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- PDB-6u3w: Crystal structure of yeast alpha/epsilon-COP of the COPI vesicula... -

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Basic information

Entry
Database: PDB / ID: 6u3w
TitleCrystal structure of yeast alpha/epsilon-COP of the COPI vesicular coat
Components
  • Coatomer subunit alpha
  • Coatomer subunit epsilon
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


vesicle coating / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding ...vesicle coating / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / late endosome to vacuole transport via multivesicular body sorting pathway / intracellular mRNA localization / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / intracellular protein transport / promoter-specific chromatin binding / protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer epsilon subunit / Coatomer, epsilon subunit / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / : / COPA/B TPR domain / Coatomer, WD associated region / : ...Coatomer epsilon subunit / Coatomer, epsilon subunit / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / Quinoprotein amine dehydrogenase, beta chain-like / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Coatomer subunit epsilon / Coatomer subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.394 Å
AuthorsTravis, S.M. / Hughson, F.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071574 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM12676 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering.
Authors: Travis, S.M. / Kokona, B. / Fairman, R. / Hughson, F.M.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coatomer subunit alpha
B: Coatomer subunit epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5523
Polymers69,4602
Non-polymers921
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-30 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.264, 84.594, 117.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Coatomer subunit alpha / Alpha-coat protein / Alpha-COP / Retrieval from endoplasmic reticulum protein 1 / Secretory protein ...Alpha-coat protein / Alpha-COP / Retrieval from endoplasmic reticulum protein 1 / Secretory protein 22 / Suppressor of osmo-sensitivity 1


Mass: 33985.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: COP1, RET1, SEC33, SOO1, YDL145C, D1578 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): (DE3) CodonPlus RIL / References: UniProt: P53622
#2: Protein Coatomer subunit epsilon / Epsilon-coat protein / Epsilon-COP


Mass: 35474.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC28, YIL076W / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): (DE3) CodonPlus RIL / References: UniProt: P40509
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.7 Å3/Da / Density % sol: 54.42 % / Description: Hexagonal rod, 0.2 x 0.05 x 0.05 mm
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.2 M Li2SO4, 15% (w/v) PEG 3350, 25% (v/v) glycerol Cryoprotected with 23% (w/v) PEG 3350, 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9782 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2015
RadiationMonochromator: Single-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.39→35 Å / Num. obs: 29047 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.047 / Rrim(I) all: 0.114 / Χ2: 0.801 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.39-2.444.40.67314040.7240.360.7670.76998.1
2.44-2.495.10.66313950.7630.3230.740.76797.1
2.49-2.535.40.58314230.8170.2750.6470.74799.2
2.53-2.595.60.52714360.8280.2420.5810.79899.8
2.59-2.645.80.48514060.8730.2190.5330.76100
2.64-2.75.80.44114530.9050.1990.4850.772100
2.7-2.775.50.35514390.9170.1640.3920.789100
2.77-2.855.80.3214350.9420.1430.3510.76899.9
2.85-2.935.80.26914380.9520.1210.2960.784100
2.93-3.0260.23714510.9720.1040.2590.79499.9
3.02-3.1360.214250.9760.0880.2190.79899.9
3.13-3.265.90.16114530.9830.0720.1760.767100
3.26-3.45.50.13214500.9880.0610.1460.795100
3.4-3.585.70.09914540.9930.0450.1090.782100
3.58-3.8160.08214700.9950.0360.0890.796100
3.81-4.15.90.06514420.9960.0290.0710.769100
4.1-4.515.60.05514860.9970.0250.0610.805100
4.51-5.175.80.05314880.9970.0240.0580.78100
5.17-6.55.60.05815080.9950.0270.0640.811100
6.5-355.20.05415910.9960.0250.061.16199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MV2

3mv2


Resolution: 2.394→29.46 Å / SU ML: 0.2916 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.3856
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1997 6.9 %Random selection
Rwork0.1783 ---
obs0.1824 28927 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.76 Å2
Refinement stepCycle: LAST / Resolution: 2.394→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 6 182 4915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754818
X-RAY DIFFRACTIONf_angle_d0.88456526
X-RAY DIFFRACTIONf_chiral_restr0.0489750
X-RAY DIFFRACTIONf_plane_restr0.005836
X-RAY DIFFRACTIONf_dihedral_angle_d14.77052938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.394-2.450.30661350.22431818X-RAY DIFFRACTION95.08
2.45-2.520.32321370.22661847X-RAY DIFFRACTION97.78
2.52-2.590.31471420.21981912X-RAY DIFFRACTION99.85
2.59-2.680.27021420.21481911X-RAY DIFFRACTION100
2.68-2.770.25991410.20261909X-RAY DIFFRACTION100
2.77-2.880.26391430.20091920X-RAY DIFFRACTION99.95
2.88-3.020.27431430.20751929X-RAY DIFFRACTION99.9
3.02-3.170.29911420.21531921X-RAY DIFFRACTION99.95
3.17-3.370.29621440.20121929X-RAY DIFFRACTION100
3.37-3.630.25141420.1891920X-RAY DIFFRACTION100
3.63-40.24661440.16211944X-RAY DIFFRACTION100
4-4.570.17741460.14621965X-RAY DIFFRACTION100
4.57-5.760.19441460.15681980X-RAY DIFFRACTION100
5.76-29.460.19031500.14942025X-RAY DIFFRACTION97.23

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