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- PDB-13uw: Orf9b homodimer in complex with fragment ZINC000002386971 -

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Basic information

Entry
Database: PDB / ID: 13uw
TitleOrf9b homodimer in complex with fragment ZINC000002386971
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: 1.85 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)22,0335
Polymers21,6172
Non-polymers4163
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-13 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.568, 64.992, 73.498
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-A1C1M / 6-chloro-1H-indole-2-carboxylic acid


Mass: 195.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 1.96 Å3/Da / Density % sol: 37.4 %
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: 1.85→36.75 Å / Num. obs: 13211 / % possible obs: 89.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.047 / Rrim(I) all: 0.096 / Χ2: 0.92 / Net I/σ(I): 7.9 / Num. measured all: 46465
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 93 % / Redundancy: 3.5 % / Rmerge(I) obs: 2.445 / Num. measured all: 2936 / Num. unique obs: 843 / CC1/2: 0.331 / Rpim(I) all: 1.438 / Rrim(I) all: 2.866 / Χ2: 0.73 / Net I/σ(I) obs: 0.5

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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: 1.85→36.75 Å / SU ML: 0.3245 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2658 1027 7.79 %
Rwork0.2427 12156 -
obs0.2445 13183 87.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 27 35 1359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071343
X-RAY DIFFRACTIONf_angle_d0.7661820
X-RAY DIFFRACTIONf_chiral_restr0.0515228
X-RAY DIFFRACTIONf_plane_restr0.007224
X-RAY DIFFRACTIONf_dihedral_angle_d19.1818524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.950.40071450.36091760X-RAY DIFFRACTION90.71
1.95-2.070.36521530.32021742X-RAY DIFFRACTION89.68
2.07-2.230.32731450.27151768X-RAY DIFFRACTION88.69
2.23-2.450.31221520.2551725X-RAY DIFFRACTION88.5
2.45-2.810.27111470.25171722X-RAY DIFFRACTION86.97
2.81-3.540.27541480.24511750X-RAY DIFFRACTION86.55
3.54-36.750.21811370.21271689X-RAY DIFFRACTION79.6
Refinement TLS params.Method: refined / Origin x: 8.53144380879 Å / Origin y: -1.298605706 Å / Origin z: -4.55729644054 Å
111213212223313233
T0.239394546646 Å20.00973593381291 Å2-0.00722964697932 Å2-0.25330273035 Å20.0696135887087 Å2--0.257874747646 Å2
L1.19087949143 °2-0.956775199928 °2-0.791042272411 °2-3.1890201208 °22.5777069793 °2--3.22553118915 °2
S-0.0845717646897 Å °0.0211756063962 Å °-0.103342512653 Å °0.124382258846 Å °-0.0387696568669 Å °0.0706953273531 Å °0.293367907658 Å °-0.0583052544746 Å °0.149259146536 Å °
Refinement TLS groupSelection details: all

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