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- PDB-13ub: Orf9b homodimer in complex with fragment ZINC000000053963 -

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Basic information

Entry
Database: PDB / ID: 13ub
TitleOrf9b homodimer in complex with fragment ZINC000000053963
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
1-benzofuran-2-carboxylic acid / DECANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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)22,0005
Polymers21,6172
Non-polymers3833
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-8 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.857, 64.827, 73.319
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-BZ2 / 1-benzofuran-2-carboxylic acid


Mass: 162.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 37.59 %
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: 1.71→48.57 Å / Num. obs: 18961 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 33.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Χ2: 0.92 / Net I/σ(I): 14.6 / Num. measured all: 117935
Reflection shellResolution: 1.71→1.75 Å / % possible obs: 95.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 2.231 / Num. measured all: 5468 / Num. unique obs: 927 / CC1/2: 0.307 / Rpim(I) all: 0.986 / Rrim(I) all: 2.445 / Χ2: 0.59 / Net I/σ(I) obs: 0.6

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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: 1.71→48.57 Å / SU ML: 0.2617 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5987
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 1479 7.82 %
Rwork0.2142 17426 -
obs0.216 18905 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.58 Å2
Refinement stepCycle: LAST / Resolution: 1.71→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 26 40 1331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121309
X-RAY DIFFRACTIONf_angle_d1.25571774
X-RAY DIFFRACTIONf_chiral_restr0.079224
X-RAY DIFFRACTIONf_plane_restr0.011218
X-RAY DIFFRACTIONf_dihedral_angle_d17.7736508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.770.40261260.35041510X-RAY DIFFRACTION97.15
1.77-1.830.35261320.29221543X-RAY DIFFRACTION100
1.83-1.910.26411330.25791577X-RAY DIFFRACTION100
1.91-1.990.35441320.25141568X-RAY DIFFRACTION99.94
1.99-2.10.31071350.22051568X-RAY DIFFRACTION99.94
2.1-2.230.2681310.20481565X-RAY DIFFRACTION100
2.23-2.40.27371340.20051585X-RAY DIFFRACTION100
2.4-2.640.28161360.21721585X-RAY DIFFRACTION100
2.64-3.030.24851380.22051599X-RAY DIFFRACTION99.94
3.03-3.810.22511360.20911612X-RAY DIFFRACTION99.94
3.81-48.570.19651460.20131714X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: 8.0255042284 Å / Origin y: -1.07566639555 Å / Origin z: -4.23927585478 Å
111213212223313233
T0.228247519349 Å20.0219775067293 Å2-0.0150844519085 Å2-0.241389249223 Å20.0521952859684 Å2--0.238390903952 Å2
L1.01475707141 °2-0.743537906169 °2-0.82415626362 °2-3.10388734356 °22.03960250185 °2--3.13819694681 °2
S-0.0698996489772 Å °-0.00890579849371 Å °0.00114283657093 Å °0.0897147388857 Å °-0.0283552308061 Å °-0.0269045137385 Å °0.399220407706 Å °-0.0199733029322 Å °0.10281733542 Å °
Refinement TLS groupSelection details: all

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