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- EMDB-4633: Cryo-EM structure of SH1 full particle. -

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Basic information

Entry
Database: EMDB / ID: EMD-4633
TitleCryo-EM structure of SH1 full particle.
Map dataBlock-based reconstruction of SH1 capsid, filtered at 3.8 Angstrom and sharpened with a B-factor=-90
Sample
  • Virus: Haloarcula hispanica virus SH1
    • Protein or peptide: ORF 25
    • Protein or peptide: ORF 25
    • Protein or peptide: ORF 24
    • Protein or peptide: ORF 24
    • Protein or peptide: ORF 24
    • Protein or peptide: ORF 31
    • Protein or peptide: VP12
    • Protein or peptide: VP13
Keywordseuryarcheal virus / SH1 / VIRUS
Function / homologyORF 31 / ORF 25 / ORF 24
Function and homology information
Biological speciesHaloarcula hispanica virus SH1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDe Colibus L / Roine E / Walter TS / Ilca SL
Funding support United Kingdom, Finland, 4 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N00065X/1 United Kingdom
European Research Council649053 United Kingdom
Academy of Finland255342 Finland
Academy of Finland256518 Finland
CitationJournal: Nat Commun / Year: 2019
Title: Assembly of complex viruses exemplified by a halophilic euryarchaeal virus.
Authors: Luigi De Colibus / Elina Roine / Thomas S Walter / Serban L Ilca / Xiangxi Wang / Nan Wang / Alan M Roseman / Dennis Bamford / Juha T Huiskonen / David I Stuart /
Abstract: Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). ...Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). Here, by high-resolution cryo-EM analysis, we show that a class of archaeal viruses possess hetero-hexameric MCPs which mimic the PRD1-adeno lineage trimer. These hetero-hexamers are built from heterodimers and utilise a jigsaw-puzzle system of pegs and holes, and underlying minor capsid proteins, to assemble the capsid laterally from the 5-fold vertices. At these vertices proteins engage inwards with the internal membrane vesicle whilst 2-fold symmetric horn-like structures protrude outwards. The horns are assembled from repeated globular domains attached to a central spine, presumably facilitating multimeric attachment to the cell receptor. Such viruses may represent precursors of the main PRD1-adeno lineage, similarly engaging cell-receptors via 5-fold spikes and using minor proteins to define particle size.
History
DepositionFeb 22, 2019-
Header (metadata) releaseApr 10, 2019-
Map releaseApr 10, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.25
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qt9
  • Surface level: 2.25
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qt9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4633.png

Downloads & links

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Map

FileDownload / File: emd_4633.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBlock-based reconstruction of SH1 capsid, filtered at 3.8 Angstrom and sharpened with a B-factor=-90
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 800 pix.
= 1080. Å		1.35 Å/pix.
x 800 pix.
= 1080. Å		1.35 Å/pix.
x 800 pix.
= 1080. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.25 / Movie #1: 2.25
Minimum - Maximum-8.843221 - 13.590450000000001
Average (Standard dev.)0.002663619 (±0.5492085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1080.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z1080.0001080.0001080.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-8.84313.5900.003

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Supplemental data

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Additional map: Sharpened and non-icosahedrally averaged map of VP7 protein

Fileemd_4633_additional_1.map
AnnotationSharpened and non-icosahedrally averaged map of VP7 protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened and non-icosahedrally averaged map of VP4 protein

Fileemd_4633_additional_2.map
AnnotationSharpened and non-icosahedrally averaged map of VP4 protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Block-based reconstruction of SH1 capsid, halfmap 2

Fileemd_4633_half_map_1.map
AnnotationBlock-based reconstruction of SH1 capsid, halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Block-based reconstruction of SH1 capsid. halfmap 1

Fileemd_4633_half_map_2.map
AnnotationBlock-based reconstruction of SH1 capsid. halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Haloarcula hispanica virus SH1

EntireName: Haloarcula hispanica virus SH1
Components
  • Virus: Haloarcula hispanica virus SH1
    • Protein or peptide: ORF 25
    • Protein or peptide: ORF 25
    • Protein or peptide: ORF 24
    • Protein or peptide: ORF 24
    • Protein or peptide: ORF 24
    • Protein or peptide: ORF 31
    • Protein or peptide: VP12
    • Protein or peptide: VP13

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Supramolecule #1: Haloarcula hispanica virus SH1

SupramoleculeName: Haloarcula hispanica virus SH1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 326574 / Sci species name: Haloarcula hispanica virus SH1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloarcula hispanica virus SH1
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1000.0 Å / T number (triangulation number): 28

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Macromolecule #1: ORF 25

MacromoleculeName: ORF 25 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica virus SH1
Molecular weightTheoretical: 25.042207 KDa
SequenceString: EYTISHTGGT LGSSKVTTAA NQTSPQRETA IIGFECPRKF AEIEYVGQRD STRFIPRTTE SITGTAGDDT VVSLTANIQP VAGETAIED QDYPVAVAYN VTQGVQVDID AVDYAADEVT LADNPADGDT VKVWPIMGDG DVQFRLVNQF GQEEGRVYPW A TPLYRWHD ...String:
EYTISHTGGT LGSSKVTTAA NQTSPQRETA IIGFECPRKF AEIEYVGQRD STRFIPRTTE SITGTAGDDT VVSLTANIQP VAGETAIED QDYPVAVAYN VTQGVQVDID AVDYAADEVT LADNPADGDT VKVWPIMGDG DVQFRLVNQF GQEEGRVYPW A TPLYRWHD FPQLKRGREI NLHGSVTWEE NETVEVLLDA PQAITWEDSD YPEGQYVSTF EQDVEITL

UniProtKB: ORF 25

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Macromolecule #2: ORF 25

MacromoleculeName: ORF 25 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica virus SH1
Molecular weightTheoretical: 24.913094 KDa
SequenceString: YTISHTGGTL GSSKVTTAAN QTSPQRETAI IGFECPRKFA EIEYVGQRDS TRFIPRTTES ITGTAGDDTV VSLTANIQPV AGETAIEDQ DYPVAVAYNV TQGVQVDIDA VDYAADEVTL ADNPADGDTV KVWPIMGDGD VQFRLVNQFG QEEGRVYPWA T PLYRWHDF ...String:
YTISHTGGTL GSSKVTTAAN QTSPQRETAI IGFECPRKFA EIEYVGQRDS TRFIPRTTES ITGTAGDDTV VSLTANIQPV AGETAIEDQ DYPVAVAYNV TQGVQVDIDA VDYAADEVTL ADNPADGDTV KVWPIMGDGD VQFRLVNQFG QEEGRVYPWA T PLYRWHDF PQLKRGREIN LHGSVTWEEN ETVEVLLDAP QAITWEDSDY PEGQYVSTFE QDVEITL

UniProtKB: ORF 25

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Macromolecule #3: ORF 24

MacromoleculeName: ORF 24 / type: protein_or_peptide / ID: 3 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica virus SH1
Molecular weightTheoretical: 18.840627 KDa
SequenceString:
GNIGNLSAEK QISVYDGQPF VDEQDVPADD PNTPALTIEG PDGYVIAVDA GTPIAPEFRD SNGNKLDPST RVIVQKCDRQ GNPLGDGIV FNDTLGRFDY EQMRTDPDFM RKTAKSLMID EREIVKVFVD IPAGANGYDA DKSRLTLGDD TSDFGKAVEI V DHDELSDA ETRAV

UniProtKB: ORF 24

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Macromolecule #4: ORF 24

MacromoleculeName: ORF 24 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica virus SH1
Molecular weightTheoretical: 18.272 KDa
SequenceString:
SAEKQISVYD GQPFVDEQDV PADDPNTPAL TIEGPDGYVI AVDAGTPIAP EFRDSNGNKL DPSTRVIVQK CDRQGNPLGD GIVFNDTLG RFDYEQMRTD PDFMRKTAKS LMIDEREIVK VFVDIPAGAN GYDADKSRLT LGDDTSDFGK AVEIVDHDEL S DAETRAV

UniProtKB: ORF 24

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Macromolecule #5: ORF 24

MacromoleculeName: ORF 24 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica virus SH1
Molecular weightTheoretical: 19.040887 KDa
SequenceString:
GNIGNLSAEK QISVYDGQPF VDEQDVPADD PNTPALTIEG PDGYVIAVDA GTPIAPEFRD SNGNKLDPST RVIVQKCDRQ GNPLGDGIV FNDTLGRFDY EQMRTDPDFM RKTAKSLMID EREIVKVFVD IPAGANGYDA DKSRLTLGDD TSDFGKAVEI V DHDELSDA ETRAVKA

UniProtKB: ORF 24

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Macromolecule #6: ORF 31

MacromoleculeName: ORF 31 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica virus SH1
Molecular weightTheoretical: 14.982346 KDa
SequenceString:
ERLGRLVDVL ETKEFGDTTV ERSVTQNIDR TRTDSPNNEN QPIYFSTGPE AIAVENTEEW ERLDFGIVAE TVNIRTTDDI DIAFADPNK NGPVIRVREG ESPFTIGGDA GIESAFIWLR QAETASNTPG IQIIAF

UniProtKB: ORF 31

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Macromolecule #7: VP12

MacromoleculeName: VP12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica virus SH1
Molecular weightTheoretical: 2.060531 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #8: VP13

MacromoleculeName: VP13 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula hispanica virus SH1
Molecular weightTheoretical: 6.826406 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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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

Concentration15 mg/mL
BufferpH: 7.2 / Details: 20mM Tris-HCl pH 7.2, 1M NaCl, 10 mM MnCl2
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.027 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 4.4 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 160000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 16185
Details: This number of particle was generated by merging the datasets of full particles with and without spikes.
Startup modelType of model: EMDB MAP / Details: EMDB-1353
Final reconstructionApplied symmetry - Point group: C532 (532 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 16185
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) / Software - details: custom
Final 3D classificationSoftware - Name: RELION (ver. 2.1) / Software - details: custom

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 144.281 / Target criteria: Cross-correlation coefficient
Output model

PDB-6qt9:
Cryo-EM structure of SH1 full particle.

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