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- PDB-13um: Orf9b homodimer in complex with fragment ZINC000001389101 -

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Basic information

Entry
Database: PDB / ID: 13um
TitleOrf9b homodimer in complex with fragment ZINC000001389101
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
6-methyl-1H-indole-2-carboxylic acid / DECANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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)22,0135
Polymers21,6172
Non-polymers3963
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-7 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.703, 65.053, 73.528
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-4BL / 6-methyl-1H-indole-2-carboxylic acid


Mass: 175.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 37.72 %
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: 1.79→48.72 Å / Num. obs: 14439 / % possible obs: 87.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 29.24 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.038 / Rrim(I) all: 0.075 / Χ2: 0.88 / Net I/σ(I): 9.5 / Num. measured all: 44111
Reflection shellResolution: 1.79→1.83 Å / % possible obs: 53 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.69 / Num. measured all: 808 / Num. unique obs: 497 / CC1/2: 0.62 / Rpim(I) all: 0.542 / Rrim(I) all: 0.884 / Χ2: 0.61 / 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: 1.79→32.53 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.0955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242 1122 7.78 %
Rwork0.2055 13295 -
obs0.2083 14417 86.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.8 Å2
Refinement stepCycle: LAST / Resolution: 1.79→32.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 27 66 1358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271310
X-RAY DIFFRACTIONf_angle_d1.26841776
X-RAY DIFFRACTIONf_chiral_restr0.0697224
X-RAY DIFFRACTIONf_plane_restr0.0117218
X-RAY DIFFRACTIONf_dihedral_angle_d19.0275508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.870.439940.34281127X-RAY DIFFRACTION59.65
1.87-1.970.27441210.2561528X-RAY DIFFRACTION79.82
1.97-2.090.2771460.21161726X-RAY DIFFRACTION90.96
2.09-2.260.25861550.20861777X-RAY DIFFRACTION94.2
2.26-2.480.25061510.19681798X-RAY DIFFRACTION93.61
2.48-2.840.27461500.20951777X-RAY DIFFRACTION92.29
2.84-3.580.2391510.20311773X-RAY DIFFRACTION90.41
3.58-32.530.21081540.19261789X-RAY DIFFRACTION87.44
Refinement TLS params.Method: refined / Origin x: 8.08523927244 Å / Origin y: -0.618988909046 Å / Origin z: -4.1645076226 Å
111213212223313233
T0.160095699586 Å20.00798277567509 Å2-0.00259055483739 Å2-0.188560200426 Å20.050693741459 Å2--0.203219210853 Å2
L1.08945549709 °2-1.18836348714 °2-0.938898883153 °2-3.12420210192 °22.5960837685 °2--3.57156768479 °2
S-0.0663672618015 Å °0.00977053669551 Å °-0.0395112546209 Å °0.0736260411396 Å °-0.0255225008544 Å °0.0314780821627 Å °0.326019231269 Å °-0.0349100701913 Å °0.10313410811 Å °
Refinement TLS groupSelection details: all

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