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- PDB-8enw: Crystal structure of beta'-COPI-WD40 domain in complex with SARS-... -

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Basic information

Entry
Database: PDB / ID: 8enw
TitleCrystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike tail heptapeptide.
Components
  • Clientized spike tail peptide
  • Coatomer 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)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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

Downloads & links

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Assembly

Deposited unit
A: Coatomer subunit beta'
B: Coatomer subunit beta'
C: Clientized spike tail peptide
D: Clientized spike tail peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,13815
Polymers70,4554
Non-polymers68311
Water9,548530
1
A: Coatomer subunit beta'
C: Clientized spike tail peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,72410
Polymers35,2282
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint15 kcal/mol
Surface area12370 Å2
MethodPISA
2
B: Coatomer subunit beta'
D: Clientized spike tail peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4145
Polymers35,2282
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint14 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.711, 46.012, 84.319
Angle α, β, γ (deg.)81.240, 81.520, 69.010
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: 34380.730 Da / Num. of mol.: 2
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 peptide


Mass: 846.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: F0-Fc electron density of Glycine is not detected.
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.0, 15% 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: Dec 14, 2021 / 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: 1.45→82.91 Å / Num. obs: 100965 / % possible obs: 96.55 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.25 Å2 / CC1/2: 0.996 / Rsym value: 0.096 / Net I/σ(I): 6.8
Reflection shellResolution: 1.45→1.47 Å / Num. unique obs: 4966 / CC1/2: 0.62 / Rsym value: 0.884 / % possible all: 94.78

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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: 1.45→42.71 Å / SU ML: 0.1339 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.3177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1796 5049 5 %
Rwork0.1533 95889 -
obs0.1546 100938 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.04 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 44 530 5546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00535145
X-RAY DIFFRACTIONf_angle_d0.94586987
X-RAY DIFFRACTIONf_chiral_restr0.0871766
X-RAY DIFFRACTIONf_plane_restr0.009881
X-RAY DIFFRACTIONf_dihedral_angle_d8.5541680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.29811750.25583109X-RAY DIFFRACTION94.8
1.47-1.480.27811780.25683190X-RAY DIFFRACTION94.87
1.48-1.50.25111420.24283106X-RAY DIFFRACTION94.69
1.5-1.520.28521770.23563210X-RAY DIFFRACTION95.57
1.52-1.540.24971820.23093082X-RAY DIFFRACTION94.8
1.54-1.560.25771550.21673150X-RAY DIFFRACTION95.35
1.56-1.580.23521720.21443202X-RAY DIFFRACTION95.18
1.58-1.610.21181500.19893115X-RAY DIFFRACTION95.89
1.61-1.630.21651690.19553204X-RAY DIFFRACTION95.74
1.63-1.660.19271610.18443195X-RAY DIFFRACTION95.78
1.66-1.690.2231720.18433146X-RAY DIFFRACTION95.87
1.69-1.720.22811740.18633164X-RAY DIFFRACTION96.17
1.72-1.750.21511620.18813178X-RAY DIFFRACTION96.12
1.75-1.790.23321640.17923233X-RAY DIFFRACTION96.31
1.79-1.830.20321670.15913172X-RAY DIFFRACTION96.61
1.83-1.870.17641590.14593230X-RAY DIFFRACTION96.64
1.87-1.920.16041660.14233211X-RAY DIFFRACTION96.49
1.92-1.970.16631830.13353138X-RAY DIFFRACTION96.65
1.97-2.030.17681440.13223279X-RAY DIFFRACTION97.3
2.03-2.090.17831670.12963244X-RAY DIFFRACTION97.37
2.09-2.170.17371710.13423200X-RAY DIFFRACTION97.29
2.17-2.250.17561760.14043210X-RAY DIFFRACTION97.64
2.25-2.360.16621730.13613231X-RAY DIFFRACTION97.56
2.36-2.480.15121790.13813212X-RAY DIFFRACTION97.72
2.48-2.630.15281700.13553267X-RAY DIFFRACTION97.86
2.63-2.840.15731520.13493240X-RAY DIFFRACTION97.84
2.84-3.120.1751700.1393201X-RAY DIFFRACTION96.92
3.12-3.580.14951980.13513235X-RAY DIFFRACTION97.75
3.58-4.50.14951580.1333248X-RAY DIFFRACTION98.67
4.51-42.710.19091830.17393287X-RAY DIFFRACTION99.28

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