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- PDB-7dhg: Crystal structure of SARS-CoV-2 Orf9b complex with human TOM70 -

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Basic information

Entry
Database: PDB / ID: 7dhg
TitleCrystal structure of SARS-CoV-2 Orf9b complex with human TOM70
Components
  • Mitochondrial import receptor subunit TOM70
  • ORF9b protein
KeywordsIMMUNE SYSTEM / HSP90 / orf9b
Function / homology
Function and homology information


Translation of Accessory Proteins / outer mitochondrial membrane protein complex / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / negative regulation of defense response to virus / protein import into mitochondrial matrix / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of autophagosome assembly / protein insertion into mitochondrial inner membrane ...Translation of Accessory Proteins / outer mitochondrial membrane protein complex / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / negative regulation of defense response to virus / protein import into mitochondrial matrix / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of autophagosome assembly / protein insertion into mitochondrial inner membrane / response to thyroxine / Mitochondrial protein import / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / host cell mitochondrion / negative regulation of mitochondrial fission / protein transmembrane transporter activity / positive regulation of defense response to virus by host / protein sequestering activity / PINK1-PRKN Mediated Mitophagy / activation of innate immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / positive regulation of interferon-beta production / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / SARS-CoV-1 activates/modulates innate immune responses / regulation of apoptotic process / mitochondrial outer membrane / molecular adaptor activity / Ub-specific processing proteases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / mitochondrion / extracellular exosome / identical protein binding / membrane
Similarity search - Function
Protein 9b, Betacoronavirus / Protein 9b, SARS-CoV / Betacoronavirus lipid binding protein / Sarbecovirus 9b domain profile. / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...Protein 9b, Betacoronavirus / Protein 9b, SARS-CoV / Betacoronavirus lipid binding protein / Sarbecovirus 9b domain profile. / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM70 / ORF9b protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGao, X. / Zhu, K. / Qin, B. / Olieric, V. / Wang, M. / Cui, S.
CitationJournal: Nat Commun / Year: 2021
Title: Crystal structure of SARS-CoV-2 Orf9b in complex with human TOM70 suggests unusual virus-host interactions.
Authors: Gao, X. / Zhu, K. / Qin, B. / Olieric, V. / Wang, M. / Cui, S.
History
DepositionNov 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Structure summary / Category: audit_author / citation / struct / Item: _citation.title / _struct.title
Revision 1.2Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Mitochondrial import receptor subunit TOM70
B: ORF9b protein


Theoretical massNumber of molelcules
Total (without water)78,3542
Polymers78,3542
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-34 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.655, 79.438, 124.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitochondrial import receptor subunit TOM70 / Mitochondrial precursor proteins import receptor / Translocase of outer membrane 70 kDa subunit / ...Mitochondrial precursor proteins import receptor / Translocase of outer membrane 70 kDa subunit / Translocase of outer mitochondrial membrane protein 70


Mass: 67545.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM70, KIAA0719, TOM70, TOMM70A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O94826
#2: Protein ORF9b protein / ORF9b / Accessory protein 9b / ORF-9b / Protein 9b


Mass: 10808.636 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 1.72 Å3/Da / Density % sol: 28.41 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1m Bis-tris ph5.5,21%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→66.89 Å / Num. obs: 51880 / % possible obs: 98.1 % / Redundancy: 5.78 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.33
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 2.99 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 0.71 / Num. unique obs: 7594 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7kdt

7kdt


Resolution: 2.2→50.01 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 2552 4.94 %
Rwork0.2241 --
obs0.2263 51681 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 0 61 4079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024079
X-RAY DIFFRACTIONf_angle_d0.4445482
X-RAY DIFFRACTIONf_dihedral_angle_d20.1321569
X-RAY DIFFRACTIONf_chiral_restr0.033601
X-RAY DIFFRACTIONf_plane_restr0.002714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.37081140.34552205X-RAY DIFFRACTION79
2.24-2.290.37611180.32842495X-RAY DIFFRACTION88
2.29-2.340.3428990.32452701X-RAY DIFFRACTION95
2.34-2.390.30851640.3092725X-RAY DIFFRACTION99
2.39-2.450.36351340.29012796X-RAY DIFFRACTION100
2.45-2.520.31031360.28572785X-RAY DIFFRACTION100
2.52-2.590.29381870.27172767X-RAY DIFFRACTION100
2.59-2.680.28471290.26612807X-RAY DIFFRACTION100
2.68-2.770.34931370.27272790X-RAY DIFFRACTION100
2.77-2.880.28661300.25392823X-RAY DIFFRACTION100
2.88-3.020.29791560.25512802X-RAY DIFFRACTION100
3.02-3.170.35731280.25942778X-RAY DIFFRACTION100
3.17-3.370.28541320.26162823X-RAY DIFFRACTION100
3.37-3.630.29761320.23652785X-RAY DIFFRACTION100
3.63-40.22712180.20482738X-RAY DIFFRACTION100
4-4.580.20051620.17652772X-RAY DIFFRACTION100
4.58-5.760.28521350.19852788X-RAY DIFFRACTION100
5.77-50.010.23171410.17242749X-RAY DIFFRACTION98

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