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- PDB-7mx9: Crystal structure of the SARS-CoV-2 ORF8 accessory protein -

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Basic information

Entry
Database: PDB / ID: 7mx9
TitleCrystal structure of the SARS-CoV-2 ORF8 accessory protein
ComponentsORF8 protein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / COVID19 / ORF8 / immunoglobulin fold
Function / homology
Function and homology information


Translation of Accessory Proteins / positive regulation of immunoglobulin mediated immune response / Interleukin-17 signaling / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / negative regulation of interferon-beta production / cytokine activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lysosome / virus-mediated perturbation of host defense response / SARS-CoV-2 activates/modulates innate and adaptive immune responses ...Translation of Accessory Proteins / positive regulation of immunoglobulin mediated immune response / Interleukin-17 signaling / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / negative regulation of interferon-beta production / cytokine activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lysosome / virus-mediated perturbation of host defense response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / extracellular space / extracellular region / identical protein binding
Similarity search - Function
SARS-like ORF8 accessory protein, Ig-like domain / SARS ORF8 accessory protein immunoglobulin (Ig)-like domain profile. / Non-structural protein ORF8, betacoronavirus / ORF8, SARS-CoV-2 / Betacoronavirus NS8 protein
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBailey-Elkin, B.A. / Stetefeld, J.
Funding support2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-004954-2017
Canadian Institutes of Health Research (CIHR)201610PJT-152935
CitationJournal: To Be Published
Title: The unique ORF8 protein of SARS-CoV-2 binds to human dendritic cells and induces a cytokine storm
Authors: Hamdorf, M. / Imhof, T. / Theobald, S.J. / Simonis, A. / Di Cristanziano, V. / Gieselmann, L. / Dewald, F. / Lehmann, C. / Augustin, M. / Klein, F. / Alejandre Alcazar, M.A. / Rongisch, R. / ...Authors: Hamdorf, M. / Imhof, T. / Theobald, S.J. / Simonis, A. / Di Cristanziano, V. / Gieselmann, L. / Dewald, F. / Lehmann, C. / Augustin, M. / Klein, F. / Alejandre Alcazar, M.A. / Rongisch, R. / Fabri, M. / Cursiefen, C. / Rybniker, J. / Bailey-Elkin, B.A. / Stetefeld, J. / Koch, M. / Bock, F.
History
DepositionMay 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF8 protein


Theoretical massNumber of molelcules
Total (without water)12,9071
Polymers12,9071
Non-polymers00
Water19811
1
A: ORF8 protein

A: ORF8 protein


Theoretical massNumber of molelcules
Total (without water)25,8132
Polymers25,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.349, 51.349, 74.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein ORF8 protein / ORF8 / Non-structural protein 8 / ns8


Mass: 12906.724 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2 M Lithium chloride, 20% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.6→42.2 Å / Num. obs: 3379 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 48.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.8
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.796 / Num. unique obs: 400 / CC1/2: 0.932

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Processing

Software
NameVersionClassification
PHENIX(1.18.2-3874_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JTL

7jtl


Resolution: 2.6→30.04 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2966 336 10.02 %
Rwork0.2432 --
obs0.2487 3353 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms715 0 0 11 726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004759
X-RAY DIFFRACTIONf_angle_d0.7481037
X-RAY DIFFRACTIONf_dihedral_angle_d6.864101
X-RAY DIFFRACTIONf_chiral_restr0.05114
X-RAY DIFFRACTIONf_plane_restr0.005133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-3.280.37251610.29821456X-RAY DIFFRACTION100
3.28-30.040.2711750.2241561X-RAY DIFFRACTION100

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