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- PDB-3grl: Crystal Structure of the Monomer of the p115 Tether Globular Head... -

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Basic information

Entry
Database: PDB / ID: 3grl
TitleCrystal Structure of the Monomer of the p115 Tether Globular Head Domain
ComponentsGeneral vesicular transport factor p115
KeywordsTRANSPORT PROTEIN / vesicle transport / membrane trafficking / membrane tethering / membrane fusion / SNARE / Rab GTPase / armadillo repeats / ER-Golgi transport / Golgi apparatus / Membrane / Phosphoprotein / Protein transport / Transport
Function / homology
Function and homology information


COPII-mediated vesicle transport / inter-Golgi cisterna vesicle-mediated transport / Golgi vesicle docking / cytoplasmic side of Golgi membrane / vesicle fusion with Golgi apparatus / COPI-mediated anterograde transport / Golgi stack / transcytosis / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport ...COPII-mediated vesicle transport / inter-Golgi cisterna vesicle-mediated transport / Golgi vesicle docking / cytoplasmic side of Golgi membrane / vesicle fusion with Golgi apparatus / COPI-mediated anterograde transport / Golgi stack / transcytosis / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / ER to Golgi transport vesicle membrane / protein homooligomerization / membrane fusion / perinuclear region of cytoplasm / endoplasmic reticulum / identical protein binding / 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 / Leucine-rich Repeat Variant ...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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / General vesicular transport factor p115
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsAn, Y. / Elsliger, M.A. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and functional analysis of the globular head domain of p115 provides insight into membrane tethering.
Authors: An, Y. / Chen, C.Y. / Moyer, B. / Rotkiewicz, P. / Elsliger, M.A. / Godzik, A. / Wilson, I.A. / Balch, W.E.
History
DepositionMar 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)72,7622
Polymers72,6671
Non-polymers951
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: General vesicular transport factor p115
hetero molecules

A: General vesicular transport factor p115
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5244
Polymers145,3342
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area3440 Å2
ΔGint-27 kcal/mol
Surface area49000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.629, 174.715, 87.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein General vesicular transport factor p115 / Protein USO1 homolog / Transcytosis-associated protein / TAP / Vesicle-docking protein


Mass: 72666.984 Da / Num. of mol.: 1
Fragment: p115 Tether Globular Head Domain (UNP residues 1-651)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: USO1, VDP / Production host: Escherichia coli (E. coli) / References: UniProt: P41541
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.2 M NaH2PO4/K2HPO4, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211
SYNCHROTRONALS 8.2.120.9794, 0.9796, 0.9537
DetectorDate: Dec 8, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
30.97961
40.95371
ReflectionResolution: 2→50 Å / Num. obs: 79589 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rsym value: 0.049 / Net I/σ(I): 34.3
Reflection shellResolution: 2→2.03 Å / % possible all: 94.6

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementResolution: 2→48.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.177 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.864 / SU B: 7.528 / SU ML: 0.09 / SU R Cruickshank DPI: 0.131 / SU Rfree: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.204 7124 10 %RANDOM
Rwork0.178 ---
obs0.181 71158 88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.52 Å2 / Biso mean: 35.891 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å20 Å20 Å2
2--2.44 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 5 390 5085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224769
X-RAY DIFFRACTIONr_bond_other_d0.0010.023184
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9756464
X-RAY DIFFRACTIONr_angle_other_deg0.92237848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1295599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01525.571210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74615870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3321522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02871
X-RAY DIFFRACTIONr_mcbond_it1.59232992
X-RAY DIFFRACTIONr_mcbond_other0.41231213
X-RAY DIFFRACTIONr_mcangle_it2.80254846
X-RAY DIFFRACTIONr_scbond_it4.72381777
X-RAY DIFFRACTIONr_scangle_it6.945111618
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 416 -
Rwork0.296 3971 -
all-4387 -
obs--74.24 %
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)
17.7668-2.3227-3.1677.2869-0.879713.79580.23430.5239-0.36880.0103-0.17770.47550.6292-0.3603-0.05660.3337-0.00330.03530.175-0.02230.331518.3765-5.940211.6047
26.0079-1.1829-0.12755.77041.07935.9717-0.154-0.2258-0.98090.51650.1410.51570.8905-0.21540.0130.5811-0.12450.26750.2080.07460.51617.0397.63614.4591
33.0675-0.0712-0.61214.92740.57245.2051-0.2478-0.0111-0.50440.0046-0.09810.17260.9043-0.36570.3460.2297-0.10960.13960.0795-0.04290.189222.483420.69973.9097
44.59820.7735-0.93323.3934-1.81184.1042-0.09080.0956-0.0818-0.0121-0.0879-0.02580.25030.04430.17870.02710.00240.0280.07430.00250.037734.124235.027-1.6023
53.695-2.47520.00427.3866-4.35588.9707-0.1123-0.2968-0.010.2454-0.008-0.2315-0.13340.63630.12030.01730.0030.01570.12420.03220.081747.026139.2216-5.7814
63.539-0.4558-0.99093.8949-0.39654.37610.0267-0.43-0.01530.1877-0.0459-0.43080.08120.79440.01930.01650.0241-0.01150.23420.05560.088259.269541.2973-13.4977
73.7751-1.9701-0.97256.9163-1.22774.7675-0.1787-0.23170.18430.31250.0611-0.5916-0.2160.90140.11760.0352-0.0023-0.02320.28310.01410.053566.808144.2438-29.2841
83.7663-0.35670.44162.7256-0.29172.9509-0.05060.3266-0.4046-0.169-0.0477-0.34270.34260.81450.09830.05770.1130.0340.3366-0.02620.142269.670834.7053-41.2268
93.70910.2936-0.08735.3313-0.56545.7964-0.01770.5078-0.8081-0.6601-0.1186-0.08831.1460.37640.13640.2970.12970.00550.2557-0.14060.281358.776727.7422-48.6392
103.1971-0.54132.46482.2117-0.95179.93390.0829-0.0783-0.2776-0.06950.00150.23640.7167-0.4669-0.08440.0833-0.00520.02080.06220.01240.216651.747429.5828-34.7576
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 24
2X-RAY DIFFRACTION2A25 - 85
3X-RAY DIFFRACTION3A86 - 180
4X-RAY DIFFRACTION4A181 - 255
5X-RAY DIFFRACTION5A256 - 307
6X-RAY DIFFRACTION6A308 - 394
7X-RAY DIFFRACTION7A395 - 464
8X-RAY DIFFRACTION8A465 - 524
9X-RAY DIFFRACTION9A525 - 590
10X-RAY DIFFRACTION10A591 - 632

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