7KDT

Human Tom70 in complex with SARS CoV2 Orf9b


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

Gordon, D.E.Hiatt, J.Bouhaddou, M.Rezelj, V.V.Ulferts, S.Braberg, H.Jureka, A.S.Obernier, K.Guo, J.Z.Batra, J.Kaake, R.M.Weckstein, A.R.Owens, T.W.Gupta, M.Pourmal, S.Titus, E.W.Cakir, M.Soucheray, M.McGregor, M.Cakir, Z.Jang, G.O'Meara, M.J.Tummino, T.A.Zhang, Z.Foussard, H.Rojc, A.Zhou, Y.Kuchenov, D.Huttenhain, R.Xu, J.Eckhardt, M.Swaney, D.L.Fabius, J.M.Ummadi, M.Tutuncuoglu, B.Rathore, U.Modak, M.Haas, P.Haas, K.M.Naing, Z.Z.C.Pulido, E.H.Shi, Y.Barrio-Hernandez, I.Memon, D.Petsalaki, E.Dunham, A.Marrero, M.C.Burke, D.Koh, C.Vallet, T.Silvas, J.A.Azumaya, C.M.Billesbolle, C.Brilot, A.F.Campbell, M.G.Diallo, A.Dickinson, M.S.Diwanji, D.Herrera, N.Hoppe, N.Kratochvil, H.T.Liu, Y.Merz, G.E.Moritz, M.Nguyen, H.C.Nowotny, C.Puchades, C.Rizo, A.N.Schulze-Gahmen, U.Smith, A.M.Sun, M.Young, I.D.Zhao, J.Asarnow, D.Biel, J.Bowen, A.Braxton, J.R.Chen, J.Chio, C.M.Chio, U.S.Deshpande, I.Doan, L.Faust, B.Flores, S.Jin, M.Kim, K.Lam, V.L.Li, F.Li, J.Li, Y.L.Li, Y.Liu, X.Lo, M.Lopez, K.E.Melo, A.A.Moss 3rd, F.R.Nguyen, P.Paulino, J.Pawar, K.I.Peters, J.K.Pospiech Jr., T.H.Safari, M.Sangwan, S.Schaefer, K.Thomas, P.V.Thwin, A.C.Trenker, R.Tse, E.Tsui, T.K.M.Wang, F.Whitis, N.Yu, Z.Zhang, K.Zhang, Y.Zhou, F.Saltzberg, D.Hodder, A.J.Shun-Shion, A.S.Williams, D.M.White, K.M.Rosales, R.Kehrer, T.Miorin, L.Moreno, E.Patel, A.H.Rihn, S.Khalid, M.M.Vallejo-Gracia, A.Fozouni, P.Simoneau, C.R.Roth, T.L.Wu, D.Karim, M.A.Ghoussaini, M.Dunham, I.Berardi, F.Weigang, S.Chazal, M.Park, J.Logue, J.McGrath, M.Weston, S.Haupt, R.Hastie, C.J.Elliott, M.Brown, F.Burness, K.A.Reid, E.Dorward, M.Johnson, C.Wilkinson, S.G.Geyer, A.Giesel, D.M.Baillie, C.Raggett, S.Leech, H.Toth, R.Goodman, N.Keough, K.C.Lind, A.L.Klesh, R.J.Hemphill, K.R.Carlson-Stevermer, J.Oki, J.Holden, K.Maures, T.Pollard, K.S.Sali, A.Agard, D.A.Cheng, Y.Fraser, J.S.Frost, A.Jura, N.Kortemme, T.Manglik, A.Southworth, D.R.Stroud, R.M.Alessi, D.R.Davies, P.Frieman, M.B.Ideker, T.Abate, C.Jouvenet, N.Kochs, G.Shoichet, B.Ott, M.Palmarini, M.Shokat, K.M.Garcia-Sastre, A.Rassen, J.A.Grosse, R.Rosenberg, O.S.Verba, K.A.Basler, C.F.Vignuzzi, M.Peden, A.A.Beltrao, P.Krogan, N.J.

(2020) Science 370

  • DOI: https://doi.org/10.1126/science.abe9403
  • Primary Citation of Related Structures:  
    7KDT

  • PubMed 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 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.


  • Organizational Affiliation

    Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM70500Homo sapiensMutation(s): 0 
Gene Names: TOMM70KIAA0719TOM70TOMM70A
UniProt & NIH Common Fund Data Resources
Find proteins for O94826 (Homo sapiens)
Explore O94826 
Go to UniProtKB:  O94826
PHAROS:  O94826
GTEx:  ENSG00000154174 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94826
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ORF9b protein97Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: 9b
UniProt
Find proteins for P0DTD2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD2 
Go to UniProtKB:  P0DTD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv2.15.0
MODEL REFINEMENTRosetta2020.08.61146
MODEL REFINEMENTISOLDE1.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DARPAUnited StatesHR0011-19-2-0020
FastGrantsUnited StatesCOVID19 grant
Laboratory for Genomics ResearchUnited StatesExcellence in Research Award COVID19
Quantitative Biosciences InstituteUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description