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- EMDB-33404: 3.4 Angstrom cryoEM D5 reconstruction of mud crab reovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-33404
Title3.4 Angstrom cryoEM D5 reconstruction of mud crab reovirus
Map data
Sample
  • Virus: Scylla serrata reovirus SZ-2007
    • Protein or peptide: VP3
    • Protein or peptide: VP1
KeywordsReovirus / ds-RNA virus / VIRUS
Function / homologyVP3 / VP1
Function and homology information
Biological speciesScylla serrata reovirus SZ-2007
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang QF / Gao YZ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570736 China
National Natural Science Foundation of China (NSFC)31672677 China
CitationJournal: PLoS Pathog / Year: 2023
Title: The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization.
Authors: Qinfen Zhang / Yuanzhu Gao / Matthew L Baker / Shanshan Liu / Xudong Jia / Haidong Xu / Jianguo He / Jason T Kaelber / Shaoping Weng / Wen Jiang /
Abstract: Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell ...Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.
History
DepositionMay 9, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33404.png

Downloads & links

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Map

FileDownload / File: emd_33404.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 800 pix.
= 872. Å		1.09 Å/pix.
x 800 pix.
= 872. Å		1.09 Å/pix.
x 800 pix.
= 872. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-21.309729999999998 - 33.537272999999999
Average (Standard dev.)0.08086818 (±1.814282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 872.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33404_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33404_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Scylla serrata reovirus SZ-2007

EntireName: Scylla serrata reovirus SZ-2007
Components
  • Virus: Scylla serrata reovirus SZ-2007
    • Protein or peptide: VP3
    • Protein or peptide: VP1

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Supramolecule #1: Scylla serrata reovirus SZ-2007

SupramoleculeName: Scylla serrata reovirus SZ-2007 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 458682 / Sci species name: Scylla serrata reovirus SZ-2007 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Scylla serrata (giant mud crab)

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Macromolecule #1: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Scylla serrata reovirus SZ-2007
Molecular weightTheoretical: 97.019383 KDa
SequenceString: MASTTRLVND RKQLEQQVKD DARILADARG LNITTVANDS ATGGQAIRNV GPNDEATIKA LDNVIKQIEA LSVIVNRSEK ADDAQILGP NTYKQLLEHL FSPEENVYIL LPIQAYTGGV IDRRDASFSN FAYSIASKLM MELSAATHNK IFTDYTRIAA S ALGPEIST ...String:
MASTTRLVND RKQLEQQVKD DARILADARG LNITTVANDS ATGGQAIRNV GPNDEATIKA LDNVIKQIEA LSVIVNRSEK ADDAQILGP NTYKQLLEHL FSPEENVYIL LPIQAYTGGV IDRRDASFSN FAYSIASKLM MELSAATHNK IFTDYTRIAA S ALGPEIST EGMPLFSLIE SLELTEAETS RLPVIQDSMV IQKSTATVGN AQQGISTINI KRVPFVGSAF QQVIDQLLWE YS TTSLTTK EQRRQRITEM VNDRRIMIQK LTLAEKPQVM RHVTTEINND LFFKMSPVAQ LYIYHLDRAF LDGVGFTPLA EKQ QQLQLQ LKTNILTANL IRSAINGMNT ESNLEVAIKM MQAAQLHRAS IEIAFPMNVS LSPEIIVQCF IVWMSIPEQL LSDR SNFII AAVIWAGFSA DDSYADIMRR SARASDRQNY DIIKAALSSR KFKLPRASTT LFDENEPVVR RYQIGRVYAP FPVDR YGSP VYSNCTKVEL ASDYNAEGFT IRKDDFRALQ AVLRIDEDRA ADMFTTLRIM ISSIPAVWYD AEVVHYPHTA VELEQL AAY GLTGAYPRTN HSVDTIVKTV NNISATYSTI AQMLSTIDLD PTRYGTSESI DKFKIAWENV ESVLNMEGND FVKTIMY AY EDNFPKKDFY MMLKQIASDG QGAHPIAAAI DQLRTIVYRE PERFGYIDSV ILTHNPDVDT AYNRFFHLHP IVTNQPSN T IKNAQLWNEM RLEQQVEHIK AGPVRIIGPF HVTYNYLSEE EDMPATSHII MKDNMILNDH LTFNFVKRER RNNKKRVSS FRYKAVEMYV AVRISRFQLE VLRDLHDLVR SRTYLDVSKS PLATTPIRVV EYVR

UniProtKB: VP3

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Macromolecule #2: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Scylla serrata reovirus SZ-2007
Molecular weightTheoretical: 161.488531 KDa
SequenceString: MRIMAQRLKE LQREIDKKKK ERIAEAYLSS VEVTNSSPSL SKQDDALTLP KVSPFLDSTP FTTLHNSLYG QQIHSIDDEL AQICKLEYE LQTQIADEQI TALKHFLTIR TGSPQEIQYV DKEWMKSNQH VPSFLGDVKL MFGDTAGKFR STSKSVDSIH S ITSDVQVT ...String:
MRIMAQRLKE LQREIDKKKK ERIAEAYLSS VEVTNSSPSL SKQDDALTLP KVSPFLDSTP FTTLHNSLYG QQIHSIDDEL AQICKLEYE LQTQIADEQI TALKHFLTIR TGSPQEIQYV DKEWMKSNQH VPSFLGDVKL MFGDTAGKFR STSKSVDSIH S ITSDVQVT RKKQTRSQIR NSYRVQKKHK VQQPLKPNTL YVYKYKGLPR VVLRFVPKVD TTSNSNSSSA SDSKKDKDAF SC DDLSPTW KYILTEAKRA FPDRSYSDCI HPMTWEEWLE ENQDHVKVLT QYAHQLDYVT LLQDFNLYVS GGASRVRNID MST LPTSIN VLDHFELYGD ASMKEYVRSG EWYGLLREIE QEGMTVNESE KVFANPDTYV LNVKKYFLRR FQQEIASTGM TPLT DELLN IMFVHWNIIV TAEPKLQVIK DDLLKYYSRY GVDATFDYNM KRSEMTVVTR GHLLAHKVLE CALRIVETIY TYDIQ DETF KDILIDLGRL IMRDPIYGTT TVRDATTVMK QLMYTQGTQF RRIMFKKYDY SNFNEKLVLK GEQMTNEPPT LLATTH YEE MDKKRIDALI KANQRAGNIL SQSSIERCRY TDSLDLVGDA NRYFSALTTL EAVAGFASSD LLSGFIDSNE SIEFTGT AH LRKLLYHSVR EQITTLNTST VPRPSLPKVL LSSAKDTASA SIEPLTFRIY KTTPEYDGES LNLVESTVEM STRQKKPN L MKAAEILRST VTTNQEMIIS GGTRAVQGGK GARAVYPTKQ PYHIAGSLLF HKVDTIVNAN KKYRGVSNKY GQGISNAIP HIGVPEIIAV SSDGMAICLA LDVSAFDVAQ KYTEADIELA MRDGFLDSEI SMISGETVLE RMNPADLANN LLTNTPPRYK YQTALGDII ILQHDNRSGV PWTGTQNDLV NVSNHHMAYD EYKKRVAELQ RQGKISIDVN DKHHIVRVFG DDSTFIMTYD E PPSAEEVH LMCATFVESY QDTAGTLGFA INARKGMIGR YGSEYLKNSA IYGNIKSVNQ VKFRGSEKSA SYHFGVSEKV SM IRDITDL TITRGCDETR KWKYNLMMLP VDLTTRAGAF RMHNLCSIMT GVGKMYLGGT LNNKLIASYH GSSFGWNFDD NLI KTANSI GAISDSSYDA ISTKITNLAD FKDSQQRITR DIITSGRLPQ HLNRYGKSNI LRHILASAAM GPLSQIEKNV NAYN VVMGI LNGKLEAPTV LERLNMGFKY VVMSDLKQDD YSPYSCQGLQ YRRMLVHWGL NDSRITSFDP KGKLQHLLAK NSQIL PIHF DIEFVYRLYL QAGTMGFLQV MSYYQLPDTL THEMLAAVVA LELQLGNDKY AVDMGVYSSQ AGQIRINDAL MDSIIQ HRR GPPLPIIDRT LNRLLLHTYM LMFGLMGKSI DSTKIDPTLS WRAILESNDQ RIAQLSELLT AV

UniProtKB: VP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K / Max: 100.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-16 / Number grids imaged: 1 / Number real images: 3595 / Average exposure time: 1.1 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 128440 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 58095
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr (ver. 2014) / Number images used: 58095
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: jspr (ver. 2014)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: jspr (ver. 2014)
FSC plot (resolution estimation)

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