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- PDB-8ewx: N-terminal WD40 domain of beta'-COPI subunit with two chains in t... -

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Basic information

Entry
Database: PDB / ID: 8ewx
TitleN-terminal WD40 domain of beta'-COPI subunit with two chains in the asymmetric unit
ComponentsCoatomer subunit beta'
KeywordsCYTOSOLIC PROTEIN / COATOMER / TRAFFICKING / SECRETION / ENDOPLASMIC RETICULUM / GOLGI / ER-GOLGI INTERMEDIATE COMPARTMENT / COPI
Function / homology
Function and homology information


COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat ...Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / 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 Beta
Similarity search - Domain/homology
Coatomer subunit beta'
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsDey, D. / Hasan, S.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA134274 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Protein Expr.Purif. / Year: 2023
Title: Strategies for rapid production of crystallization quality coatomer WD40 domains.
Authors: Dey, D. / Hasan, S.S.
History
DepositionOct 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit beta'
B: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)68,7612
Polymers68,7612
Non-polymers00
Water11,223623
1
A: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,3811
Polymers34,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,3811
Polymers34,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.997, 89.821, 69.070
Angle α, β, γ (deg.)90.000, 93.690, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Coatomer subunit beta'


Mass: 34380.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: G2WDW6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.24→29.33 Å / Num. obs: 160014 / % possible obs: 95.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 11.23 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.1
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5385 / CC1/2: 0.572 / % possible all: 64.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J73

4j73


Resolution: 1.24→27.46 Å / SU ML: 0.1025 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.0348
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.161 7794 4.87 %
Rwork0.1331 152173 -
obs0.1345 159967 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.49 Å2
Refinement stepCycle: LAST / Resolution: 1.24→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4744 0 0 623 5367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914928
X-RAY DIFFRACTIONf_angle_d1.09726729
X-RAY DIFFRACTIONf_chiral_restr0.0992740
X-RAY DIFFRACTIONf_plane_restr0.012854
X-RAY DIFFRACTIONf_dihedral_angle_d13.43461766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.250.22941680.24283398X-RAY DIFFRACTION63.45
1.25-1.270.24371890.23133607X-RAY DIFFRACTION68.5
1.27-1.280.24972080.22713936X-RAY DIFFRACTION73.48
1.28-1.30.29132180.20854329X-RAY DIFFRACTION81.2
1.3-1.320.22912350.19964679X-RAY DIFFRACTION88
1.32-1.340.23352360.18574956X-RAY DIFFRACTION93.57
1.34-1.350.21112440.16775125X-RAY DIFFRACTION95.6
1.35-1.380.19772500.16175134X-RAY DIFFRACTION96.37
1.38-1.40.17952790.15285192X-RAY DIFFRACTION97.14
1.4-1.420.20452410.14785190X-RAY DIFFRACTION97.75
1.42-1.440.17342610.14375305X-RAY DIFFRACTION98.5
1.44-1.470.18372440.13835286X-RAY DIFFRACTION99.25
1.47-1.50.16092650.13385308X-RAY DIFFRACTION99.39
1.5-1.530.17592870.1255323X-RAY DIFFRACTION99.63
1.53-1.560.17192950.11345228X-RAY DIFFRACTION99.69
1.56-1.60.14192540.11545352X-RAY DIFFRACTION99.72
1.6-1.640.15663050.1115287X-RAY DIFFRACTION99.71
1.64-1.680.15762680.10955337X-RAY DIFFRACTION99.88
1.68-1.730.14592400.10775347X-RAY DIFFRACTION99.87
1.73-1.790.11972290.11595360X-RAY DIFFRACTION99.95
1.79-1.850.1412700.11495336X-RAY DIFFRACTION99.98
1.85-1.930.12632530.1175366X-RAY DIFFRACTION100
1.93-2.010.14433040.11225298X-RAY DIFFRACTION100
2.01-2.120.15093330.11375301X-RAY DIFFRACTION100
2.12-2.250.14783280.11485290X-RAY DIFFRACTION100
2.25-2.430.14392600.11755383X-RAY DIFFRACTION100
2.43-2.670.13992700.12695341X-RAY DIFFRACTION100
2.67-3.060.15262650.13185400X-RAY DIFFRACTION100
3.06-3.850.16253030.13575339X-RAY DIFFRACTION100
3.85-27.460.17362920.15365440X-RAY DIFFRACTION99.95

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