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- PDB-8evl: Crystal structure of alpha-COPI N-terminal WD40 domain -

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Basic information

Entry
Database: PDB / ID: 8evl
TitleCrystal structure of alpha-COPI N-terminal WD40 domain
ComponentsPutative coatomer subunit alpha
KeywordsPROTEIN TRANSPORT / COPI / protein trafficking / SARS-CoV-2 spike / dibasic motif
Function / homology
Function and homology information


COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity ...COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity / Golgi apparatus / cytoplasm
Similarity search - Function
: / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / Coatomer WD associated region / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...: / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / Coatomer WD associated region / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Putative coatomer subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Brookhaven National Laboratory (BNL)DE-SC0012704 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 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative coatomer subunit alpha
B: Putative coatomer subunit alpha
C: Putative coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)113,2773
Polymers113,2773
Non-polymers00
Water7,134396
1
A: Putative coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)37,7591
Polymers37,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)37,7591
Polymers37,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)37,7591
Polymers37,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.687, 171.416, 69.991
Angle α, β, γ (deg.)90.000, 97.340, 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 Putative coatomer subunit alpha / Alpha-coat protein / Alpha-COP


Mass: 37759.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q96WV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium citrate tribasic dihydrate, 18% PEG3350

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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 14, 2022 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→29.66 Å / Num. obs: 67199 / % possible obs: 100 % / Redundancy: 4 % / Biso Wilson estimate: 18.92 Å2 / CC1/2: 0.993 / Net I/σ(I): 5.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.7 % / Num. unique obs: 6741 / CC1/2: 0.706 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487+SVNrefinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S22

7s22


Resolution: 1.9→29.66 Å / SU ML: 0.2237 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.6522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2334 6501 4.93 %
Rwork0.1918 125252 -
obs0.1938 131753 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7376 0 0 396 7772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037603
X-RAY DIFFRACTIONf_angle_d0.661710324
X-RAY DIFFRACTIONf_chiral_restr0.05161103
X-RAY DIFFRACTIONf_plane_restr0.00621309
X-RAY DIFFRACTIONf_dihedral_angle_d6.9525987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.35362120.31354081X-RAY DIFFRACTION94.04
1.92-1.940.28782210.28783911X-RAY DIFFRACTION92.92
1.94-1.970.31492040.28233959X-RAY DIFFRACTION94.76
1.97-1.990.29661750.27384194X-RAY DIFFRACTION99.34
1.99-2.020.27412430.26614251X-RAY DIFFRACTION99.89
2.02-2.050.31462050.26274237X-RAY DIFFRACTION99.91
2.05-2.080.31432100.26094225X-RAY DIFFRACTION99.98
2.08-2.110.30292130.25274177X-RAY DIFFRACTION99.86
2.11-2.140.26382170.2474258X-RAY DIFFRACTION99.78
2.14-2.170.26622240.22684211X-RAY DIFFRACTION99.71
2.17-2.210.28642390.22734104X-RAY DIFFRACTION99.77
2.21-2.250.23752220.2284300X-RAY DIFFRACTION99.85
2.25-2.30.25272310.21474235X-RAY DIFFRACTION99.71
2.3-2.340.28431980.20624183X-RAY DIFFRACTION99.82
2.34-2.390.231940.21194207X-RAY DIFFRACTION99.71
2.39-2.450.24042590.20814250X-RAY DIFFRACTION99.45
2.45-2.510.25522150.20044147X-RAY DIFFRACTION99.52
2.51-2.580.25512210.19834192X-RAY DIFFRACTION99.26
2.58-2.650.24822400.20074158X-RAY DIFFRACTION99.32
2.65-2.740.21741920.19034172X-RAY DIFFRACTION99.11
2.74-2.840.24732620.18854214X-RAY DIFFRACTION99.16
2.84-2.950.25752130.18724106X-RAY DIFFRACTION99.04
2.95-3.090.23072080.1734142X-RAY DIFFRACTION96.39
3.09-3.250.19612470.17434100X-RAY DIFFRACTION98.26
3.25-3.450.20921790.16124218X-RAY DIFFRACTION99.64
3.45-3.720.21711840.16654276X-RAY DIFFRACTION99.22
3.72-4.090.2142120.15054150X-RAY DIFFRACTION98.04
4.09-4.680.17312230.13094209X-RAY DIFFRACTION100
4.68-5.890.16462270.14134196X-RAY DIFFRACTION99.91
5.89-29.660.20352110.1794189X-RAY DIFFRACTION99.12

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