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

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Basic information

Entry
Database: PDB / ID: 8ens
TitleCrystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail hepta-peptide
Components
  • Coatomer subunit beta'
  • spike tail hepta-peptide
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) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / G-protein beta WD-40 repeat / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Coatomer beta' subunit (COPB2) / : / COPA/B TPR domain / Coatomer, WD associated region / : / COPA/B second beta-propeller / G-protein beta WD-40 repeat / WD domain, G-beta 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'
C: spike tail hepta-peptide


Theoretical massNumber of molelcules
Total (without water)35,2002
Polymers35,2002
Non-polymers00
Water8,449469
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.966, 51.359, 85.276
Angle α, β, γ (deg.)90.000, 101.670, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-554-

HOH

31A-800-

HOH

41A-804-

HOH

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Components

#1: Protein Coatomer subunit beta'


Mass: 34380.730 Da / Num. of mol.: 1
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 spike tail hepta-peptide


Mass: 818.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fo-Fc electron density of Glycine not detected.
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.2, 19% PEG 4000

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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: Nov 30, 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→28.06 Å / Num. obs: 56398 / % possible obs: 99.78 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.39 Å2 / CC1/2: 1 / Rsym value: 0.107 / Net I/σ(I): 9.1
Reflection shellResolution: 1.45→1.47 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2705 / CC1/2: 0.84 / Rsym value: 0.671 / % possible all: 98.4

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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→28.06 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.172 --
Rwork0.1509 53570 -
obs-56384 98.39 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 0 469 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842554
X-RAY DIFFRACTIONf_angle_d1.08583481
X-RAY DIFFRACTIONf_chiral_restr0.0893384
X-RAY DIFFRACTIONf_plane_restr0.0108439
X-RAY DIFFRACTIONf_dihedral_angle_d7.5108335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.24011520.22542584X-RAY DIFFRACTION97.06
1.47-1.50.23071320.21562686X-RAY DIFFRACTION99.72
1.5-1.530.19631550.20232621X-RAY DIFFRACTION99.78
1.53-1.560.22311440.18862698X-RAY DIFFRACTION99.58
1.56-1.60.23741330.18842628X-RAY DIFFRACTION99.82
1.6-1.630.1941420.17372683X-RAY DIFFRACTION100
1.63-1.670.19191570.16562653X-RAY DIFFRACTION100
1.67-1.720.19111530.16522657X-RAY DIFFRACTION99.96
1.72-1.770.21460.15862639X-RAY DIFFRACTION100
1.77-1.830.18231350.15712710X-RAY DIFFRACTION100
1.83-1.890.17451300.15152685X-RAY DIFFRACTION99.93
1.89-1.970.18811370.15012659X-RAY DIFFRACTION99.96
1.97-2.060.16471470.14152698X-RAY DIFFRACTION100
2.06-2.160.14541440.14572651X-RAY DIFFRACTION99.96
2.16-2.30.17071190.14182714X-RAY DIFFRACTION100
2.3-2.480.20061500.14522666X-RAY DIFFRACTION100
2.48-2.730.19471270.14682707X-RAY DIFFRACTION99.96
2.73-3.120.1681270.14852732X-RAY DIFFRACTION100
3.12-3.930.1571420.13282718X-RAY DIFFRACTION100
3.93-28.060.12921420.1442781X-RAY DIFFRACTION99.9

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