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- EMDB-61592: Cryo-EM structure of Full particle of prokaryotic dsRNA virus phiYY -

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Basic information

Entry
Database: EMDB / ID: EMD-61592
TitleCryo-EM structure of Full particle of prokaryotic dsRNA virus phiYY
Map dataBlock-Refine of Full particle at 5-fold axis.
Sample
  • Virus: Pseudomonas phage phiYY (virus)
    • Protein or peptide: Phage procapsid protein
    • Protein or peptide: Nucleocapsid shell protein
KeywordsCryo-EM / dsRNA virus / Full particle / capsid protein / genome package / VIRUS
Function / homology: / Phi6 bacteriophage P8 capsid protein / : / Major inner capsid protein P1 / viral nucleocapsid / Phage procapsid protein / Nucleocapsid shell protein
Function and homology information
Biological speciesPseudomonas phage phiYY (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMeng KW / Cui CX / Huyan YN / Meng G
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structure assembly and genome packaging of a prokaryotic Double-strand RNA virus
Authors: Huyan YN / Meng KW / Cui CX / Meng G
History
DepositionSep 19, 2024-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61592.png

Downloads & links

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Map

FileDownload / File: emd_61592.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBlock-Refine of Full particle at 5-fold axis.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 224 pix.
= 304.64 Å		1.36 Å/pix.
x 224 pix.
= 304.64 Å		1.36 Å/pix.
x 224 pix.
= 304.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.04832632 - 0.07583977
Average (Standard dev.)0.0002530234 (±0.0051483163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Block-Refine of Full particle at 5-fold axis.

Fileemd_61592_half_map_1.map
AnnotationBlock-Refine of Full particle at 5-fold axis.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Block-Refine of Full particle at 5-fold axis.

Fileemd_61592_half_map_2.map
AnnotationBlock-Refine of Full particle at 5-fold axis.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas phage phiYY

EntireName: Pseudomonas phage phiYY (virus)
Components
  • Virus: Pseudomonas phage phiYY (virus)
    • Protein or peptide: Phage procapsid protein
    • Protein or peptide: Nucleocapsid shell protein

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Supramolecule #1: Pseudomonas phage phiYY

SupramoleculeName: Pseudomonas phage phiYY / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1852644 / Sci species name: Pseudomonas phage phiYY / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Phage procapsid protein

MacromoleculeName: Phage procapsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiYY (virus)
Molecular weightTheoretical: 87.548891 KDa
SequenceString: MLKFNLREIY KALPRLTQAN LIGMTEGAIP VASVVKPIAF NTLHAASHEG EFFYEFGKGV VDPKLIARVM MHYAASSTRV PSFQALVDE FLEYQYSVAS NSTLWRNLVA FVTGSSNDRA VKPDSMGRMP AEAIRERLGD EAKKQGIVSS HADFFNLIVA D YAISMLAQ ...String:
MLKFNLREIY KALPRLTQAN LIGMTEGAIP VASVVKPIAF NTLHAASHEG EFFYEFGKGV VDPKLIARVM MHYAASSTRV PSFQALVDE FLEYQYSVAS NSTLWRNLVA FVTGSSNDRA VKPDSMGRMP AEAIRERLGD EAKKQGIVSS HADFFNLIVA D YAISMLAQ ARLVLPGTPM VYRISRLVSF PDYGLYVDAV RAANLSRLLE GLATSDLGLV KKTMEKKEAV SPSFIAHQLA SA CIRAADR VRGSYNPDKV VEAVFYSLGT VWDPSTPAAN VATASVQSSE GFSRLLVNAT MFVAYQRRVA TVGAFPAPSF SDM VIAREV IPLFLEAVER ISPYAERTLA QAVGHLGMRS NTEVDGAKSH VAVYEAWNFS RSAVAFVPVR NNRNDLGRFL MEEV AVSDA MSSAMGPIAE TFSVDGFVER HLTALATAVP GAYNVKANGT EMLLALPSVS AAPLTLGVTT EALLSSMRNA GPFEP AVDQ LYAEGVEHVI SDSEGMGSDT HRAAVARGEA LINSYYVLML ARALLTGGMT RVGSVPVSNN ANTESNVALY WELTTS SKV PFGPTGILGG RLETSEPVER VAYGTDEEPT LSVTPPALPL SAHDRALHVW NWHDSSSKVE YNDRFETTIS NQKVIVQ LN EIDILSLGYR RERLRFMVPM SARAIAEMWV TWYTETDKEL QAMKAKTKDT AALAAIEGRQ LSAGVLLVQR LRSVGRSP V GSNLARVINS RIVASLRKSA QIDSMKHVYT VPHQIRLEVY CGLILLELLG VLDPAEVSKL TASLSATNAL ATVMTMGLD DSNNN

UniProtKB: Phage procapsid protein

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Macromolecule #2: Nucleocapsid shell protein

MacromoleculeName: Nucleocapsid shell protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiYY (virus)
Molecular weightTheoretical: 15.429834 KDa
SequenceString:
MYPAVAAALR AAPGAVKLLA TRLGVPSSVS GVLNFAKANP TTFMLAAKET FDQGVAIYDL LGEAIGEVEQ SANAQKISFK QIDSVGGNV LDQLDALADE MQDIDVAIRV VGSLHELLAL RRALLMSEEH FTMYQRLKRL KGRI

UniProtKB: Nucleocapsid shell 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 IS (4k x 4k) / 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 / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18004
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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