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- PDB-8enx: Crystal structure of beta'-COPI-WD40 domain Y33A mutant in comple... -

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Basic information

Entry
Database: PDB / ID: 8enx
TitleCrystal structure of beta'-COPI-WD40 domain Y33A mutant in complex with SARS-CoV-2 clientized spike tail heptapeptide.
Components
  • Clientized spike tail heptapeptide
  • Coatomer subunit beta'
KeywordsPROTEIN TRANSPORT / COPI / protein trafficking / SARS-CoV-2 spike / dibasic motif
Function / homology
Function and homology information


COPI-coated vesicle membrane / membrane coat / vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / Coatomer WD associated region / G-protein beta WD-40 repeat / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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)
Severe acute respiratory syndrome coronavirus 2
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
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: Coatomer subunit beta'
B: Coatomer subunit beta'
C: Clientized spike tail heptapeptide


Theoretical massNumber of molelcules
Total (without water)69,4243
Polymers69,4243
Non-polymers00
Water14,880826
1
A: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,2891
Polymers34,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coatomer subunit beta'


Theoretical massNumber of molelcules
Total (without water)34,2891
Polymers34,2891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Clientized spike tail heptapeptide


Theoretical massNumber of molelcules
Total (without water)8471
Polymers8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.746, 46.241, 84.520
Angle α, β, γ (deg.)81.070, 81.700, 69.500
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Coatomer subunit beta' /


Mass: 34288.633 Da / Num. of mol.: 2 / Mutation: Y33A
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: Protein/peptide Clientized spike tail heptapeptide


Mass: 846.970 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 44.35 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1M MES pH 6.2, 17% PEG20000

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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 17, 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→28.33 Å / Num. obs: 53029 / % possible obs: 96.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 16.09 Å2 / CC1/2: 0.989 / Rsym value: 0.137 / Net I/σ(I): 3.7
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2959 / CC1/2: 0.551 / Rsym value: 0.713

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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: 4J79

4j79


Resolution: 1.8→28.33 Å / SU ML: 0.2042 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.0525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1964 2606 4.92 %
Rwork0.1491 50412 -
obs0.1513 53018 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 0 826 5728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00465039
X-RAY DIFFRACTIONf_angle_d0.75886867
X-RAY DIFFRACTIONf_chiral_restr0.0556758
X-RAY DIFFRACTIONf_plane_restr0.0064870
X-RAY DIFFRACTIONf_dihedral_angle_d7.3997660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.29911530.25942452X-RAY DIFFRACTION89.83
1.84-1.870.26931380.22772648X-RAY DIFFRACTION96.23
1.87-1.910.24051540.20722615X-RAY DIFFRACTION96.41
1.91-1.950.24151580.1862668X-RAY DIFFRACTION96.29
1.95-20.23631550.17732568X-RAY DIFFRACTION96.39
2-2.050.21411530.1612685X-RAY DIFFRACTION96.79
2.05-2.10.22831130.16052660X-RAY DIFFRACTION96.96
2.1-2.160.20511150.16132672X-RAY DIFFRACTION97.14
2.16-2.230.21621180.15252703X-RAY DIFFRACTION97.38
2.23-2.310.22961340.14432704X-RAY DIFFRACTION97.49
2.31-2.410.19061470.14352667X-RAY DIFFRACTION97.47
2.41-2.520.17841280.14342681X-RAY DIFFRACTION97.7
2.52-2.650.21511500.13362657X-RAY DIFFRACTION96.99
2.65-2.810.21731460.14122665X-RAY DIFFRACTION97.54
2.81-3.030.17041420.14062673X-RAY DIFFRACTION97.17
3.03-3.340.16971210.13272662X-RAY DIFFRACTION96.7
3.34-3.820.14131040.11762688X-RAY DIFFRACTION96.88
3.82-4.810.14291170.11572691X-RAY DIFFRACTION97.2
4.81-28.330.19691600.17382653X-RAY DIFFRACTION97.78

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