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- PDB-2v8s: VTI1B HABC DOMAIN - EPSINR ENTH DOMAIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2v8s
TitleVTI1B HABC DOMAIN - EPSINR ENTH DOMAIN COMPLEX
Components
  • CLATHRIN INTERACTOR 1
  • VESICLE TRANSPORT THROUGH INTERACTION WITH T-SNARES HOMOLOG 1B
KeywordsPROTEIN TRANSPORT / CYTOPLASMIC VESICLE / LIPID-BINDING / TRANSMEMBRANE / PHOSPHORYLATION / ALTERNATIVE SPLICING / VTI1B-EPSINR COMPLEX / CYTOPLASM / TRANSPORT / ENDOCYTOSIS / COILED COIL / SNARE / CARGO / ADAPTOR / VESICLE / MEMBRANE / CLATHRIN
Function / homology
Function and homology information


vesicle fusion with Golgi apparatus / clathrin vesicle coat / Golgi to vacuole transport / platelet degranulation / chloride channel inhibitor activity / clathrin coat assembly / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / protein targeting to vacuole ...vesicle fusion with Golgi apparatus / clathrin vesicle coat / Golgi to vacuole transport / platelet degranulation / chloride channel inhibitor activity / clathrin coat assembly / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / protein targeting to vacuole / vesicle docking involved in exocytosis / retrograde transport, endosome to Golgi / clathrin binding / Golgi Associated Vesicle Biogenesis / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of protein localization to plasma membrane / vesicle-mediated transport / SNARE binding / platelet alpha granule lumen / phospholipid binding / ER to Golgi transport vesicle membrane / recycling endosome / endocytosis / recycling endosome membrane / synaptic vesicle / Platelet degranulation / late endosome membrane / early endosome membrane / vesicle / membrane fusion / membrane => GO:0016020 / endosome / cadherin binding / lysosomal membrane / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
t-snare proteins / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE, N-terminal domain superfamily / Vesicle transport v-SNARE protein N-terminus / ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / SNARE ...t-snare proteins / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE, N-terminal domain superfamily / Vesicle transport v-SNARE protein N-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 / 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
Clathrin interactor 1 / Vesicle transport through interaction with t-SNAREs homolog 1B / Vesicle transport through interaction with t-SNAREs homolog 1B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsOwen, D.J. / McCoy, A.J. / Collins, B.M. / Miller, S.E.
CitationJournal: Nature / Year: 2007
Title: A Snare-Adaptor Interaction is a New Mode of Cargo Recognition in Clathrin Coated Vesicles
Authors: Miller, S.E. / Collins, B.M. / Mccoy, A.J. / Robinson, M.S. / Owen, D.J.
History
DepositionAug 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: CLATHRIN INTERACTOR 1
V: VESICLE TRANSPORT THROUGH INTERACTION WITH T-SNARES HOMOLOG 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1497
Polymers28,6892
Non-polymers4605
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-1.9 kcal/mol
Surface area16650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.231, 60.935, 40.998
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CLATHRIN INTERACTOR 1 / EPSINR / EPSIN-4 / EPSIN-RELATED PROTEIN / ENTHOPROTIN / CLATHRIN-INTERACTING PROTEIN LOCALIZED IN ...EPSINR / EPSIN-4 / EPSIN-RELATED PROTEIN / ENTHOPROTIN / CLATHRIN-INTERACTING PROTEIN LOCALIZED IN THE TRANS-GOLGI REGION / CLINT


Mass: 17434.732 Da / Num. of mol.: 1 / Fragment: ENTH, RESIDUES 20-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 PLYSS / References: UniProt: Q14677
#2: Protein VESICLE TRANSPORT THROUGH INTERACTION WITH T-SNARES HOMOLOG 1B / VTI1B / VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1 / VTI1-RP1


Mass: 11253.795 Da / Num. of mol.: 1 / Fragment: HABC DOMAIN, RESIDUES 1-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 PLYSS / References: UniProt: Q96J28, UniProt: Q9UEU0*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.2 Å3/Da / Density % sol: 43.75 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19.9 Å / Num. obs: 11925 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.5 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNCOMPLEXED STRUCTURES

Resolution: 2.22→19.55 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.973 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 591 4.9 %RANDOM
Rwork0.196 ---
obs0.201 11579 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.06 Å2
2---0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.22→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 30 75 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212021
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.9782700
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.255240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48623.514111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.24815409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.241524
X-RAY DIFFRACTIONr_chiral_restr0.1540.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021522
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2922
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21329
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3411.51234
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.15721881
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3373920
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8714.5816
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: 2.22→2.27 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.39 51
Rwork0.227 767

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