[English] 日本語
Yorodumi
- EMDB-4633: Cryo-EM structure of SH1 full particle. -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.25
  • Imaged by UCSF Chimera
  • Download
  • 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4633.png

Downloads & links

-
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

-
Supplemental data

-
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)

-
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)

-
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)

-
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)

-
Sample components

-
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

-
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

-
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

-
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

-
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

-
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

-
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

-
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

-
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)

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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

-
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.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more