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- PDB-13ug: Orf9b homodimer in complex with fragment ZINC000004787230 -

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Basic information

Entry
Database: PDB / ID: 13ug
TitleOrf9b homodimer in complex with fragment ZINC000004787230
ComponentsORF9b protein
KeywordsVIRAL PROTEIN / Homodimer / SARS-CoV-2 / Innate immunity
Function / homology
Function and homology information


Translation of Accessory Proteins / negative regulation of defense response to virus / positive regulation of autophagosome assembly / negative regulation of mitochondrial fission / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / DDX58/IFIH1-mediated induction of interferon-alpha/beta / mitochondrial membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...Translation of Accessory Proteins / negative regulation of defense response to virus / positive regulation of autophagosome assembly / negative regulation of mitochondrial fission / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / DDX58/IFIH1-mediated induction of interferon-alpha/beta / mitochondrial membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / identical protein binding
Similarity search - Function
Protein 9b, Betacoronavirus / Protein 9b, SARS-CoV / Betacoronavirus lipid binding protein / Sarbecovirus 9b domain profile.
Similarity search - Domain/homology
2-hydroxy-5-(methylsulfanyl)benzoic acid / DECANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSan Felipe, C.J. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171110 United States
CitationJournal: to be published
Title: Orf9b homodimer in complex with fragments
Authors: San Felipe, C.J. / Fraser, J.S.
History
DepositionOct 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF9b protein
B: ORF9b protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0225
Polymers21,6172
Non-polymers4053
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-8 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.717, 64.690, 73.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ORF9b protein / ORF9b / Accessory protein 9b / ORF-9b / Protein 9b


Mass: 10808.636 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: 9b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD2
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#4: Chemical ChemComp-3R6 / 2-hydroxy-5-(methylsulfanyl)benzoic acid


Mass: 184.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG3350, 10% PEG1000, 10% MPD, 0.15M Ethylene Glycol, 0.1M MES pH 6.5, 0.1M Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.77→48.58 Å / Num. obs: 15450 / % possible obs: 90 % / Redundancy: 5.8 % / Biso Wilson estimate: 31.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.02 / Rrim(I) all: 0.049 / Χ2: 0.91 / Net I/σ(I): 19.5 / Num. measured all: 89336
Reflection shellResolution: 1.77→1.81 Å / % possible obs: 44.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.764 / Num. measured all: 863 / Num. unique obs: 421 / CC1/2: 0.403 / Rpim(I) all: 0.599 / Rrim(I) all: 0.978 / Χ2: 0.53 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→36.79 Å / SU ML: 0.238 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.4562
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 1223 7.94 %
Rwork0.2078 14187 -
obs0.2109 15410 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.02 Å2
Refinement stepCycle: LAST / Resolution: 1.77→36.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 26 38 1329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211308
X-RAY DIFFRACTIONf_angle_d1.18661772
X-RAY DIFFRACTIONf_chiral_restr0.0671224
X-RAY DIFFRACTIONf_plane_restr0.0088218
X-RAY DIFFRACTIONf_dihedral_angle_d17.4011509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.840.5282800.3947843X-RAY DIFFRACTION49.54
1.84-1.930.30381070.27681183X-RAY DIFFRACTION69.06
1.93-2.030.30031330.22021524X-RAY DIFFRACTION88.7
2.03-2.150.25821470.19431733X-RAY DIFFRACTION99.21
2.16-2.320.2311480.19941739X-RAY DIFFRACTION99.63
2.32-2.550.27111510.20351758X-RAY DIFFRACTION99.9
2.56-2.920.27161470.21721754X-RAY DIFFRACTION99.89
2.92-3.680.26671490.2081779X-RAY DIFFRACTION99.33
3.69-36.790.20911610.19781874X-RAY DIFFRACTION99.46

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