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- PDB-13uq: Orf9b homodimer in complex with fragment ZINC000001689349 -

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Basic information

Entry
Database: PDB / ID: 13uq
TitleOrf9b homodimer in complex with fragment ZINC000001689349
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
: / DECANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)22,0495
Polymers21,6172
Non-polymers4323
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-6 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.882, 64.522, 73.490
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-A1C1L / 1-(benzenesulfonyl)pyrrolidine


Mass: 211.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 37.49 %
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: 2→48.49 Å / Num. obs: 11788 / % possible obs: 98.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 40.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Χ2: 0.96 / Net I/σ(I): 12.7 / Num. measured all: 75127
Reflection shellResolution: 2→2.05 Å / % possible obs: 93 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.906 / Num. measured all: 4671 / Num. unique obs: 788 / CC1/2: 0.246 / Rpim(I) all: 0.832 / Rrim(I) all: 2.086 / Χ2: 0.83 / Net I/σ(I) obs: 0.9

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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: 2→48.49 Å / SU ML: 0.3126 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.4282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2881 918 7.81 %
Rwork0.2538 10837 -
obs0.2564 11755 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.97 Å2
Refinement stepCycle: LAST / Resolution: 2→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 28 33 1326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01481311
X-RAY DIFFRACTIONf_angle_d1.43841777
X-RAY DIFFRACTIONf_chiral_restr0.073224
X-RAY DIFFRACTIONf_plane_restr0.0113217
X-RAY DIFFRACTIONf_dihedral_angle_d22.5786514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.36411260.33881461X-RAY DIFFRACTION94.69
2.11-2.240.33831310.29491514X-RAY DIFFRACTION97.57
2.24-2.410.32781250.29511526X-RAY DIFFRACTION98.04
2.41-2.650.3311320.26151524X-RAY DIFFRACTION97.76
2.65-3.040.37091290.27571575X-RAY DIFFRACTION98.67
3.04-3.830.27521330.24441568X-RAY DIFFRACTION98.55
3.83-48.490.24991420.23331669X-RAY DIFFRACTION98.58
Refinement TLS params.Method: refined / Origin x: 8.17293757327 Å / Origin y: -0.973046363776 Å / Origin z: -4.32984570204 Å
111213212223313233
T0.249099972145 Å2-0.00229960458835 Å2-0.0273551158045 Å2-0.324082787551 Å20.0980116371186 Å2--0.347510966847 Å2
L1.47058833815 °2-1.24544466422 °2-1.32365498267 °2-4.00645147971 °23.31274431814 °2--4.85285222891 °2
S-0.0923429026109 Å °-0.0569743412375 Å °0.1077716388 Å °0.219564407377 Å °-0.0487667387959 Å °0.0245490969262 Å °0.454389668133 Å °-0.129071083747 Å °0.139617624479 Å °
Refinement TLS groupSelection details: all

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