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- PDB-6lsu: Crystal structure of Uso1-2 -

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Basic information

Entry
Database: PDB / ID: 6lsu
TitleCrystal structure of Uso1-2
ComponentsIntracellular protein transport protein USO1Glossary of biology
KeywordsTRANSPORT PROTEIN / Tethering protein
Function / homology
Function and homology information


Golgi vesicle docking / vesicle fusion with Golgi apparatus / COPI-mediated anterograde transport / Golgi stack / SNARE complex assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / ER to Golgi transport vesicle membrane / membrane fusion / cytoskeleton ...Golgi vesicle docking / vesicle fusion with Golgi apparatus / COPI-mediated anterograde transport / Golgi stack / SNARE complex assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / ER to Golgi transport vesicle membrane / membrane fusion / cytoskeleton / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
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-like helical / Armadillo-type fold
Similarity search - Domain/homology
Intracellular protein transport protein USO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHeo, Y.Y. / Lee, H.H.
CitationJournal: Sci Rep / Year: 2020
Title: Crystal structures of Uso1 membrane tether reveal an alternative conformation in the globular head domain
Authors: Heo, Y. / Yoon, H.J. / Ko, H. / Jang, S. / Lee, H.H.
History
DepositionJan 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intracellular protein transport protein USO1


Theoretical massNumber of molelcules
Total (without water)83,2801
Polymers83,2801
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30070 Å2
2
A: Intracellular protein transport protein USO1

A: Intracellular protein transport protein USO1


Theoretical massNumber of molelcules
Total (without water)166,5612
Polymers166,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area4430 Å2
ΔGint-19 kcal/mol
Surface area55720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.376, 104.376, 231.842
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Intracellular protein transport protein USO1 / Glossary of biology / Int-1


Mass: 83280.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: USO1 / Production host: Escherichia coli (E. coli) / References: UniProt: P25386
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 4.38 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Bis-Tris: HCl pH 6.0, 2M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 41061 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.043 / Rrim(I) all: 0.104 / Χ2: 2.148 / Net I/σ(I): 9.2 / Num. measured all: 243939
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.756.10.91320350.7360.3980.9981.566100
2.75-2.86.20.78120250.7560.3390.8531.565100
2.8-2.856.20.67119880.8080.2930.7331.533100
2.85-2.916.10.56220580.860.2450.6141.553100
2.91-2.976.10.45320350.9050.1970.4941.602100
2.97-3.046.10.34519900.9410.1510.3771.687100
3.04-3.126.10.28520500.9620.1250.3121.706100
3.12-3.26.10.23620040.9740.1030.2581.719100
3.2-3.36.10.18620530.9820.0810.2031.769100
3.3-3.46.10.15920320.9850.070.1741.834100
3.4-3.526.10.12720280.9910.0560.1391.96100
3.52-3.666.10.10720450.9920.0470.1172.097100
3.66-3.8360.0920670.9940.040.0982.244100
3.83-4.0360.07920540.9950.0350.0872.413100
4.03-4.295.90.07320580.9950.0330.082.601100
4.29-4.625.80.06920700.9950.0320.0762.974100
4.62-5.085.80.06920820.9950.0310.0762.966100
5.08-5.815.70.07321110.9940.0330.082.916100
5.81-7.325.50.0721080.9940.0320.0773.02999.9
7.32-504.80.06221680.9930.0320.073.78195.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LST

6lst


Resolution: 2.7→48.79 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.568 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.051
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 2058 5 %RANDOM
Rwork0.1977 ---
obs0.1994 38865 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 230.66 Å2 / Biso mean: 74.053 Å2 / Biso min: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 2.7→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5449 0 0 124 5573
Biso mean---75.35 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135558
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175217
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.6357541
X-RAY DIFFRACTIONr_angle_other_deg1.3911.56912111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57423.241290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85715991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2371529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026098
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021141
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 155 -
Rwork0.225 2810 -
all-2965 -
obs--99.53 %

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