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- PDB-8szx: Crystal structure of b'-WD40 Lys17Ala mutant -

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Basic information

Entry
Database: PDB / ID: 8szx
TitleCrystal structure of b'-WD40 Lys17Ala mutant
ComponentsCoatomer subunit beta'
KeywordsPROTEIN TRANSPORT / COPI / protein trafficking / SARS-CoV-2 spike / dibasic motif
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) / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / WD domain, G-beta repeat / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / WD domain, G-beta repeat / G-protein beta WD-40 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
Similarity search - Domain/homology
Coatomer subunit beta'
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,6452
Polymers68,6452
Non-polymers00
Water8,359464
1
A: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,3231
Polymers34,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,3231
Polymers34,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.189, 158.189, 47.567
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Coatomer subunit beta'


Mass: 34322.629 Da / Num. of mol.: 2 / Mutation: K17A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EC1118_1G1_1453g / Production host: Escherichia coli (E. coli) / References: UniProt: C8Z8B3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.5, PEG 19% 20000

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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 16M / Detector: PIXEL / Date: May 22, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→27.96 Å / Num. obs: 40138 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.08 Å2 / CC1/2: 0.955 / Χ2: 0.97 / Net I/σ(I): 3.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2931 / CC1/2: 0.683 / Χ2: 1 / % 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 / Resolution: 2→27.96 Å / SU ML: 0.2292 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 23.1685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 3634 4.74 %RANDOM
Rwork0.1901 73027 --
obs0.1921 40131 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.14 Å2
Refinement stepCycle: LAST / Resolution: 2→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 0 464 5306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00294992
X-RAY DIFFRACTIONf_angle_d0.64446810
X-RAY DIFFRACTIONf_chiral_restr0.0529751
X-RAY DIFFRACTIONf_plane_restr0.0072863
X-RAY DIFFRACTIONf_dihedral_angle_d13.81221780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.33441440.25982760X-RAY DIFFRACTION98.57
2.03-2.050.26961580.24092801X-RAY DIFFRACTION98.18
2.05-2.080.27981400.23532824X-RAY DIFFRACTION97.95
2.08-2.110.30151290.23932835X-RAY DIFFRACTION97.73
2.11-2.150.26331320.23752788X-RAY DIFFRACTION97.56
2.15-2.180.27331660.22942705X-RAY DIFFRACTION97.29
2.18-2.220.30451080.21912813X-RAY DIFFRACTION97.95
2.22-2.260.23781210.22062861X-RAY DIFFRACTION98.29
2.26-2.30.24441500.21732810X-RAY DIFFRACTION98.96
2.3-2.350.24721330.21522796X-RAY DIFFRACTION99.15
2.35-2.40.28221050.21132888X-RAY DIFFRACTION98.97
2.4-2.460.27141810.21452760X-RAY DIFFRACTION98.2
2.46-2.520.24521600.21022763X-RAY DIFFRACTION98.88
2.52-2.590.24871410.21312847X-RAY DIFFRACTION99.34
2.59-2.660.25161430.19292877X-RAY DIFFRACTION99.51
2.66-2.750.28861270.19442815X-RAY DIFFRACTION99.53
2.75-2.850.26931350.18822861X-RAY DIFFRACTION99.47
2.85-2.960.25711230.18492861X-RAY DIFFRACTION99.43
2.96-3.10.21291390.18012837X-RAY DIFFRACTION99.33
3.1-3.260.21021460.17092822X-RAY DIFFRACTION98.77
3.26-3.460.20741380.16742778X-RAY DIFFRACTION97.85
3.46-3.730.19661410.15672724X-RAY DIFFRACTION96.53
3.73-4.10.20531410.16062773X-RAY DIFFRACTION96.62
4.11-4.70.15891280.13662830X-RAY DIFFRACTION98.37
4.7-5.910.19681390.15662788X-RAY DIFFRACTION97.37
5.91-27.960.21331660.20572810X-RAY DIFFRACTION99.73

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