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- EMDB-20091: Singapore Grouper Iridovirus (SGIV) at 8.6 Angstrom Resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-20091
TitleSingapore Grouper Iridovirus (SGIV) at 8.6 Angstrom Resolution
Map dataIndependent reconstruction half of the micrographs
Sample
  • Virus: Singapore grouper iridovirus
    • Protein or peptide: Major capsid protein
Keywordsicosahedral / trimers / outer coat / anchor proteins / zip proteins / VIRAL PROTEIN
Function / homologyMajor capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesSingapore grouper iridovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsPintilie G / Chen D-H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM103832 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM079429 United States
CitationJournal: Structure / Year: 2019
Title: Segmentation and Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus.
Authors: Grigore Pintilie / Dong-Hua Chen / Bich Ngoc Tran / Joanita Jakana / Jinlu Wu / Choy Leong Hew / Wah Chiu /
Abstract: SGIV, or Singapore grouper iridovirus, is a large double-stranded DNA virus, reaching a diameter of 220 nm and packaging a genome of 140 kb. We present a 3D cryoelectron microscopy (cryo-EM) ...SGIV, or Singapore grouper iridovirus, is a large double-stranded DNA virus, reaching a diameter of 220 nm and packaging a genome of 140 kb. We present a 3D cryoelectron microscopy (cryo-EM) icosahedral reconstruction of SGIV determined at 8.6-Å resolution. It reveals several layers including a T = 247 icosahedral outer coat, anchor proteins, a lipid bilayer, and the encapsidated DNA. A new segmentation tool, iSeg, was applied to extract these layers from the reconstructed map. The outer coat was further segmented into major and minor capsid proteins. None of the proteins extracted by segmentation have known atomic structures. We generated models for the major coat protein using three comparative modeling tools, and evaluated each model using the cryo-EM map. Our analysis reveals a new architecture in the Iridoviridae family of viruses. It shares similarities with others in the same family, e.g., Chilo iridescent virus, but also shows new features of the major and minor capsid proteins.
History
DepositionApr 11, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ojn
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ojn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20091.png

Downloads & links

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Map

FileDownload / File: emd_20091.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIndependent reconstruction half of the micrographs
Voxel sizeX=Y=Z: 2.37 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 4
Minimum - Maximum-13.887831 - 21.549627000000001
Average (Standard dev.)-0.04749717 (±1.4707036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-600-600-600
Dimensions120012001200
Spacing120012001200
CellA=B=C: 2843.9998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.372.372.37
M x/y/z120012001200
origin x/y/z0.0000.0000.000
length x/y/z2844.0002844.0002844.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-600-600-600
NC/NR/NS120012001200
D min/max/mean-13.88821.550-0.047

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Supplemental data

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Additional map: Independent reconstruction other half of the micrographs

Fileemd_20091_additional_1.map
AnnotationIndependent reconstruction other half of the micrographs
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Additional map: A pentasymmetron

Fileemd_20091_additional_10.map
AnnotationA pentasymmetron
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Additional map: Averaged densities from trimers from a trisymmetron within...

Fileemd_20091_additional_11.map
AnnotationAveraged densities from trimers from a trisymmetron within the asymmetric unit
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Additional map: Trisymmetron 1 of 5 around a pentasymmetron

Fileemd_20091_additional_12.map
AnnotationTrisymmetron 1 of 5 around a pentasymmetron
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Additional map: Trisymmetron 2 of 5 around a pentasymmetron

Fileemd_20091_additional_13.map
AnnotationTrisymmetron 2 of 5 around a pentasymmetron
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Additional map: Trisymmetron 3 of 5 around a pentasymmetron

Fileemd_20091_additional_14.map
AnnotationTrisymmetron 3 of 5 around a pentasymmetron
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Supplemental map: emd 20091 additional 15.map

Fileemd_20091_additional_15.map
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Additional map: Trisymmetron 5 of 5 around a pentasymmetron

Fileemd_20091_additional_16.map
AnnotationTrisymmetron 5 of 5 around a pentasymmetron
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Additional map: Zip proteins 1

Fileemd_20091_additional_17.map
AnnotationZip proteins 1
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Additional map: Zip proteins 2

Fileemd_20091_additional_18.map
AnnotationZip proteins 2
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Additional map: Zip proteins 3

Fileemd_20091_additional_19.map
AnnotationZip proteins 3
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Additional map: Anchor protein 1

Fileemd_20091_additional_2.map
AnnotationAnchor protein 1
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Additional map: Zip proteins 4

Fileemd_20091_additional_20.map
AnnotationZip proteins 4
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Additional map: Zip proteins 5

Fileemd_20091_additional_21.map
AnnotationZip proteins 5
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Additional map: Anchor protein 2

Fileemd_20091_additional_3.map
AnnotationAnchor protein 2
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Additional map: Anchor protein 3

Fileemd_20091_additional_4.map
AnnotationAnchor protein 3
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Additional map: Anchor protein 4

Fileemd_20091_additional_5.map
AnnotationAnchor protein 4
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Additional map: Anchor protein 5

Fileemd_20091_additional_6.map
AnnotationAnchor protein 5
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Additional map: An asymmetric unit from the icosahedrally-symmetric map

Fileemd_20091_additional_7.map
AnnotationAn asymmetric unit from the icosahedrally-symmetric map
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Additional map: Inner half of the bilayer lipid membrane

Fileemd_20091_additional_8.map
AnnotationInner half of the bilayer lipid membrane
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Additional map: Outer half of the bilayer lipid membrane

Fileemd_20091_additional_9.map
AnnotationOuter half of the bilayer lipid membrane
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Sample components

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Entire : Singapore grouper iridovirus

EntireName: Singapore grouper iridovirus
Components
  • Virus: Singapore grouper iridovirus
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Singapore grouper iridovirus

SupramoleculeName: Singapore grouper iridovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 262968 / Sci species name: Singapore grouper iridovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Epinephelus tauvina (greasy grouper)
Virus shellShell ID: 1 / Name: Outer coat / Diameter: 2200.0 Å / T number (triangulation number): 247

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Singapore grouper iridovirus
Molecular weightTheoretical: 50.573141 KDa
SequenceString: MTCTTGAGVT SGFIDLATYD NLDRALYGGK DATTYFIKEH YPVGWFTKLP TMATRVSGNP AFGQEFSVGV PRSGDYVLNA WLTLKTPEI KLLETNRLGA NGTVRWTKNL MHNAVEHASL TFNDICAQQF NTAYLDAWTQ FNMCEGKRIG YDNMIGNTSD M TNPTPAQG ...String:
MTCTTGAGVT SGFIDLATYD NLDRALYGGK DATTYFIKEH YPVGWFTKLP TMATRVSGNP AFGQEFSVGV PRSGDYVLNA WLTLKTPEI KLLETNRLGA NGTVRWTKNL MHNAVEHASL TFNDICAQQF NTAYLDAWTQ FNMCEGKRIG YDNMIGNTSD M TNPTPAQG QDGARTLPSK NLVLPLPFFF SRDCGLALPT VVLPYNEIRI NIKLRSLQEL LVFQNKDTGN VIPISATDIA GG LADTVEA YVYMTVGLVS NVERCAMAGT VRDMVVEQMQ AAPTHIVNPQ NTNNVHVDMR FSHAVKALFF MVQNVTYKSV GSN YTCVTP VNGPGNTVME PAMSVDPIKS ASLTYENTTR LANMGVEYYS LVQPWYFSAS IPVYTGYHMY SYALNVGSVH PSGS TNYGR LTNASITVTM SPESVVAAAG GGNNNSGYNE PQRFALVVIA VNHNVIRIMN GSMGFPIL

UniProtKB: Major capsid 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: 7.4
GridModel: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Blotted for 1 second before plunging..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 63290 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19628
Startup modelType of model: OTHER / Details: EMAN1 starticos was used.
Initial angle assignmentType: COMMON LINE / Software - Name: MPSA
Final 3D classificationNumber classes: 1
Final angle assignmentType: COMMON LINE / Software - Name: MPSA
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN / Number images used: 9422
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1m3y
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Z-score of Cross Correlation scores
Output model

PDB-6ojn:
Comparative Model of SGIV Major Coat Protein (MCP) Trimer Based on Cryo-EM Map

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