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- PDB-9mzb: X-ray crystallographic structure of Orf9b Apo Homodimer -

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Basic information

Entry
Database: PDB / ID: 9mzb
TitleX-ray crystallographic structure of Orf9b Apo Homodimer
ComponentsORF9b protein
KeywordsVIRAL PROTEIN / Refolded / Apo-Homodimer / Type-1 Interferon Suppressor / Fold-switcher
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
GLYCINE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 Refolded Apo-Orf9b Homodimer
Authors: San Felipe, C.J. / Fraser, J.S.
History
DepositionJan 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: 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)21,6923
Polymers21,6172
Non-polymers751
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.280, 75.280, 80.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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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 (E. coli) / Strain (production host): DE3 / References: UniProt: P0DTD2
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.04 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.2M Sodium Phosphate, 0.8M Potassium Phosphate, 0.2M Lithium Sulfate, and 0.1M Glycine pH 10.5

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Data collection

DiffractionMean temperature: 193.15 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 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.8→37.64 Å / Num. obs: 12518 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 97.42 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06155 / Rpim(I) all: 0.03073 / Rrim(I) all: 0.06893 / Net I/σ(I): 11.49
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.187 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 1367 / CC1/2: 0.319 / CC star: 0.696 / Rpim(I) all: 0.7572 / Rrim(I) all: 1.414 / % possible all: 98.06

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→37.64 Å / SU ML: 0.6145 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 50.012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3414 1248 9.98 %
Rwork0.2856 11263 -
obs0.2914 12511 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 129.53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 5 1 1174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571183
X-RAY DIFFRACTIONf_angle_d0.8431602
X-RAY DIFFRACTIONf_chiral_restr0.0502210
X-RAY DIFFRACTIONf_plane_restr0.009197
X-RAY DIFFRACTIONf_dihedral_angle_d19.2418454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.910.44261380.42591226X-RAY DIFFRACTION98.06
2.91-3.040.44111340.37991282X-RAY DIFFRACTION100
3.04-3.20.43261420.3571223X-RAY DIFFRACTION100
3.2-3.40.481470.40581269X-RAY DIFFRACTION100
3.4-3.670.42461380.3721242X-RAY DIFFRACTION100
3.67-4.030.36181440.32441244X-RAY DIFFRACTION100
4.04-4.620.35171430.26681252X-RAY DIFFRACTION100
4.62-5.80.31181270.23491272X-RAY DIFFRACTION99.64
5.82-37.640.28091350.24711253X-RAY DIFFRACTION99.57
Refinement TLS params.Method: refined / Origin x: 22.3149426092 Å / Origin y: -29.4025059655 Å / Origin z: -14.6729628711 Å
111213212223313233
T0.544435364076 Å2-0.126181380801 Å2-0.132572402604 Å2-0.71634705581 Å2-0.140933295824 Å2--0.771568758771 Å2
L9.21758057428 °2-4.48905561347 °2-4.6296323822 °2-7.24025629122 °21.88465686473 °2--4.42197339773 °2
S-0.264641144548 Å °-0.13089238344 Å °0.528448070443 Å °0.43529050625 Å °0.203722537003 Å °0.484807343706 Å °0.167015568377 Å °-0.140067119431 Å °-0.0362787541035 Å °
Refinement TLS groupSelection details: all

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