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- PDB-2w3c: Globular head region of the human general vesicular transport fac... -

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Basic information

Entry
Database: PDB / ID: 2w3c
TitleGlobular head region of the human general vesicular transport factor p115
ComponentsGENERAL VESICULAR TRANSPORT FACTOR P115
KeywordsTRANSPORT PROTEIN / MEMBRANE VESICLE TETHERING / ARMADILLO FOLD / GOLGI APPARATUS / ER-GOLGI TRANSPORT / ENDOPLASMATIC RETICULUM / P115 / GOLGI / USO1P / GOLGIN / MEMBRANE
Function / homology
Function and homology information


: / vesicle fusion with Golgi apparatus / transcytosis / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / microtubule organizing center / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / transport vesicle / intracellular protein transport ...: / vesicle fusion with Golgi apparatus / transcytosis / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / microtubule organizing center / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / transport vesicle / intracellular protein transport / ER to Golgi transport vesicle membrane / membrane fusion / cadherin binding / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / RNA binding / membrane / cytosol
Similarity search - Function
Vesicle tethering protein p115, armadillo tether-repeat / Armadillo tether-repeat of vescicular transport factor / Vesicle tethering protein Uso1/P115-like , head domain / Uso1/p115-like vesicle tethering protein, C-terminal / : / Uso1 / p115 like vesicle tethering protein, head region / Uso1 / p115 like vesicle tethering protein, C terminal region / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeats / Armadillo ...Vesicle tethering protein p115, armadillo tether-repeat / Armadillo tether-repeat of vescicular transport factor / Vesicle tethering protein Uso1/P115-like , head domain / Uso1/p115-like vesicle tethering protein, C-terminal / : / Uso1 / p115 like vesicle tethering protein, head region / Uso1 / p115 like vesicle tethering protein, C terminal region / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / General vesicular transport factor p115
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsStriegl, H. / Roske, Y. / Kummel, D. / Heinemann, U.
CitationJournal: Plos One / Year: 2009
Title: Unusual Armadillo Fold in the Human General Vesicular Transport Factor P115
Authors: Striegl, H. / Roske, Y. / Kummel, D. / Heinemann, U.
History
DepositionNov 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENERAL VESICULAR TRANSPORT FACTOR P115
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6614
Polymers64,3431
Non-polymers3183
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)175.550, 68.890, 85.750
Angle α, β, γ (deg.)90.00, 108.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GENERAL VESICULAR TRANSPORT FACTOR P115 / PROTEIN USO1 HOMOLOG / TRANSCYTOSIS-ASSOCIATED PROTEIN / VESICLE-DOCKING PROTEIN


Mass: 64342.543 Da / Num. of mol.: 1
Fragment: ARMADILLO HELICAL DOMAIN, USO1 HEAD DOMAIN, RESIDUES 53-629
Source method: isolated from a genetically manipulated source
Details: LACKING N-TERMINAL RESIDUES 1-53 AND PUTATIVE C-TERMINAL COILED-COIL DOMAIN (630-962)
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60763
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.8 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.22→19.85 Å / Num. obs: 43877 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.2
Reflection shellResolution: 2.22→2.35 Å / % possible all: 82.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.22→19.85 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.501 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2352 5 %RANDOM
Rwork0.219 ---
obs0.222 44669 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å22.46 Å2
2--2.76 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.22→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4275 0 21 123 4419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9745940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72425.532188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0115781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2431518
X-RAY DIFFRACTIONr_chiral_restr0.10.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023223
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.22086
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23069
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.852836
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.91364455
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.66971730
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.63371485
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→2.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.444 167
Rwork0.401 3159
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)
16.4444-3.8107-1.78744.01571.09953.63450.1596-0.35590.19650.44-0.11910.27960.17820.0598-0.04050.1120.0074-0.0142-0.27380.05470.1792-54.82355.767340.4236
23.6385-1.2043-1.02011.6750.73880.41860.36510.93240.2538-0.3324-0.2059-0.014-0.2426-0.0241-0.15920.0270.1077-0.0540.22810.1074-0.1818-23.8672-8.645915.409
32.5349-0.2188-0.75731.20660.0422.0460.00110.0584-0.0772-0.0168-0.0276-0.4240.03850.64390.0265-0.0530.0477-0.04640.1942-0.0082-0.1013-0.0667-21.401129.8074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 158
2X-RAY DIFFRACTION2A159 - 407
3X-RAY DIFFRACTION3A408 - 575

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