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- PDB-7xmn: Structure of SARS-CoV-2 ORF8 -

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Basic information

Entry
Database: PDB / ID: 7xmn
TitleStructure of SARS-CoV-2 ORF8
Components
  • Maltodextrin-binding protein
  • ORF8 protein
KeywordsVIRAL PROTEIN / ORF8
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 / carbohydrate transmembrane transporter activity / cytokine activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / outer membrane-bounded periplasmic space / lysosome ...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 / carbohydrate transmembrane transporter activity / cytokine activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / outer membrane-bounded periplasmic space / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
NOR-N-OMEGA-HYDROXY-L-ARGININE / Maltodextrin-binding protein / ORF8 protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, X. / Xu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32041005,82130101 China
CitationJournal: Microbiol Spectr / Year: 2023
Title: Glycosylated, Lipid-Binding, CDR-Like Domains of SARS-CoV-2 ORF8 Indicate Unique Sites of Immune Regulation.
Authors: Wu, F. / Chen, X. / Ma, Y. / Wu, Y. / Li, R. / Huang, Y. / Zhang, R. / Zhou, Y. / Zhan, J. / Liu, S. / Xu, W.
History
DepositionApr 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 16, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein
B: ORF8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,88911
Polymers52,4732
Non-polymers1,4159
Water1,54986
1
A: Maltodextrin-binding protein
B: ORF8 protein
hetero molecules

A: Maltodextrin-binding protein
B: ORF8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,77722
Polymers104,9474
Non-polymers2,83018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10370 Å2
ΔGint-164 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.088, 146.693, 74.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Maltodextrin-binding protein


Mass: 40236.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, GUB92_19955, NCTC8450_00456, NCTC9775_03059 / Cell (production host): 293F / Production host: Mammalia (mammals) / References: UniProt: A0A376KDN7
#2: Protein ORF8 protein / ORF8 / Non-structural protein 8 / ns8


Mass: 12236.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Mammalia (mammals) / References: UniProt: P0DTC8

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Sugars , 2 types, 2 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 93 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NNH / NOR-N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N4O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH6.1, 2%Polyethylene glycol 400, 2.1 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→101.31 Å / Num. obs: 33261 / % possible obs: 96.8 % / Redundancy: 4.4 % / CC1/2: 0.989 / Net I/σ(I): 7.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.5 % / Num. unique obs: 3311 / CC1/2: 0.726 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SET

3set


Resolution: 2.3→60.13 Å / SU ML: 0.2855 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 1667 5.01 %
Rwork0.2149 31582 -
obs0.2164 33249 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→60.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 86 86 3824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253828
X-RAY DIFFRACTIONf_angle_d0.57015213
X-RAY DIFFRACTIONf_chiral_restr0.0429573
X-RAY DIFFRACTIONf_plane_restr0.0037664
X-RAY DIFFRACTIONf_dihedral_angle_d7.3399527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.30581560.28472636X-RAY DIFFRACTION99.08
2.37-2.440.26421150.27372703X-RAY DIFFRACTION98.84
2.44-2.530.32481410.26022680X-RAY DIFFRACTION98.71
2.53-2.630.33151410.27422661X-RAY DIFFRACTION98.59
2.63-2.750.28921420.25582674X-RAY DIFFRACTION98.36
2.75-2.90.32411100.24882587X-RAY DIFFRACTION94.2
2.9-3.080.25061180.24672709X-RAY DIFFRACTION98.67
3.08-3.320.27831660.25082668X-RAY DIFFRACTION98.68
3.32-3.650.24011600.20812628X-RAY DIFFRACTION97.11
3.65-4.180.23341350.18912342X-RAY DIFFRACTION84.92
4.18-5.260.15921450.15892680X-RAY DIFFRACTION96.61
5.27-60.130.23381380.18582614X-RAY DIFFRACTION90.29

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