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- PDB-13tv: Orf9b homodimer in complex with fragment ZINC000000146551 -

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Basic information

Entry
Database: PDB / ID: 13tv
TitleOrf9b homodimer in complex with fragment ZINC000000146551
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: 1.56 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)22,0625
Polymers21,6172
Non-polymers4453
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-6 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.905, 65.167, 73.648
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-A1C1J / (2,3-dihydro-1H-indol-1-yl)(pyridin-3-yl)methanone


Mass: 224.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 38.28 %
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: 1.56→48.8 Å / Num. obs: 25099 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 27.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.029 / Rrim(I) all: 0.071 / Χ2: 0.93 / Net I/σ(I): 13.7 / Num. measured all: 154590
Reflection shellResolution: 1.56→1.59 Å / % possible obs: 94.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 1.662 / Num. measured all: 5466 / Num. unique obs: 1143 / CC1/2: 0.397 / Rpim(I) all: 0.838 / Rrim(I) all: 1.868 / 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: 1.56→36.82 Å / SU ML: 0.2414 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.4491
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2408 1965 7.85 %
Rwork0.2086 23070 -
obs0.2111 25035 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.11 Å2
Refinement stepCycle: LAST / Resolution: 1.56→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 31 61 1357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01241315
X-RAY DIFFRACTIONf_angle_d1.20661782
X-RAY DIFFRACTIONf_chiral_restr0.069224
X-RAY DIFFRACTIONf_plane_restr0.0101219
X-RAY DIFFRACTIONf_dihedral_angle_d21.1126512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.44711310.41611528X-RAY DIFFRACTION95.56
1.6-1.650.38141380.35351638X-RAY DIFFRACTION99.89
1.65-1.690.32321410.29771629X-RAY DIFFRACTION99.94
1.69-1.750.27541390.25441609X-RAY DIFFRACTION99.94
1.75-1.810.25671380.23261654X-RAY DIFFRACTION99.89
1.81-1.880.23161390.22651615X-RAY DIFFRACTION99.94
1.88-1.970.30381390.22921652X-RAY DIFFRACTION99.94
1.97-2.070.27241400.19961634X-RAY DIFFRACTION99.89
2.07-2.20.23491410.19041650X-RAY DIFFRACTION100
2.2-2.370.2321410.17961661X-RAY DIFFRACTION100
2.37-2.610.23091410.19611664X-RAY DIFFRACTION99.89
2.61-2.990.24691420.21431673X-RAY DIFFRACTION99.45
2.99-3.760.25551420.20121681X-RAY DIFFRACTION99.67
3.77-36.820.20771530.19931782X-RAY DIFFRACTION99.13
Refinement TLS params.Method: refined / Origin x: 8.16418799746 Å / Origin y: -0.667357066756 Å / Origin z: -4.2651413028 Å
111213212223313233
T0.179476326762 Å20.0223533268812 Å2-0.00128739955395 Å2-0.167808754463 Å20.0571864932591 Å2--0.175544716301 Å2
L1.19438989957 °2-0.420706813015 °2-0.413463966202 °2-2.87281071769 °21.7788475842 °2--3.11061254035 °2
S-0.0723391867414 Å °-0.0118551588931 Å °-0.00790083547584 Å °0.0602559264652 Å °-5.25509990942E-5 Å °-0.0584001371524 Å °0.415051918812 Å °0.0789966419039 Å °0.095638466275 Å °
Refinement TLS groupSelection details: all

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