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- PDB-2qyw: Crystal structure of mouse vti1b Habc domain -

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Basic information

Entry
Database: PDB / ID: 2qyw
TitleCrystal structure of mouse vti1b Habc domain
ComponentsVesicle transport through interaction with t-SNAREs 1B homolog
KeywordsPROTEIN TRANSPORT / ENDOCYTOSIS / Habc domain
Function / homology
Function and homology information


vesicle fusion with Golgi apparatus / Golgi to vacuole transport / Platelet degranulation / SNARE complex / chloride channel inhibitor activity / SNAP receptor activity / intra-Golgi vesicle-mediated transport / retrograde transport, endosome to Golgi / regulation of protein localization to plasma membrane / vesicle-mediated transport ...vesicle fusion with Golgi apparatus / Golgi to vacuole transport / Platelet degranulation / SNARE complex / chloride channel inhibitor activity / SNAP receptor activity / intra-Golgi vesicle-mediated transport / retrograde transport, endosome to Golgi / regulation of protein localization to plasma membrane / vesicle-mediated transport / SNARE binding / macroautophagy / intracellular protein transport / ER to Golgi transport vesicle membrane / recycling endosome membrane / synaptic vesicle / late endosome membrane / early endosome membrane / lysosomal membrane / neuronal cell body / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / membrane / cytosol
Similarity search - Function
t-snare proteins / 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 / SNARE / Helical region found in SNAREs / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vesicle transport through interaction with t-SNAREs homolog 1B / Vesicle transport through interaction with t-SNAREs 1B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsMiller, S.E. / Collins, B.M. / McCoy, A.J. / Robinson, M.S. / Owen, D.J.
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 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vesicle transport through interaction with t-SNAREs 1B homolog


Theoretical massNumber of molelcules
Total (without water)11,9751
Polymers11,9751
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.227, 25.167, 80.115
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vesicle transport through interaction with t-SNAREs 1B homolog


Mass: 11974.978 Da / Num. of mol.: 1 / Fragment: Habc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vti1b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/plysS / References: UniProt: Q91XH6, UniProt: O88384*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Tris, 30% ethanol and 20% glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→79 Å / Num. obs: 6751 / % possible obs: 96.9 % / Observed criterion σ(F): 4 / Redundancy: 9.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.884 / SU B: 9.984 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29653 648 10 %RANDOM
Rwork0.21815 ---
obs0.22518 5850 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.105 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.13 Å2
2--1.38 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 0 52 839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022798
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.991066
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.508595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93623.72143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.03115162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.968159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02603
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2314
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2870.2519
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2781.5503
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8482763
X-RAY DIFFRACTIONr_scbond_it3.3443334
X-RAY DIFFRACTIONr_scangle_it4.8664.5303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 38 -
Rwork0.199 326 -
obs--73.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.45651.8286.51821.18063.910416.96660.04990.44030.0764-0.14840.1323-0.1866-0.25260.6928-0.1822-0.0340.0530.0580.02290.0165-0.0019-0.312615.001620.481
20.63710.77350.98282.02044.060511.4253-0.00840.14420.02330.0915-0.01520.07140.61350.01010.02360.01660.0174-0.0125-0.01290.0116-0.0008-6.72527.305119.6444
30.97491.39833.39152.04275.349818.151-0.1015-0.01860.3917-0.1164-0.43980.3404-0.3167-1.1320.5413-0.05640.106-0.02210.08830.0088-0.0197-11.346118.471122.8726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 367 - 42
2X-RAY DIFFRACTION2AA37 - 7043 - 76
3X-RAY DIFFRACTION3AA71 - 9677 - 102

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