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- PDB-7kdt: Human Tom70 in complex with SARS CoV2 Orf9b -

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Basic information

Entry
Database: PDB / ID: 7kdt
TitleHuman Tom70 in complex with SARS CoV2 Orf9b
Components
  • Mitochondrial import receptor subunit TOM70
  • ORF9b protein
KeywordsVIRAL PROTEIN / Orf9b / Tom70 / mitochondria / virus infection / SARS CoV2
Function / homology
Function and homology information


Translation of Accessory Proteins / TOM complex / outer mitochondrial membrane protein complex / mitochondrion targeting sequence binding / negative regulation of defense response to virus / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial inner membrane / protein import into mitochondrial matrix / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of autophagosome assembly ...Translation of Accessory Proteins / TOM complex / outer mitochondrial membrane protein complex / mitochondrion targeting sequence binding / negative regulation of defense response to virus / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial inner membrane / protein import into mitochondrial matrix / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of autophagosome assembly / 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 / protein transmembrane transporter activity / negative regulation of mitochondrial fission / positive regulation of defense response to virus by host / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / PINK1-PRKN Mediated Mitophagy / activation of innate immune response / positive regulation of interferon-beta production / protein sequestering activity / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / mitochondrion / extracellular exosome / membrane / identical protein binding
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsQCRG Structural Biology Consortium
Funding support United States, 4items
OrganizationGrant numberCountry
DARPAHR0011-19-2-0020 United States
FastGrantsCOVID19 grant United States
Laboratory for Genomics ResearchExcellence in Research Award COVID19 United States
Quantitative Biosciences Institute United States
CitationJournal: Science / Year: 2020
Title: Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
Authors: David E Gordon / Joseph Hiatt / Mehdi Bouhaddou / Veronica V Rezelj / Svenja Ulferts / Hannes Braberg / Alexander S Jureka / Kirsten Obernier / Jeffrey Z Guo / Jyoti Batra / Robyn M Kaake / ...Authors: David E Gordon / Joseph Hiatt / Mehdi Bouhaddou / Veronica V Rezelj / Svenja Ulferts / Hannes Braberg / Alexander S Jureka / Kirsten Obernier / Jeffrey Z Guo / Jyoti Batra / Robyn M Kaake / Andrew R Weckstein / Tristan W Owens / Meghna Gupta / Sergei Pourmal / Erron W Titus / Merve Cakir / Margaret Soucheray / Michael McGregor / Zeynep Cakir / Gwendolyn Jang / Matthew J O'Meara / Tia A Tummino / Ziyang Zhang / Helene Foussard / Ajda Rojc / Yuan Zhou / Dmitry Kuchenov / Ruth Hüttenhain / Jiewei Xu / Manon Eckhardt / Danielle L Swaney / Jacqueline M Fabius / Manisha Ummadi / Beril Tutuncuoglu / Ujjwal Rathore / Maya Modak / Paige Haas / Kelsey M Haas / Zun Zar Chi Naing / Ernst H Pulido / Ying Shi / Inigo Barrio-Hernandez / Danish Memon / Eirini Petsalaki / Alistair Dunham / Miguel Correa Marrero / David Burke / Cassandra Koh / Thomas Vallet / Jesus A Silvas / Caleigh M Azumaya / Christian Billesbølle / Axel F Brilot / Melody G Campbell / Amy Diallo / Miles Sasha Dickinson / Devan Diwanji / Nadia Herrera / Nick Hoppe / Huong T Kratochvil / Yanxin Liu / Gregory E Merz / Michelle Moritz / Henry C Nguyen / Carlos Nowotny / Cristina Puchades / Alexandrea N Rizo / Ursula Schulze-Gahmen / Amber M Smith / Ming Sun / Iris D Young / Jianhua Zhao / Daniel Asarnow / Justin Biel / Alisa Bowen / Julian R Braxton / Jen Chen / Cynthia M Chio / Un Seng Chio / Ishan Deshpande / Loan Doan / Bryan Faust / Sebastian Flores / Mingliang Jin / Kate Kim / Victor L Lam / Fei Li / Junrui Li / Yen-Li Li / Yang Li / Xi Liu / Megan Lo / Kyle E Lopez / Arthur A Melo / Frank R Moss / Phuong Nguyen / Joana Paulino / Komal Ishwar Pawar / Jessica K Peters / Thomas H Pospiech / Maliheh Safari / Smriti Sangwan / Kaitlin Schaefer / Paul V Thomas / Aye C Thwin / Raphael Trenker / Eric Tse / Tsz Kin Martin Tsui / Feng Wang / Natalie Whitis / Zanlin Yu / Kaihua Zhang / Yang Zhang / Fengbo Zhou / Daniel Saltzberg / / Anthony J Hodder / Amber S Shun-Shion / Daniel M Williams / Kris M White / Romel Rosales / Thomas Kehrer / Lisa Miorin / Elena Moreno / Arvind H Patel / Suzannah Rihn / Mir M Khalid / Albert Vallejo-Gracia / Parinaz Fozouni / Camille R Simoneau / Theodore L Roth / David Wu / Mohd Anisul Karim / Maya Ghoussaini / Ian Dunham / Francesco Berardi / Sebastian Weigang / Maxime Chazal / Jisoo Park / James Logue / Marisa McGrath / Stuart Weston / Robert Haupt / C James Hastie / Matthew Elliott / Fiona Brown / Kerry A Burness / Elaine Reid / Mark Dorward / Clare Johnson / Stuart G Wilkinson / Anna Geyer / Daniel M Giesel / Carla Baillie / Samantha Raggett / Hannah Leech / Rachel Toth / Nicola Goodman / Kathleen C Keough / Abigail L Lind / / Reyna J Klesh / Kafi R Hemphill / Jared Carlson-Stevermer / Jennifer Oki / Kevin Holden / Travis Maures / Katherine S Pollard / Andrej Sali / David A Agard / Yifan Cheng / James S Fraser / Adam Frost / Natalia Jura / Tanja Kortemme / Aashish Manglik / Daniel R Southworth / Robert M Stroud / Dario R Alessi / Paul Davies / Matthew B Frieman / Trey Ideker / Carmen Abate / Nolwenn Jouvenet / Georg Kochs / Brian Shoichet / Melanie Ott / Massimo Palmarini / Kevan M Shokat / Adolfo García-Sastre / Jeremy A Rassen / Robert Grosse / Oren S Rosenberg / Kliment A Verba / Christopher F Basler / Marco Vignuzzi / Andrew A Peden / Pedro Beltrao / Nevan J Krogan /
Abstract: The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more ...The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,6842
Polymers67,6842
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 56875.727 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(DE3) (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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Orf9b-Tom70 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.FormulaBuffer-ID
1150 mMKCl1
220 mMHEPES-NaOH1
30.5 mMTHP1
SpecimenConc.: 12.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Blot for 5 seconds before plunging into liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 1534

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv2.15.0particle selection
2SerialEM3,8image acquisition
4cryoSPARCv2.15.0CTF correction
7Rosetta2020.08.61146model fitting
10cryoSPARCv2.15.0final Euler assignment
12cryoSPARCv2.15.03D reconstruction
13Rosetta2020.08.61146model refinement
14ISOLDE1model refinement
CTF correctionDetails: Done at the reconstruction stage as is standard for cryoSPARC
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2805121
Details: Template picked based on previous low resolution reconstruction (which was picked with a blob picker)
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178373 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3FP3

3fp3


Accession code: 3FP3 / Source name: PDB / Type: experimental model

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