE IS AN 1:1 COMPLEX FORMING BY TWO MONOMERIC PROTEIN.

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Components

#1: Protein Epsin-3 / ENT3


Mass: 17621.947 Da / Num. of mol.: 2 / Fragment: ENTH domain, residues 28-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: P47160
#2: Protein t-SNARE VTI1 / Vesicle transport v-SNARE protein VTI1 / Qb-SNARE VTI1 / VPS10-interacting protein 1


Mass: 10995.161 Da / Num. of mol.: 1 / Fragment: Habc domain, residues 3-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q04338
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2M tri-Lithium Citrate tetrahydrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23733 / % possible obs: 98.4 %
Reflection shellResolution: 2.2→2.28 Å / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3ONJ and 3ONK

3onj

3onk


Resolution: 2.2→33.71 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1213 5.1 %RANDOM
Rwork0.2233 ---
obs0.2256 23725 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 113.15 Å2 / Biso mean: 38.5679 Å2 / Biso min: 17.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 0 180 3157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223020
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.9524068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2345368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48724.088159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30415561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1211530
X-RAY DIFFRACTIONr_chiral_restr0.0760.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022279
X-RAY DIFFRACTIONr_mcbond_it2.041.51843
X-RAY DIFFRACTIONr_mcangle_it3.91922961
X-RAY DIFFRACTIONr_scbond_it4.42231177
X-RAY DIFFRACTIONr_scangle_it7.4784.51107
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 88 -
Rwork0.28 1528 -
all-1616 -
obs--91.25 %

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