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- PDB-7ye7: Crystal structure of SARS-CoV-2 soluble dimeric ORF9b -

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Basic information

Entry
Database: PDB / ID: 7ye7
TitleCrystal structure of SARS-CoV-2 soluble dimeric ORF9b
ComponentsORF9b protein
KeywordsVIRAL PROTEIN / ORF9b / SARS-CoV-2 / immune escape / viral antagonist / membrane association / fold switch / lipid binding
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 / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta ...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 / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / mitochondrial outer 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
nonane / N-OCTANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsJin, X. / Chai, Y. / Qi, J. / Song, H. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Sci China Life Sci / Year: 2023
Title: Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism.
Authors: Jin, X. / Sun, X. / Chai, Y. / Bai, Y. / Li, Y. / Hao, T. / Qi, J. / Song, H. / Wong, C.C.L. / Gao, G.F.
History
DepositionJul 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Jan 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,7936
Polymers46,5504
Non-polymers2422
Water0
1
C: ORF9b protein
D: ORF9b protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4033
Polymers23,2752
Non-polymers1281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-21 kcal/mol
Surface area9220 Å2
MethodPISA
2
A: ORF9b protein
B: ORF9b protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3893
Polymers23,2752
Non-polymers1141
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-10 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.579, 73.579, 175.616
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein
ORF9b protein / ORF9b / Accessory protein 9b / ORF-9b / Protein 9b


Mass: 11637.517 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: 9b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DTD2
#2: Chemical ChemComp-DD9 / nonane / Nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.0M ammonium phosphate monobasic, 0.1M Tris pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 12167 / % possible obs: 99.8 % / Redundancy: 17.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 34.357
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 16.2 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 4.569 / Num. unique obs: 12059 / % possible all: 100

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CME

2cme


Resolution: 2.95→31.15 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.0019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2892 561 4.65 %
Rwork0.2657 11498 -
obs0.2691 12059 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.99 Å2
Refinement stepCycle: LAST / Resolution: 2.95→31.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 17 0 2323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472359
X-RAY DIFFRACTIONf_angle_d0.73293195
X-RAY DIFFRACTIONf_chiral_restr0.0456414
X-RAY DIFFRACTIONf_plane_restr0.0037391
X-RAY DIFFRACTIONf_dihedral_angle_d21.0066916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.250.35751260.30962744X-RAY DIFFRACTION92.89
3.25-3.720.34561420.29232845X-RAY DIFFRACTION95.25
3.72-4.680.27191320.23832900X-RAY DIFFRACTION95.65
4.68-31.150.26211600.26193010X-RAY DIFFRACTION94.59

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