[English] 日本語
Yorodumi
- EMDB-43730: Cryo-EM structure of BTV core -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43730
TitleCryo-EM structure of BTV core
Map data
Sample
  • Virus: Bluetongue virus (serotype 1 / isolate South Africa)
    • Protein or peptide: Core protein VP3
    • Protein or peptide: RNA-directed RNA polymeraseRNA-dependent RNA polymerase
KeywordsBluetongue virus / capsid protein / assembly intermediate / core / VIRAL PROTEIN
Function / homology
Function and homology information


viral genome replication / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / structural molecule activity / RNA binding
Similarity search - Function
RNA-dependent RNA polymerase, orbiviral / Orbivirus RNA-dependent RNA polymerase (VP1) / Inner layer core protein VP3, Orbivirus / Orbivirus VP3 (T2) protein / Inner layer core protein VP3, Reovirus / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Core protein VP3 / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesBluetongue virus (serotype 1 / isolate South Africa)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsXia X / Sung PY / Martynowycz MW / Gonen T / Roy P / Zhou ZH
Funding support United States, United Kingdom, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
Wellcome TrustWT221749/20/Z United Kingdom
CitationJournal: Cell / Year: 2024
Title: RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells.
Authors: Xian Xia / Po-Yu Sung / Michael W Martynowycz / Tamir Gonen / Polly Roy / Z Hong Zhou /
Abstract: Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques ...Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8 Å, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed "duality" characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond.
History
DepositionFeb 17, 2024-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43730.png

Downloads & links

-
Map

FileDownload / File: emd_43730.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.0013770491 - 2.022719
Average (Standard dev.)0.03214469 (±0.14281966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_43730_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43730_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bluetongue virus (serotype 1 / isolate South Africa)

EntireName: Bluetongue virus (serotype 1 / isolate South Africa)
Components
  • Virus: Bluetongue virus (serotype 1 / isolate South Africa)
    • Protein or peptide: Core protein VP3
    • Protein or peptide: RNA-directed RNA polymeraseRNA-dependent RNA polymerase

-
Supramolecule #1: Bluetongue virus (serotype 1 / isolate South Africa)

SupramoleculeName: Bluetongue virus (serotype 1 / isolate South Africa) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10905
Sci species name: Bluetongue virus (serotype 1 / isolate South Africa)
Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Ovis aries (sheep)

-
Macromolecule #1: Core protein VP3

MacromoleculeName: Core protein VP3 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Bluetongue virus (serotype 1 / isolate South Africa)
Molecular weightTheoretical: 103.410508 KDa
SequenceString: MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILDD IKALAAEQVY KIVKVPSIS FRHIVMQSRD RVLRVDTYYE EMSQVGDVIT EDEPEKFYST IIKKVRFIRG KGSFILHDIP TRDHRGMEVA E PEVLGVEF ...String:
MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILDD IKALAAEQVY KIVKVPSIS FRHIVMQSRD RVLRVDTYYE EMSQVGDVIT EDEPEKFYST IIKKVRFIRG KGSFILHDIP TRDHRGMEVA E PEVLGVEF KNVLPVLTAE HRAMIQNALD GSIIENGNVA TRDVDVFIGA CSEPVYRIYN RLQGYIEAVQ LQELRNSIGW LE RLGHRKR ITYSQEVLTD FRRQDTIWVL ALQLPVNPQV VWDVPRSSIA NLIMNIATCL PTGEYIAPNP RISSITLTQR ITT TGPFAI LTGSTPTAQQ LNDVRKIYLA LMFPGQIILD LKIDPGERMD PAVRMVAGVV GHLLFTAGGR FTNLTQNMAR QLDI ALNDY LLYMYNTRVQ VNYGPTGEPL DFQIGRNQYD CNVFRADFAT GTGYNGWATI DVEYREPAPY VHAQRYIRYC GIDSR ELIN PTTYGIGMTY HCYNEMLRML VAAGKDSEAA YFRSMLPFHM VRFARINQII NEDLHSVFSL PDDMFNALLP DLIAGA HQN ADPVVLDVSW ISLWFAFNRS FEPTHRNEML EVAPLIESVY ASELSVMKVD MRHLSLMQRR FPDVLIQARP SHFWKAV LN DSPEAVKAVM NLSHSHNFIN IRDMMRWVML PSLQPSLKLA LEEEAWAAAN DFEDLMLTDQ VYMHRDMLPE PRLDDIER F RQEGFYYTNM LEAPPEIDRV VQYTYEIARL QANMGQFRAA LRRIMDDDDW VRFGGVLRTV RVKFYDARPP DDVLQGLPF SYDTNERGGL AYATIKYATE TTIFYLIYNV EFSNTPDSLV LINPTYTMTK VFINKRIVER VRVGQILAVL NRRFVAYKGK MRIMDITQS LKMGTKLAAP TV

UniProtKB: Core protein VP3

-
Macromolecule #2: RNA-directed RNA polymerase

MacromoleculeName: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Bluetongue virus (serotype 1 / isolate South Africa)
Molecular weightTheoretical: 149.926281 KDa
SequenceString: MVAITVQGAQ LIKRVVERFY PGIAFNINEG ACYIYKFSDH IRRIRMKHGT KYRRQAEEII RNISLRKERL YGIPVLDEVE WKYVFDGQT FQSYAFEVYV NSILPWSELD PEEEFLRNYR VSREMTEVEK FIEFRAKNEM QIYGDIPIKV WCCFINELSA E LKHVPLGM ...String:
MVAITVQGAQ LIKRVVERFY PGIAFNINEG ACYIYKFSDH IRRIRMKHGT KYRRQAEEII RNISLRKERL YGIPVLDEVE WKYVFDGQT FQSYAFEVYV NSILPWSELD PEEEFLRNYR VSREMTEVEK FIEFRAKNEM QIYGDIPIKV WCCFINELSA E LKHVPLGM QVMADFVNRF DSPFHQGNRD LSNLEDFQVA YTTPLLFEMC CMESILEFNI KMRMREEEIS ALEFGDMKVD PV GLLREFF ILCLPHPKKI NNVLRAPYSW FVKMWGVGAD PIVVLQSTAG DDRNSKDVFY DKFRTEPNRY KALFRSSFYN ESR RMNEEK ILEAVKYSQK LGSHDRRLPL FEKMLKTVYT TPFYPHKSSN MILASFLLSI QTITGYGRAW VKNVSTEFDK QLKP NPSNL VQDVSDLTRE FFKQAYVEAK ERREEIVKPE DLYTSMLRLA RNTSSGFSTE IYVKKRFGPR LRDKDLIKIN SRIKA LVIF TKGHTVFTDE ELHKKYNSVE LYQTKGSRDV PIKATRTIYS INLSVLVPQL IVTLPLNEYF SRVGGITSPD YKKIGG KVI VGDLEATGSR VMDAADCFRN SADRDIFTIA IDYSEYDTHL TRHNFRTGML QGIREAMAPY RDLRYEGYTL EQIIDFG YG EGRVANTLWN GKRRLFKTTF DAYIRLDESE RDKGSFKVPK GVLPVSSVDV ANRIAVDKGF DTLIAATDGS DLALIDTH L SGENSTLIAN SMHNMAIGTL MQREVGREQP GVLTFLSEQY VGDDTLFYTK LHTTDTKVFD KVAASIFDTV AKCGHEASP SKTMMTPYSV EKTQTHAKQG CYVPQDRMMI ISSERRKDIE DVQGYVRSQV QTMITKVSRG FCHDLAQLIL MLKTTFIGAW KMKRTIKED AMYRDRKFDS NDEDGFTLIQ IRNPLALYVP IGWNGYGAHP AALNIVMTEE MYVDSIMISK LDEIMAPIRR I VHDIPPCW NETQGDKRGL ISATKMSFFS KMARPAVQAA LSDPQIINLV EELPLGEFSP GRISRTMMHS ALLKESSART LL SSGYELE YQKALNSWIT QVSMRLGEES GVISTSYAKL FDVYFEGELD GAPHMFPDQN LSPQFYIQKM MIGPRVSSRV RNS YVDRID VILRKDVVMR GFITANTILN VIEKLGTNHS VGDLVTVFTL MNIETRVAEE LAEYMTSEKI RFDALKLLKK GIAG DEFTM SLNVATQDFI DTYLAYPYQL TKTEVDAISL YCTQMIMLRA ALGLPKKKMK IVVTDDAKKR YKIRLQRFRT HVPKI KVLK KLIDPNRMTV RNLENQFV

UniProtKB: RNA-directed RNA polymerase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.8 / Component - Concentration: 20.0 mM / Component - Name: Tris
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
DetailsVirus isolated from infected BHK cells

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 62928 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 193452
Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 7 / Avg.num./class: 155590 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 96588

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 92
Output model

PDB-8w1r:
Cryo-EM structure of BTV core

+
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