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- PDB-8eo0: Crystal structure of alpha-COPI WD40 domain R300A mutant. -

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Basic information

Entry
Database: PDB / ID: 8eo0
TitleCrystal structure of alpha-COPI WD40 domain R300A mutant.
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 / : / : / COPA/B second beta-propeller / COPA/B TPR domain / WD domain, G-beta repeat ...Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / WD domain, G-beta repeat / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ACETYL GROUP / Putative coatomer subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM150187 United States
CitationJournal: Nat Commun / Year: 2023
Title: A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Authors: Dey, D. / Qing, E. / He, Y. / Chen, Y. / Jennings, B. / Cohn, W. / Singh, S. / Gakhar, L. / Schnicker, N.J. / Pierce, B.G. / Whitelegge, J.P. / Doray, B. / Orban, J. / Gallagher, T. / Hasan, S.S.
History
DepositionOct 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4916
Polymers116,3593
Non-polymers1323
Water9,458525
1
A: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8302
Polymers38,7861
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8302
Polymers38,7861
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8302
Polymers38,7861
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.940, 171.326, 71.583
Angle α, β, γ (deg.)90.000, 100.280, 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: 38786.172 Da / Num. of mol.: 3 / Mutation: R300A
Source method: isolated from a genetically manipulated source
Details: Fo-Fc electron density for 172-199 and 332-337 was not detected.
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Homo sapiens (human) / References: UniProt: Q96WV5
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.96 Å3/Da / Density % sol: 37.34 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Potassium sodium tartrate tetrahydrate, 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: May 23, 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: 1.8→28.97 Å / Num. obs: 82865 / % possible obs: 100 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.22 Å2 / CC1/2: 0.991 / Rsym value: 0.185 / Net I/σ(I): 4.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4564 / CC1/2: 0.552 / Rsym value: 1.964 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S22

7s22


Resolution: 1.8→28.97 Å / SU ML: 0.2065 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 4054 4.9 %
Rwork0.1767 78671 -
obs0.1787 82725 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7440 0 9 525 7974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00567675
X-RAY DIFFRACTIONf_angle_d0.883510427
X-RAY DIFFRACTIONf_chiral_restr0.05721112
X-RAY DIFFRACTIONf_plane_restr0.00881318
X-RAY DIFFRACTIONf_dihedral_angle_d7.3167996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.33941360.30162742X-RAY DIFFRACTION99.79
1.82-1.840.33971170.27842670X-RAY DIFFRACTION99.79
1.84-1.870.2961400.26622722X-RAY DIFFRACTION99.69
1.87-1.890.26281460.25472759X-RAY DIFFRACTION99.69
1.89-1.920.31241430.2382643X-RAY DIFFRACTION99.79
1.92-1.940.24941230.23142677X-RAY DIFFRACTION99.89
1.94-1.970.26051230.21762787X-RAY DIFFRACTION99.79
1.97-20.27971380.20952695X-RAY DIFFRACTION99.75
2-2.040.28681280.20092691X-RAY DIFFRACTION99.93
2.04-2.070.2551340.19222698X-RAY DIFFRACTION100
2.07-2.110.20571370.19232797X-RAY DIFFRACTION99.9
2.11-2.150.23991380.1912635X-RAY DIFFRACTION99.93
2.15-2.190.22721410.18032728X-RAY DIFFRACTION99.93
2.19-2.240.24751480.18312738X-RAY DIFFRACTION100
2.24-2.290.24341450.1812655X-RAY DIFFRACTION99.93
2.29-2.350.21971330.16952735X-RAY DIFFRACTION99.93
2.35-2.420.20581480.18052724X-RAY DIFFRACTION99.97
2.42-2.490.25221550.17272699X-RAY DIFFRACTION100
2.49-2.570.19591440.17262711X-RAY DIFFRACTION99.86
2.57-2.660.22661530.16262659X-RAY DIFFRACTION99.68
2.66-2.760.21021460.16082722X-RAY DIFFRACTION99.97
2.76-2.890.20531440.16492741X-RAY DIFFRACTION99.97
2.89-3.040.19791300.15632677X-RAY DIFFRACTION99.96
3.04-3.230.1761320.14972749X-RAY DIFFRACTION99.76
3.23-3.480.1841420.14862735X-RAY DIFFRACTION100
3.48-3.830.20271440.15342705X-RAY DIFFRACTION99.93
3.83-4.380.17741380.14532722X-RAY DIFFRACTION100
4.38-5.520.19241650.15032724X-RAY DIFFRACTION99.97
5.52-28.970.23951430.21952731X-RAY DIFFRACTION99.38

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