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- EMDB-7944: Fako virus full particles, icosahedral reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-7944
TitleFako virus full particles, icosahedral reconstruction
Map dataAn icosahedral reconstruction of Fako virus full particles
Sample
  • Virus: Fako virus
    • Protein or peptide: Clamp protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Turret protein
Keywordscapsid / virion / Reoviridae / T=2 / VIRUS
Function / homology
Function and homology information


: / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 / : / Inner layer core protein VP1-like, C-terminal
Similarity search - Domain/homology
Major capsid protein / Turret protein / Clamp protein
Similarity search - Component
Biological speciesFako virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKaelber JT / Jiang W / Weaver SC / Auguste AJ / Chiu W
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
Welch FoundationQ1242 United States
CitationJournal: Structure / Year: 2020
Title: Arrangement of the Polymerase Complexes inside a Nine-Segmented dsRNA Virus.
Authors: Jason T Kaelber / Wen Jiang / Scott C Weaver / Albert J Auguste / Wah Chiu /
Abstract: Members of the family Reoviridae package several copies of the viral polymerase complex into their capsid to carry out replication and transcription within viral particles. Classical single-particle ...Members of the family Reoviridae package several copies of the viral polymerase complex into their capsid to carry out replication and transcription within viral particles. Classical single-particle reconstruction encounters difficulties resolving structures such as the intraparticle polymerase complex because refinement can converge to an incorrect map and because the map could depict a nonrepresentative subset of particles or an average of heterogeneous particles. Using the nine-segmented Fako virus, we tested hypotheses for the arrangement and number of polymerase complexes within the virion by measuring how well each hypothesis describes the set of cryoelectron microscopy images of individual viral particles. We find that the polymerase complex in Fako virus binds at ten possible sites despite having only nine genome segments. A single asymmetric configuration describes the arrangement of these complexes in both virions and genome-free capsids. Similarities between the arrangements of Reoviridae with 9, 10, and 11 segments indicate the generalizability of this architecture.
History
DepositionMay 27, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJan 16, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 32
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 32
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6djy
  • Surface level: 32
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6djy
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7944.png

Downloads & links

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Map

FileDownload / File: emd_7944.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAn icosahedral reconstruction of Fako virus full particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 576 pix.
= 867.456 Å		1.51 Å/pix.
x 576 pix.
= 867.456 Å		1.51 Å/pix.
x 576 pix.
= 867.456 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.506 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 32.0 / Movie #1: 32
Minimum - Maximum-82.149789999999996 - 144.327100000000002
Average (Standard dev.)0.6931533 (±8.784292000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-288-288-288
Dimensions576576576
Spacing576576576
CellA=B=C: 867.45605 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5061.5061.506
M x/y/z576576576
origin x/y/z0.0000.0000.000
length x/y/z867.456867.456867.456
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-288-288-288
NC/NR/NS576576576
D min/max/mean-82.150144.3270.693

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Supplemental data

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Additional map: Another icosahedral reconstruction of Fako virus full particles

Fileemd_7944_additional.map
AnnotationAnother icosahedral reconstruction of Fako virus full particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fako virus

EntireName: Fako virus
Components
  • Virus: Fako virus
    • Protein or peptide: Clamp protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Turret protein

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Supramolecule #1: Fako virus

SupramoleculeName: Fako virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1567404 / Sci species name: Fako virus / Sci species strain: CSW77 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Culicinae (mosquito)
Molecular weightTheoretical: 43 MDa
Virus shellShell ID: 1 / T number (triangulation number): 2

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Macromolecule #1: Clamp protein

MacromoleculeName: Clamp protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fako virus / Strain: CSW77
Molecular weightTheoretical: 39.589691 KDa
SequenceString: MTLTYWDKEK RMTLKQMIQQ VAINEQENEL THYVFTTPLS MPTFGKPMLG YVPLNEVATS KFFSNVNDFD RDNQLAMAHF PDTTITQAY NLTNSIKPGD TSLPDAEVAA LKWFWKFFTS INLVRQPPMD NVMYWACQFL SSGTSFLPLE RDVEIVFSGF K GSHICMFS ...String:
MTLTYWDKEK RMTLKQMIQQ VAINEQENEL THYVFTTPLS MPTFGKPMLG YVPLNEVATS KFFSNVNDFD RDNQLAMAHF PDTTITQAY NLTNSIKPGD TSLPDAEVAA LKWFWKFFTS INLVRQPPMD NVMYWACQFL SSGTSFLPLE RDVEIVFSGF K GSHICMFS NLRQMNLSPI LCPYYDLITN FKTTTEIRAY VDAHEELKSL LTYLCLCTIV GLCDTFTETR NMDTGEYVWK VR DVVSRNH TPAQNVEKFC YTIQNAKYMI QLVHVLLFPL TDNKYADLPN YVAVITQGAI NQSRSHNVIN TTDESNSNTT SDT AASTSG IVSGDTGTVA SLYPDEFKYV QS

UniProtKB: Clamp protein

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Fako virus / Strain: CSW77
Molecular weightTheoretical: 136.689766 KDa
SequenceString: MRPIRMYKNN QERTNLKHQE INEEQQNEQT TSNQGFTRSD NSGKINIERI SSSRNQITDG KTVSSYSKIE TNRSSQDSVQ HGGSSITYT SDTTGNPRIT NARTNNDETH ATGPIEDLNS TSHGREPEIE SFADRAELAM MIQGMTVGAL TVQPMRSIRS T FANLANVL ...String:
MRPIRMYKNN QERTNLKHQE INEEQQNEQT TSNQGFTRSD NSGKINIERI SSSRNQITDG KTVSSYSKIE TNRSSQDSVQ HGGSSITYT SDTTGNPRIT NARTNNDETH ATGPIEDLNS TSHGREPEIE SFADRAELAM MIQGMTVGAL TVQPMRSIRS T FANLANVL IFHDVFTTED KPSAFIEYHS DEMIVNMPKQ TYNPIDNLAK ILYLPSLEKF KYGTGIVQLN YSPHISKLYQ NT NNIINTI TDGITYANRT EFFIRVMVLM MMDRKILTME FYDVDTSAIS NTAILPTIPT TTGVSPLLRI DTRTEPIWYN DAI KTLITN LTIQYGKIKT VLDANAVKRY SVVGYPIDQY RAYLYNHNLL EYLGKKVKRE DIMSLIKALS YEFDLITISD LEYQ NIPKW FSDNDLSRFI FSICMFPDIV RQFHALNIDY FSQANVFTVK SENAIVKMLN SNQNMEPTII NWFLFRICAI DKTVI DDYF SLEMTPIIMR PKLYDFDMKR GEPVSLLYIL ELILFSIMFP NVTQHMLGQI QARILYISMY AFRQEYLKFI TKFGFY YKI VNGRKEYIQV TNQNERMTEN NDVLTGNLYP SLFTDDPTLS AIAPTLAKIA RLMKPTTSLT PDDRAIAAKF PRFKDSA HL NPYSSLNIGG RTQHSVTYTR MYDAIEEMFN LILRAFASSF AQRPRAGVTQ LKSLLTQLAD PLCLALDGHV YHLYNVMA N MMQNFIPNTD GQFHSFRACS YAVKDGGNIY RVVQNGDELN ESLLIDTAIV WGLLGNTDSS YGNAIGATGT ANVPTKVQP VIPTPDNFIT PTIHLKTSID AICSVEGILL LILSRQTTIP GYEDELNKLR TGISQPKVTE RQYRRARESI KNMLGSGDYN VAPLHFLLH TEHRSTKLSK PLIRRVLDNV VQPYVANLDP AEFENTPQLI ENSNMTRLQI ALKMLTGDMD DIVKGLILHK R ACAKFDVY ETLTIPTDVK TIVLTMQHIS TQTQNNMVYY VFLIDGVKIL AEDIKNVNFQ IDITGIWPEY VITLLLRAIN NG FNTYVSM PNILYKPTIT ADVRQFMNTT KAETLLISNK SIVHEIMFFD NALQPKMSSD TLALSEAVYR TIWNSSIITQ RIS ARGLMN LEDARPPEAK ISHQSELDMG KIDETSGEPI YTSGLQKMQS SKVSMANVVL SAGSDVIRQA AIKYNVVRTQ EIIL FE

UniProtKB: Major capsid protein

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Macromolecule #3: Turret protein

MacromoleculeName: Turret protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Fako virus / Strain: CSW77
Molecular weightTheoretical: 121.23257 KDa
SequenceString: MIDLRLEEDI LTATLPEFLS TRPKYRYAYT NTKQQDIRFQ GPMRHVRLTH LYKQTKLWNL QYIERELAIS EIDDALDEFI QTFSLPYVI EQGTYKYNML LGMHAHNVNY QDDVSELIAN NPQLLNYLDD NPFSAIFELV NVDLQIYQYG QNIFNNEAEH T ILFLKDNT ...String:
MIDLRLEEDI LTATLPEFLS TRPKYRYAYT NTKQQDIRFQ GPMRHVRLTH LYKQTKLWNL QYIERELAIS EIDDALDEFI QTFSLPYVI EQGTYKYNML LGMHAHNVNY QDDVSELIAN NPQLLNYLDD NPFSAIFELV NVDLQIYQYG QNIFNNEAEH T ILFLKDNT NYGVIQALQK HPFSATHINW HLHKHIFVFH SREQLLNKLL SAGLEDSQLY QRQKTYSTKR GDRPTERMVT YI EDDHIRR IQAVFPLLLD NIFDVKLHKD SSMTWLKSYA DMIYDSVKNS NSTITPEIRK LYLRMYNQYM RIFLPIEQYM LYD NTCWPF SEKITLKINV RLISSRENQP VLWKTPIDTE NLISIVQPDE PINKLNFTAI PSTMIRLNDN ITMYRAVKDM FSAI EYLPD AIENIPTLTM KEQALSRYIS PDSEAQNFFN NQPPYLNSIM NVNRQVFEAV KRGNIQVSTG SMEHLCLCMH VKSGL IVGR TVLIDDKVVL RRNFNASTAK MITCYVKAFA QLYGEGSLIN PGLRMVFFGV ETEPAIDILK LFYGDKSLYI QGFGDR GIG RDKFRTKIED ALTLRIGCDI LISDIDQADY EDPNEEKFDD ITDFVCYVTE LVISNATVGL VKISMPTYYI MNKISST LN NKFSNVAINI VKLSTQKPYT YEAYIMLSHG STLTNKGYLR NPVCDVYLEK ISLQPMDLKI ISTISNEINY DKPTLYRF V VDKNDVTDVS IAMHILSIHC STITTRSVMV RSDNTGAFVT MSGIKDMKRV AIMNRMTDGT SANSYMHEQN GKLYLQKVP YLEDLISAFP NGFGSTYQND YDSSMSVINV NALIRQVVYR VISKSIPVAL LESLSRIRII GGRDLGEMNA VYKLYKTPIE VYDAVGITR EYPHVQISYR AQRYSFTESI PNHTLLLANY VIMNDVDGAP ISSLEQINTI KKIISKISLG SIAYIQVYTD I VARNINVM TKNDSFLISA NADKTVFKVQ VSGYKAVEMC NYEQLLQLVS DNTGVNIIKL TYQDVLESCV LSSGILGDTG SW LLDLVLA STYIIEIRG

UniProtKB: Turret protein

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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: 7.8
Component:
ConcentrationFormulaName
10.0 mMC4H12NO3CLTris-HCl
1.0 mMEDTA
100.0 mMNaClsodium chloride
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Number real images: 2400 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.7 mm
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 10588
Startup modelType of model: EMDB MAP
EMDB ID:

6001

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 5294
Initial angle assignmentType: OTHER / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
FSC plot (resolution estimation)

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