[English] 日本語
Yorodumi
- EMDB-22829: Human Tom70 in complex with SARS CoV2 Orf9b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22829
TitleHuman Tom70 in complex with SARS CoV2 Orf9b
Map data
Sample
  • Complex: Orf9b-Tom70 complex
    • Protein or peptide: Mitochondrial import receptor subunit TOM70
    • Protein or peptide: ORF9b protein
KeywordsOrf9b / Tom70 / mitochondria / virus infection / SARS CoV2 / VIRAL PROTEIN
Function / homology
Function and homology information


Translation of Accessory Proteins / outer mitochondrial membrane protein complex / TOM complex / mitochondrion targeting sequence binding / negative regulation of defense response to virus / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / negative regulation of cell growth involved in cardiac muscle cell development / protein insertion into mitochondrial inner membrane / positive regulation of autophagosome assembly ...Translation of Accessory Proteins / outer mitochondrial membrane protein complex / TOM complex / mitochondrion targeting sequence binding / negative regulation of defense response to virus / mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / negative regulation of cell growth involved in cardiac muscle cell development / protein insertion into mitochondrial inner membrane / 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 / protein transmembrane transporter activity / negative regulation of mitochondrial fission / host cell mitochondrion / positive regulation of defense response to virus by host / activation of innate immune response / protein sequestering activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / positive regulation of interferon-beta production / PINK1-PRKN Mediated Mitophagy / 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 / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsQCRG Structural Biology Consortium
Funding support United States, 4 items
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, 2020-
Header (metadata) releaseOct 21, 2020-
Map releaseOct 21, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kdt
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22829.png

Downloads & links

-
Map

FileDownload / File: emd_22829.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 213.504 Å		0.83 Å/pix.
x 256 pix.
= 213.504 Å		0.83 Å/pix.
x 256 pix.
= 213.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.7
Minimum - Maximum-2.7296653 - 4.001267
Average (Standard dev.)-0.0003437746 (±0.105128154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.504 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8340.8340.834
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z213.504213.504213.504
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.7304.001-0.000

-
Supplemental data

-
Half map: #1

Fileemd_22829_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_22829_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Orf9b-Tom70 complex

EntireName: Orf9b-Tom70 complex
Components
  • Complex: Orf9b-Tom70 complex
    • Protein or peptide: Mitochondrial import receptor subunit TOM70
    • Protein or peptide: ORF9b protein

-
Supramolecule #1: Orf9b-Tom70 complex

SupramoleculeName: Orf9b-Tom70 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Mitochondrial import receptor subunit TOM70

MacromoleculeName: Mitochondrial import receptor subunit TOM70 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.875727 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NSLDRAQAAK NKGNKYFKAG KYEQAIQCYT EAISLCPTEK NVDLSTFYQN RAAAFEQLQK WKEVAQDCTK AVELNPKYVK ALFRRAKAH EKLDNKKECL EDVTAVCILE GFQNQQSMLL ADKVLKLLGK EKAKEKYKNR EPLMPSPQFI KSYFSSFTDD I ISQPMLKG ...String:
NSLDRAQAAK NKGNKYFKAG KYEQAIQCYT EAISLCPTEK NVDLSTFYQN RAAAFEQLQK WKEVAQDCTK AVELNPKYVK ALFRRAKAH EKLDNKKECL EDVTAVCILE GFQNQQSMLL ADKVLKLLGK EKAKEKYKNR EPLMPSPQFI KSYFSSFTDD I ISQPMLKG EKSDEDKDKE GEALEVKENS GYLKAKQYME EENYDKIISE CSKEIDAEGK YMAEALLLRA TFYLLIGNAN AA KPDLDKV ISLKEANVKL RANALIKRGS MYMQQQQPLL STQDFNMAAD IDPQNADVYH HRGQLKILLD QVEEAVADFD ECI RLRPES ALAQAQKCFA LYRQAYTGNN SSQIQAAMKG FEEVIKKFPR CAEGYALYAQ ALTDQQQFGK ADEMYDKCID LEPD NATTY VHKGLLQLQW KQDLDRGLEL ISKAIEIDNK CDFAYETMGT IEVQRGNMEK AIDMFNKAIN LAKSEMEMAH LYSLC DAAH AQTEVAKKYG LKPPTL

UniProtKB: Mitochondrial import receptor subunit TOM70

-
Macromolecule #2: ORF9b protein

MacromoleculeName: ORF9b protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 10.808636 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDPKISEMHP ALRLVDPQIQ LAVTRMENAV GRDQNNVGPK VYPIILRLGS PLSLNMARKT LNSLEDKAFQ LTPIAVQMTK LATTEELPD EFVVVTVK

UniProtKB: ORF9b protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration12.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
150.0 mMKCl
20.0 mMHEPES-NaOH
0.5 mMTHP
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot for 5 seconds before plunging into liquid ethane.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 1534 / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2805121
Details: Template picked based on previous low resolution reconstruction (which was picked with a blob picker)
Startup modelType of model: NONE / Details: Ab initio reconstruction in cryoSPARC
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2.15.0) / Number images used: 178373
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v2.15.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3fp3


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

+
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