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- PDB-8hqv: The complex structure of COPI cargo sorting module with HCoV-OC43... -

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Basic information

Entry
Database: PDB / ID: 8hqv
TitleThe complex structure of COPI cargo sorting module with HCoV-OC43 Spike KTSHxx sorting motif
Components
  • Coatomer subunit beta'
  • HCoV-OC43 Spike KTSHxx sorting motif
KeywordsTRANSPORT PROTEIN / HCoV-OC43 / Spike / COPI vesicle / KTSHxx motif / retention signal
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 / Coatomer WD associated region / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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)
Human coronavirus OC43
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 Å
AuthorsMa, W.F. / Nan, Y.N. / Yang, M.R. / Li, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Tighter ER retention of SARS-CoV-2 Omicron spike caused by a constellation of folding disruptive mutations
Authors: Li, Y.Q. / Yang, M.R. / Nan, Y.N. / Wang, J.M. / Guo, J.J. / He, P.F. / Dai, W.X. / Zhou, S.Q. / Wang, S.J. / Zhang, Y. / Ma, W.F.
History
DepositionDec 14, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: 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: HCoV-OC43 Spike KTSHxx sorting motif


Theoretical massNumber of molelcules
Total (without water)35,4522
Polymers35,4522
Non-polymers00
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.930, 51.273, 85.256
Angle α, β, γ (deg.)90.00, 101.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

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Components

#1: Protein Coatomer subunit beta'


Mass: 34293.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast)
Gene: SEC27, SCY_1929 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZU46
#2: Protein/peptide HCoV-OC43 Spike KTSHxx sorting motif


Mass: 1158.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human coronavirus OC43
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 281.15 K / Method: evaporation / Details: 0.2 M MgSO4 and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.398→50 Å / Num. obs: 56731 / % possible obs: 80.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.6
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 3.2 % / Num. unique obs: 4767 / CC1/2: 0.74 / CC star: 0.72 / % possible all: 80.2

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Processing

Software
NameVersionClassification
PHENIX1.16.3549refinement
HKL-3000data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.398→42.033 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 3744 3.54 %
Rwork0.1868 --
obs0.1876 56731 85.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.398→42.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 0 337 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132510
X-RAY DIFFRACTIONf_angle_d1.253426
X-RAY DIFFRACTIONf_dihedral_angle_d5.122880
X-RAY DIFFRACTIONf_chiral_restr0.107381
X-RAY DIFFRACTIONf_plane_restr0.008434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.398-1.41520.504410.45231068X-RAY DIFFRACTION24
1.4152-1.43380.4222780.40812077X-RAY DIFFRACTION48
1.4338-1.45350.4554870.37632366X-RAY DIFFRACTION53
1.4535-1.47430.328920.33762603X-RAY DIFFRACTION59
1.4743-1.49630.33041080.32772952X-RAY DIFFRACTION67
1.4963-1.51960.37391220.30643240X-RAY DIFFRACTION74
1.5196-1.54460.26271250.27863575X-RAY DIFFRACTION82
1.5446-1.57120.24241440.26363767X-RAY DIFFRACTION86
1.5712-1.59980.30581490.24694192X-RAY DIFFRACTION95
1.5998-1.63050.25061550.23414295X-RAY DIFFRACTION97
1.6305-1.66380.25591560.22354271X-RAY DIFFRACTION98
1.6638-1.70.26981550.21664284X-RAY DIFFRACTION97
1.7-1.73950.21451570.2144263X-RAY DIFFRACTION97
1.7395-1.7830.21141560.20364198X-RAY DIFFRACTION96
1.783-1.83130.21681530.20364201X-RAY DIFFRACTION94
1.8313-1.88510.2221560.1914224X-RAY DIFFRACTION97
1.8851-1.9460.20381590.19044237X-RAY DIFFRACTION97
1.946-2.01550.21531560.1784268X-RAY DIFFRACTION97
2.0155-2.09620.20231550.17314254X-RAY DIFFRACTION96
2.0962-2.19160.20281480.17934125X-RAY DIFFRACTION94
2.1916-2.30720.22761590.18364286X-RAY DIFFRACTION97
2.3072-2.45170.18461560.18464221X-RAY DIFFRACTION97
2.4517-2.6410.19351550.18474288X-RAY DIFFRACTION97
2.641-2.90670.20411550.18284158X-RAY DIFFRACTION95
2.9067-3.32720.17971550.17054286X-RAY DIFFRACTION97
3.3272-4.19130.17591530.15714156X-RAY DIFFRACTION94
4.1913-42.0330.19261590.16514256X-RAY DIFFRACTION97

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