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- PDB-13td: Orf9b homodimer in complex with fragment ZINC000008614810 -

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Basic information

Entry
Database: PDB / ID: 13td
TitleOrf9b homodimer in complex with fragment ZINC000008614810
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
5-chloro-1,3-benzoxazol-2-amine / DECANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)22,0065
Polymers21,6172
Non-polymers3893
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-8 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.875, 65.226, 73.511
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-36R / 5-chloro-1,3-benzoxazol-2-amine


Mass: 168.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClN2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.99 Å3/Da / Density % sol: 38.17 %
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: 1.7→48.79 Å / Num. obs: 19562 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 28.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Χ2: 0.94 / Net I/σ(I): 13.2 / Num. measured all: 124163
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 98.1 % / Redundancy: 6 % / Rmerge(I) obs: 2.475 / Num. measured all: 5966 / Num. unique obs: 994 / CC1/2: 0.324 / Rpim(I) all: 1.087 / Rrim(I) all: 2.71 / Χ2: 0.69 / Net I/σ(I) obs: 0.7

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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: 1.7→36.76 Å / SU ML: 0.2896 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2951
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2631 1530 7.84 %
Rwork0.2186 17978 -
obs0.222 19508 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.46 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 25 50 1340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321308
X-RAY DIFFRACTIONf_angle_d1.29151773
X-RAY DIFFRACTIONf_chiral_restr0.075224
X-RAY DIFFRACTIONf_plane_restr0.0103217
X-RAY DIFFRACTIONf_dihedral_angle_d19.2958507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.41181340.35681571X-RAY DIFFRACTION98.84
1.76-1.820.31681350.29641618X-RAY DIFFRACTION100
1.82-1.890.34821390.32121602X-RAY DIFFRACTION99.66
1.89-1.980.45011370.29691615X-RAY DIFFRACTION99.94
1.98-2.080.26541370.21991598X-RAY DIFFRACTION99.94
2.08-2.210.23181400.19671622X-RAY DIFFRACTION100
2.21-2.380.25851360.20281641X-RAY DIFFRACTION99.94
2.38-2.620.25981380.1971634X-RAY DIFFRACTION99.83
2.63-30.26361400.22411645X-RAY DIFFRACTION100
3-3.780.25041430.20611665X-RAY DIFFRACTION99.89
3.79-36.760.23951510.20671767X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 8.18769427033 Å / Origin y: -0.957270865748 Å / Origin z: -4.24686371532 Å
111213212223313233
T0.233887042037 Å20.0181863825195 Å2-0.00221776240509 Å2-0.212101800887 Å20.0401955111402 Å2--0.229113059248 Å2
L1.08976261358 °2-1.003440953 °2-0.950021443203 °2-2.97452121641 °22.46512568755 °2--3.69237671219 °2
S-0.0913623550499 Å °0.0313640706752 Å °-0.0289885815897 Å °0.169753434561 Å °-0.0156248378677 Å °-0.0152835477497 Å °0.52083705691 Å °-0.0271950220318 Å °0.109534673614 Å °
Refinement TLS groupSelection details: all

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