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- PDB-8eny: Crystal structure of alpha-COPI-WD40 domain R13A mutant. -

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Basic information

Entry
Database: PDB / ID: 8eny
TitleCrystal structure of alpha-COPI-WD40 domain R13A 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: 1.9 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
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
DepositionSep 30, 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
Water8,161453
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)37.444, 170.204, 71.524
Angle α, β, γ (deg.)90.000, 99.830, 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: R13A
Source method: isolated from a genetically manipulated source
Details: Fo-Fc electron density of stretches 172-199 and 332-337 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.: 453 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.14M Sodium citrate tribasic dihydrate, 16% 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: 1.9→28.8 Å / Num. obs: 67929 / % possible obs: 98.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 0.994 / Rsym value: 0.129 / Net I/σ(I): 5.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4533 / CC1/2: 0.575 / Rsym value: 0.845 / % possible all: 97.1

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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: 1.9→28.37 Å / SU ML: 0.1815 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 3342 4.93 %
Rwork0.1787 64486 -
obs0.1807 67828 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7458 0 9 453 7920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317702
X-RAY DIFFRACTIONf_angle_d0.645110464
X-RAY DIFFRACTIONf_chiral_restr0.0511116
X-RAY DIFFRACTIONf_plane_restr0.00571323
X-RAY DIFFRACTIONf_dihedral_angle_d6.9591001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.28021340.25892657X-RAY DIFFRACTION96.67
1.93-1.960.30611250.24952707X-RAY DIFFRACTION97.59
1.96-1.990.29071240.23412669X-RAY DIFFRACTION97.22
1.99-2.020.24851460.2272597X-RAY DIFFRACTION97.2
2.02-2.050.27591340.21892708X-RAY DIFFRACTION97.3
2.05-2.090.31121120.21842695X-RAY DIFFRACTION97.7
2.09-2.130.25831330.21752619X-RAY DIFFRACTION97.42
2.13-2.170.25631400.19712673X-RAY DIFFRACTION97.64
2.17-2.220.23781380.19962708X-RAY DIFFRACTION97.77
2.22-2.270.24571340.19832644X-RAY DIFFRACTION97.95
2.27-2.330.24841690.18582692X-RAY DIFFRACTION98.01
2.33-2.390.23891260.19332670X-RAY DIFFRACTION98
2.39-2.460.22041560.18692690X-RAY DIFFRACTION98.17
2.46-2.540.23421520.18182658X-RAY DIFFRACTION98.01
2.54-2.630.22161400.18192682X-RAY DIFFRACTION98.12
2.63-2.740.21681460.18382679X-RAY DIFFRACTION98.54
2.74-2.860.22521420.1792727X-RAY DIFFRACTION98.22
2.86-3.020.22081270.17062675X-RAY DIFFRACTION99.05
3.02-3.20.21081420.15982718X-RAY DIFFRACTION98.69
3.2-3.450.19611600.15722695X-RAY DIFFRACTION98.93
3.45-3.80.20031290.15742735X-RAY DIFFRACTION98.86
3.8-4.340.19051450.14562701X-RAY DIFFRACTION99.3
4.35-5.470.16651430.14472746X-RAY DIFFRACTION99.24
5.47-28.370.23221450.20692741X-RAY DIFFRACTION98.73

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