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- PDB-9n55: X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer -

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Basic information

Entry
Database: PDB / ID: 9n55
TitleX-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
ComponentsORF9b protein
KeywordsVIRAL PROTEIN / Lipid-binding protein / homodimer / SARS-CoV-2 / Innate immune suppressor
Function / homology
Function and homology information


Translation of Accessory Proteins / outer mitochondrial membrane protein complex / negative regulation of defense response to virus / positive regulation of autophagosome assembly / host cell mitochondrion / negative regulation of mitochondrial fission / 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 ...Translation of Accessory Proteins / outer mitochondrial membrane protein complex / negative regulation of defense response to virus / positive regulation of autophagosome assembly / host cell mitochondrion / negative regulation of mitochondrial fission / 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
N-OCTANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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: X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
Authors: San Felipe, C.J. / Fraser, J.S.
History
DepositionFeb 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: 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)21,7323
Polymers21,6172
Non-polymers1141
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-9 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.850, 64.230, 73.570
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DTD2
#2: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
#3: 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: 1.96 Å3/Da / Density % sol: 37.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350, PEG1K, MPD, Ethylene Glycol, Imidazole, MES

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Data collection

DiffractionMean temperature: 193 K / Ambient temp details: Cryogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.65→48.38 Å / Num. obs: 38516 / % possible obs: 98.06 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.18 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.07945 / Rrim(I) all: 0.09461 / Net I/σ(I): 7.22
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.435 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 1312 / CC1/2: 0.228 / Rrim(I) all: 1.71 / % possible all: 85.11

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→48.38 Å / SU ML: 0.2309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 3693 9.59 %
Rwork0.1984 34806 -
obs0.2006 38499 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.45 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 8 50 1367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361368
X-RAY DIFFRACTIONf_angle_d0.68561862
X-RAY DIFFRACTIONf_chiral_restr0.0502236
X-RAY DIFFRACTIONf_plane_restr0.0058234
X-RAY DIFFRACTIONf_dihedral_angle_d18.1827537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.35281250.35251173X-RAY DIFFRACTION85.11
1.68-1.70.37041420.35371361X-RAY DIFFRACTION99.87
1.7-1.720.31621460.31361344X-RAY DIFFRACTION99.53
1.72-1.750.40981510.30441360X-RAY DIFFRACTION99.41
1.75-1.780.30071480.28431371X-RAY DIFFRACTION98.7
1.78-1.80.321400.28791342X-RAY DIFFRACTION98.93
1.8-1.840.27361420.24991349X-RAY DIFFRACTION99.73
1.84-1.870.22571410.23561382X-RAY DIFFRACTION99.87
1.87-1.90.28211420.2231365X-RAY DIFFRACTION99.87
1.91-1.940.21991440.2241347X-RAY DIFFRACTION99.93
1.94-1.990.22061460.22571380X-RAY DIFFRACTION99.8
1.99-2.030.19191430.2311318X-RAY DIFFRACTION99.39
2.03-2.080.22761490.21651369X-RAY DIFFRACTION98.89
2.08-2.140.2471430.18781332X-RAY DIFFRACTION98.14
2.14-2.20.18651430.1961354X-RAY DIFFRACTION99.07
2.2-2.270.20651450.19781373X-RAY DIFFRACTION99.54
2.27-2.350.24611450.1771337X-RAY DIFFRACTION99.53
2.36-2.450.22441390.20351362X-RAY DIFFRACTION98.75
2.45-2.560.19841390.19541337X-RAY DIFFRACTION98.07
2.56-2.70.22461440.19651315X-RAY DIFFRACTION96.69
2.7-2.860.25841430.21381315X-RAY DIFFRACTION97.98
2.86-3.090.17481400.1891358X-RAY DIFFRACTION98.75
3.09-3.40.23361420.18021327X-RAY DIFFRACTION97.09
3.4-3.890.20721370.18141304X-RAY DIFFRACTION94.68
3.89-4.90.18361420.15741306X-RAY DIFFRACTION95.96
4.9-48.380.22261320.19961325X-RAY DIFFRACTION96.75
Refinement TLS params.Method: refined / Origin x: 7.4429594855 Å / Origin y: -0.71327402082 Å / Origin z: -3.80636433986 Å
111213212223313233
T0.178366800937 Å20.0090229156293 Å2-0.00526748784318 Å2-0.230232346891 Å20.0649025820844 Å2--0.190935244681 Å2
L1.14800880226 °2-0.549484220401 °2-0.331645576822 °2-4.2573241339 °21.88376196161 °2--3.43266264602 °2
S0.00760355119939 Å °-0.0279676853405 Å °-0.0546711804143 Å °0.0293129499483 Å °-0.0796811483451 Å °-0.0331222365527 Å °0.481232721502 Å °-0.00717836857299 Å °0.0479732783838 Å °
Refinement TLS groupSelection details: all

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