[English] 日本語
Yorodumi
- PDB-7kdt: Human Tom70 in complex with SARS CoV2 Orf9b -

+
Open data


ID or keywords:

Loading...

-
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 / outer mitochondrial membrane protein complex / TOM complex / negative regulation of defense response to virus / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein insertion into mitochondrial inner membrane / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of autophagosome assembly ...Translation of Accessory Proteins / outer mitochondrial membrane protein complex / TOM complex / negative regulation of defense response to virus / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein insertion into mitochondrial inner membrane / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of autophagosome assembly / response to thyroxine / Mitochondrial protein import / positive regulation of protein targeting to mitochondrion / protein targeting to mitochondrion / protein import into mitochondrial matrix / 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 / activation of innate immune response / positive regulation of interferon-beta production / protein sequestering activity / PINK1-PRKN Mediated Mitophagy / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / mitochondrial membrane / SARS-CoV-1 activates/modulates innate immune responses / regulation of apoptotic process / molecular adaptor activity / mitochondrial outer membrane / 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 / identical protein binding / membrane
Similarity search - Function
Protein 9b, Betacoronavirus / Protein 9b, SARS-CoV / Betacoronavirus lipid binding protein / Sarbecovirus 9b domain profile. / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-22829
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
1


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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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 FIELD / 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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more