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- PDB-3gq2: Crystal Structure of the Dimer of the p115 Tether Globular Head Domain -

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Basic information

Entry
Database: PDB / ID: 3gq2
TitleCrystal Structure of the Dimer 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
General vesicular transport factor p115
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 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 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_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
B: General vesicular transport factor p115


Theoretical massNumber of molelcules
Total (without water)145,3342
Polymers145,3342
Non-polymers00
Water10,935607
1


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


Theoretical massNumber of molelcules
Total (without water)72,6671
Polymers72,6671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: General vesicular transport factor p115


Theoretical massNumber of molelcules
Total (without water)72,6671
Polymers72,6671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.164, 159.817, 81.447
Angle α, β, γ (deg.)90.000, 115.130, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 17 - 640 / Label seq-ID: 17 - 640

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2
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: p115, USO1, VDP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P41541
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 10% MPD, 18% PEG 4000, 0.1M Tris-HCL, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorDate: Dec 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 91304 / % possible obs: 96.7 % / Rsym value: 0.091 / Net I/σ(I): 14.3
Reflection shellResolution: 2.18→2.25 Å / Rmerge(I) obs: 0.593 / Rsym value: 0.012 / % possible all: 76.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MOLREPphasing
RefinementResolution: 2.18→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.786 / SU B: 17.515 / SU ML: 0.188 / SU R Cruickshank DPI: 0.265 / SU Rfree: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 8222 10 %RANDOM
Rwork0.199 ---
obs0.205 82014 87.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.69 Å2 / Biso mean: 31.352 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å2-1.66 Å2
2---3.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9612 0 0 607 10219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229852
X-RAY DIFFRACTIONr_bond_other_d0.0010.026622
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.97413351
X-RAY DIFFRACTIONr_angle_other_deg0.952316315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51851240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57125.57447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.152151819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6121549
X-RAY DIFFRACTIONr_chiral_restr0.0790.21565
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021808
X-RAY DIFFRACTIONr_mcbond_it1.49236161
X-RAY DIFFRACTIONr_mcbond_other0.36332494
X-RAY DIFFRACTIONr_mcangle_it2.51559987
X-RAY DIFFRACTIONr_scbond_it4.49683691
X-RAY DIFFRACTIONr_scangle_it6.298113364
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 8023 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.385
LOOSE THERMAL2.0410
LS refinement shellResolution: 2.179→2.235 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 386 -
Rwork0.342 3284 -
all-3670 -
obs--53.43 %
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)
11.54150.02750.42810.1202-0.60173.4315-0.20730.1649-0.1362-0.19510.26280.080.7727-1.1339-0.05550.635-0.017-0.14260.76780.11030.7713-45.777721.5072-14.3489
22.63650.5894-0.27663.57980.79113.5557-0.0160.1639-0.0561-0.03650.00870.44660.1104-0.39080.00720.1780.08570.02050.33330.03020.32-36.689522.9542-8.9542
34.22460.1203-0.02122.7440.31964.5768-0.02610.1341-0.27160.17010.09810.26860.3544-0.4485-0.0720.13330.06810.01690.14970.01680.234-26.714815.4864-7.3235
44.7077-1.14121.20282.6127-0.40731.5762-0.03510.06370.52990.1014-0.01610.0558-0.3023-0.15060.05130.12390.04130.03660.02340.01990.0982-15.359521.0864-1.087
55.2909-0.4617-0.9071.83810.71664.2152-0.1255-0.53990.43980.3405-0.04820.0202-0.2161-0.0230.17370.17480.0065-0.03480.0624-0.05040.0802-3.796316.994414.7692
63.2884-0.80950.88812.6137-0.58312.286-0.0624-0.47160.09120.4732-0.0336-0.1624-0.1634-0.06790.0960.1786-0.0292-0.04480.0783-0.00210.01436.05770.834323.9745
72.639-0.21230.35621.85430.56522.11330.0229-0.396-0.10530.45370.0504-0.35330.10020.1054-0.07330.1789-0.0107-0.11090.0730.01910.082713.6222-23.818122.8983
83.7891-1.3037-0.0086.00850.67043.39380.10280.0682-0.5747-0.2973-0.1519-0.39230.32430.13070.04910.11670.01110.00890.01310.01160.158111.1021-27.71746.7032
96.9895-1.3176-4.27096.02851.86256.7570.08370.52870.0336-0.1113-0.1128-0.36240.1697-0.03670.02910.09420.0088-0.02920.06410.020.04868.1733-19.09086.8557
100.1918-0.7246-1.21672.93534.91478.2339-0.0677-0.01580.00260.0507-0.00190.04180.09540.04010.06960.16330.0013-0.00470.13090.00440.139130.1214-31.0682-5
114.32740.30431.68252.21121.1411.2327-0.6906-0.90420.41320.78890.55940.2691-0.05620.03390.13130.84110.0880.15420.69510.05640.3518-11.6191-49.511752.3586
123.76970.4271-0.77971.68640.12571.94280.0584-0.06190.15570.0564-0.06210.22520.0394-0.170.00370.327-0.05120.08370.24160.0950.1515-12.0734-51.312542.0136
135.15441.3146-0.44924.69532.24545.60980.0523-0.16680.45060.0394-0.10240.1087-0.21960.0220.05010.2445-0.09530.03470.18110.09530.1553-7.4315-45.443832.7021
143.58571.4885-0.20522.0192-0.63591.84820.01630.0723-0.39880.1081-0.05830.1030.1088-0.04410.0420.2578-0.0884-0.00420.12060.05530.1761-9.6154-52.930322.5488
154.6546-0.08270.53132.3735-0.74763.59190.19480.0338-0.32630.0898-0.17940.36230.1263-0.3482-0.01530.1352-0.0612-0.0670.078-0.01660.1459-13.7554-48.20184.5803
162.0598-0.4051-0.20492.513-1.14183.31370.08850.2116-0.2015-0.3071-0.02860.45450.1047-0.3551-0.05990.13840.0068-0.10970.062-0.03230.1238-18.5613-32.3961-12.4387
172.02710.93490.62152.53510.45152.686-0.10770.43730.133-0.50410.07840.3154-0.0104-0.0420.02930.16630.0097-0.06340.11440.01580.0398-11.0133-8.8692-20.6606
183.38653.14960.63265.7337-1.74974.89950.1520.47850.3028-0.2106-0.0085-0.2639-0.26640.7254-0.14350.17460.02460.21860.16410.07080.28383.9357-3.1156-12.3821
197.6481.2651-1.0277.6646-0.79252.68490.2457-0.1825-0.3004-0.1471-0.2684-0.14810.24670.35450.02270.06190.0366-0.01690.05110.00590.0156-2.7401-16.5887-5.9231
201.7606-1.64751.94253.13721.23529.36860.3410.1655-0.0299-0.3476-0.0404-0.1767-0.18250.0184-0.30060.3711-0.01140.03680.3732-0.05390.399621.3124-5.2034-21.6864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 36
2X-RAY DIFFRACTION2A37 - 79
3X-RAY DIFFRACTION3A80 - 131
4X-RAY DIFFRACTION4A132 - 209
5X-RAY DIFFRACTION5A210 - 272
6X-RAY DIFFRACTION6A273 - 413
7X-RAY DIFFRACTION7A414 - 531
8X-RAY DIFFRACTION8A532 - 598
9X-RAY DIFFRACTION9A599 - 633
10X-RAY DIFFRACTION10A634 - 640
11X-RAY DIFFRACTION11B17 - 36
12X-RAY DIFFRACTION12B37 - 79
13X-RAY DIFFRACTION13B80 - 130
14X-RAY DIFFRACTION14B131 - 183
15X-RAY DIFFRACTION15B184 - 270
16X-RAY DIFFRACTION16B271 - 413
17X-RAY DIFFRACTION17B414 - 531
18X-RAY DIFFRACTION18B532 - 591
19X-RAY DIFFRACTION19B592 - 630
20X-RAY DIFFRACTION20B631 - 642

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