[English] 日本語
Yorodumi
- EMDB-16774: in situ Subtomogram average of Immature Rotavirus TLP spike -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16774
Titlein situ Subtomogram average of Immature Rotavirus TLP spike
Map datamain map
Sample
  • Virus: Rotavirus A
    • Protein or peptide: Outer capsid protein VP4
    • Protein or peptide: Outer capsid glycoprotein VP7
    • Protein or peptide: Intermediate capsid protein VP6
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / membrane / metal ion binding
Similarity search - Function
Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain ...Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Viral capsid/haemagglutinin protein / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4 / Outer capsid glycoprotein VP7 / Intermediate capsid protein VP6
Similarity search - Component
Biological speciesRotavirus A
Methodsubtomogram averaging / cryo EM / Resolution: 4.5 Å
AuthorsShah PNM / Stuart DI
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Wellcome Trust03141/Z/16/Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
CitationJournal: Cell Host Microbe / Year: 2023
Title: Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography.
Authors: Pranav N M Shah / James B Gilchrist / Björn O Forsberg / Alister Burt / Andrew Howe / Shyamal Mosalaganti / William Wan / Julika Radecke / Yuriy Chaban / Geoff Sutton / David I Stuart / Mark Boyce /
Abstract: Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and ...Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.
History
DepositionFeb 27, 2023-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16774.png

Downloads & links

-
Map

FileDownload / File: emd_16774.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Voxel sizeX=Y=Z: 1.97 Å
Density
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0039085895 - 0.0059328238
Average (Standard dev.)-2.732337e-05 (±0.00039345253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 315.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half1

Fileemd_16774_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2

Fileemd_16774_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Rotavirus A

EntireName: Rotavirus A
Components
  • Virus: Rotavirus A
    • Protein or peptide: Outer capsid protein VP4
    • Protein or peptide: Outer capsid glycoprotein VP7
    • Protein or peptide: Intermediate capsid protein VP6

-
Supramolecule #1: Rotavirus A

SupramoleculeName: Rotavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 28875 / Sci species name: Rotavirus A / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Outer capsid protein VP4

MacromoleculeName: Outer capsid protein VP4 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus A
Molecular weightTheoretical: 86.767953 KDa
Recombinant expressionOrganism: Chlorocebus aethiops aethiops (mammal)
SequenceString: MASLIYRQLL TNSYTVDLSD EIQEIGSTKS QNVTINPGPF AQTGYAPVNW GPGEINDSTT VGPLLDGPYQ PTTFNPPVDY WMLLAPTTP GVIVEGTNNT DRWLATILIE PNVQSENRTY TIFGIQEQLT VSNTSQDQWK FIDVVKTTAN GSIGQYGPLL S SPKLYAVM ...String:
MASLIYRQLL TNSYTVDLSD EIQEIGSTKS QNVTINPGPF AQTGYAPVNW GPGEINDSTT VGPLLDGPYQ PTTFNPPVDY WMLLAPTTP GVIVEGTNNT DRWLATILIE PNVQSENRTY TIFGIQEQLT VSNTSQDQWK FIDVVKTTAN GSIGQYGPLL S SPKLYAVM KHNEKLYTYE GQTPNATTAH YSTTNYDSVN MTAFCDFYII PRSEESKCTE YINNGLPPIQ NTRNVVPLSL TA RDVIHYR AQANEDIVIS KTSLWKEMQY NRDITIRFKF ANTIIKSGGL GYKWSEISFK PANYQYTYTR DGEEVTAHTT CSV NGMNDF SFNGGYLPTD FVVSKFEVIK ENSYVYIDYW DDSQAFRNVV YVRSLAANLN SVMCTGGSYN FSLPVGQWPV LTGG AVSLH SAGVTLSTQF TDFVSLNSLR FRFRLAVEEP HFKLTRTRLD RLYGLPAADP NNGKEYYEIA GRFSLISLVP SNDDY QTPI ANSVTVRQDL ERQLGELREE FNALSQEIAM SQLIDLALLP LDMFSMFSGI KSTIDAAKSM ATNVMKKFKK SGLANS VST LTDSLSDAAS SISRGSSIRS IGSSASAWTD VSTQITDISS SVSSVSTQTS TISRRLRLKE MATQTEGMNF DDISAAV LK TKIDKSTQIS PNTIPDIVTE ASEKFIPNRA YRVINNDDVF EAGIDGKFFA YKVDTFEEIP FDVQKFADLV TDSPVISA I IDFKTLKNLN DNYGISRQQA FNLLRSDPRV LREFINQDNP IIRNRIEQLI MQCRL

-
Macromolecule #2: Outer capsid glycoprotein VP7

MacromoleculeName: Outer capsid glycoprotein VP7 / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus A
Molecular weightTheoretical: 37.230664 KDa
Recombinant expressionOrganism: Chlorocebus aethiops aethiops (mammal)
SequenceString: MYGIEYTTVL TFLISIILLN YILKSLTRIM DFIIYRFLFI IVILSPFLRA QNYGINLPIT GSMDIAYANS TQEEPFLTST LCLYYPTEA ATEINDNSWK DTLSQLFLTK GWPTGSVYFK EYTNIASFSV DPQLYCDYNV VLMKYDATLQ LDMSELADLI L NEWLCNPM ...String:
MYGIEYTTVL TFLISIILLN YILKSLTRIM DFIIYRFLFI IVILSPFLRA QNYGINLPIT GSMDIAYANS TQEEPFLTST LCLYYPTEA ATEINDNSWK DTLSQLFLTK GWPTGSVYFK EYTNIASFSV DPQLYCDYNV VLMKYDATLQ LDMSELADLI L NEWLCNPM DITLYYYQQT DEANKWISMG SSCTIKVCPL NTQTLGIGCL TTDATTFEEV ATAEKLVITD VVDGVNHKLD VT TATCTIR NCKKLGPREN VAVIQVGGSD ILDITADPTT APQTERMMRI NWKKWWQVFY TVVDYVDQII QVMSKRSRSL NSA AFYYRV

-
Macromolecule #3: Intermediate capsid protein VP6

MacromoleculeName: Intermediate capsid protein VP6 / type: protein_or_peptide / ID: 3 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus A
Molecular weightTheoretical: 44.910738 KDa
Recombinant expressionOrganism: Chlorocebus aethiops aethiops (mammal)
SequenceString: MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG IGNLPIRNWN FNFGLLGTTL LNLDANYVET ARNTIDYFV DFVDNVCMDE MVRESQRNGI APQSDSLRKL SAIKFKRINF DNSSEYIENW NLQNRRQRTG FTFHKPNIFP Y SASFTLNR ...String:
MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG IGNLPIRNWN FNFGLLGTTL LNLDANYVET ARNTIDYFV DFVDNVCMDE MVRESQRNGI APQSDSLRKL SAIKFKRINF DNSSEYIENW NLQNRRQRTG FTFHKPNIFP Y SASFTLNR SQPAHDNLMG TMWLNAGSEI QVAGFDYSCA INAPANIQQF EHIVPLRRVL TTATITLLPD AERFSFPRVI NS ADGATTW FFNPVILRPN NVEVEFLLNG QIINTYQARF GTIVARNFDT IRLSFQLMRP PNMTPAVAVL FPNAQPFEHH ATV GLTLRI ESAVCESVLA DASETLLANV TSVRQEYAIP VGPVFPPGMN WTDLITNYSP SREDNLQRVF TVASIRSMLI K

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
DetailsMA104 cells infected with Rotavirus

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.19 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.0.9) / Number subtomograms used: 16740
ExtractionNumber tomograms: 85 / Number images used: 16740 / Software - Name: crYOLO
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8coa:
in situ Subtomogram average of Immature Rotavirus TLP spike

+
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://pdbjlvh1.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