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- PDB-13tj: Orf9b homodimer in complex with fragment ZINC000000158540 -

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Basic information

Entry
Database: PDB / ID: 13tj
TitleOrf9b homodimer in complex with fragment ZINC000000158540
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
1,3-benzodioxole-5-carboxylic acid / DECANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,0045
Polymers21,6172
Non-polymers3873
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-8 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.768, 65.036, 73.522
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-0HN / 1,3-benzodioxole-5-carboxylic acid / benzo[d][1,3]dioxole-5-carboxylic acid


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.98 Å3/Da / Density % sol: 37.81 %
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: 2.3→48.71 Å / Num. obs: 8071 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 42.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Χ2: 0.94 / Net I/σ(I): 20.8 / Num. measured all: 50437
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 99.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.381 / Num. measured all: 4940 / Num. unique obs: 785 / CC1/2: 0.947 / Rpim(I) all: 0.163 / Rrim(I) all: 0.416 / Χ2: 0.71 / Net I/σ(I) obs: 4.3

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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: 2.3→36.76 Å / SU ML: 0.2497 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.1217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2661 631 7.85 %
Rwork0.2198 7403 -
obs0.2238 8034 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 26 28 1319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381309
X-RAY DIFFRACTIONf_angle_d0.64331774
X-RAY DIFFRACTIONf_chiral_restr0.049224
X-RAY DIFFRACTIONf_plane_restr0.0061218
X-RAY DIFFRACTIONf_dihedral_angle_d19.5183511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.35961240.2431452X-RAY DIFFRACTION99.49
2.48-2.730.30411220.23281450X-RAY DIFFRACTION99.81
2.73-3.120.28771250.23121454X-RAY DIFFRACTION100
3.12-3.930.25471270.21641487X-RAY DIFFRACTION99.63
3.94-36.760.24431330.21131560X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: 8.05760993543 Å / Origin y: -0.817133739843 Å / Origin z: -4.2488157531 Å
111213212223313233
T0.207374045196 Å20.0211052324972 Å2-0.0052937403532 Å2-0.238213471442 Å20.0707847410933 Å2--0.255150074098 Å2
L1.38310190912 °2-0.7896372384 °2-0.794601215732 °2-3.03212762206 °23.00138216732 °2--4.26965984517 °2
S-0.0993220328001 Å °-0.00580758409037 Å °0.0187531598659 Å °0.225656820775 Å °-0.0273569865498 Å °0.0801134230254 Å °0.451640028506 Å °-0.017513124784 Å °0.154882380629 Å °
Refinement TLS groupSelection details: all

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