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- PDB-7jx6: STRUCTURE OF THE SARS-CoV-2 ORF8 ENCODED ACCESSORY PROTEIN -

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Basic information

Entry
Database: PDB / ID: 7jx6
TitleSTRUCTURE OF THE SARS-CoV-2 ORF8 ENCODED ACCESSORY PROTEIN
ComponentsORF8 protein
KeywordsVIRAL PROTEIN / Immunoglobulin-like / disulfide-linked dimer / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / SYNCHROTRON / SAD / Resolution: 1.61 Å
AuthorsHall, P.D. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal Structure of the SARS-CoV-2 ORF8 Protein
Authors: Nelson, C.A. / Hall, P.D. / Fremont, D.H.
History
DepositionAug 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF8 protein
B: ORF8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9956
Polymers23,9032
Non-polymers924
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-43 kcal/mol
Surface area10920 Å2
MethodPISA
2
A: ORF8 protein
B: ORF8 protein
hetero molecules

A: ORF8 protein
B: ORF8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,99012
Polymers47,8064
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6190 Å2
ΔGint-100 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.647, 50.647, 168.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

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Components

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


Mass: 11951.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-RIL / References: UniProt: P0DTC8
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium Chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.61→42.02 Å / Num. obs: 29522 / % possible obs: 99.76 % / Redundancy: 13.4 % / Biso Wilson estimate: 24.97 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05651 / Rrim(I) all: 0.05875 / Net I/σ(I): 27.09
Reflection shellResolution: 1.61→1.668 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.631 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2877 / CC1/2: 0.762 / Rrim(I) all: 1.696 / % possible all: 99.86

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.61→42.02 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1145 3.91 %
Rwork0.2023 28369 -
obs-29522 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.44 Å2 / Biso min: 15.55 Å2
Refinement stepCycle: final / Resolution: 1.61→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 4 261 1822
Biso mean--42.07 40.71 -
Num. residues----192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.61-1.680.28881400.26723412355298
1.68-1.770.30171400.233634703610100
1.77-1.880.26291440.227835133657100
1.88-2.020.24981420.225735083650100
2.02-2.230.27161420.213935083650100
2.23-2.550.28971430.221735503693100
2.55-3.210.22581480.20336123760100
3.21-42.020.19941540.18043796395099

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