[English] 日本語
Yorodumi
- EMDB-34815: One asymmetric unit of Singapore grouper iridovirus capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34815
TitleOne asymmetric unit of Singapore grouper iridovirus capsid
Map dataThis is a composite density map generated by combining the density maps of five blocks with the accession codes EMD-34227, EMD-34230, EMD-34235, EMD-34229, and EMD-34236, respectively.
Sample
  • Virus: Singapore grouper iridovirus
    • Protein or peptide: Major capsid protein
    • Protein or peptide: VP38
    • Protein or peptide: VP137
    • Protein or peptide: VP88
    • Protein or peptide: VP59
    • Protein or peptide: VP139
    • Protein or peptide: Penton protein (VP14)
Function / homology
Function and homology information


viral capsid / structural molecule activity / membrane
Similarity search - Function
Protein of unknown function DUF5850 / Family of unknown function (DUF5850) / Virion membrane protein, poxvirus L1-related / Lipid membrane protein of large eukaryotic DNA viruses / Major 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
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Major capsid protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesSingapore grouper iridovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhao ZN / Liu CC / Zhu DJ / Qi JX / Zhang XZ / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2023
Title: Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly.
Authors: Zhennan Zhao / Youhua Huang / Congcong Liu / Dongjie Zhu / Shuaixin Gao / Sheng Liu / Ruchao Peng / Ya Zhang / Xiaohong Huang / Jianxun Qi / Catherine C L Wong / Xinzheng Zhang / Peiyi Wang ...Authors: Zhennan Zhao / Youhua Huang / Congcong Liu / Dongjie Zhu / Shuaixin Gao / Sheng Liu / Ruchao Peng / Ya Zhang / Xiaohong Huang / Jianxun Qi / Catherine C L Wong / Xinzheng Zhang / Peiyi Wang / Qiwei Qin / George F Gao /
Abstract: Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and ...Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and significantly threatens global biodiversity. In recent years, high morbidity and mortality in aquatic animals have been caused by iridovirid infections worldwide. Effective control and prevention strategies are urgently needed. Here, we present a near-atomic architecture of the SGIV capsid and identify eight types of capsid proteins. The viral inner membrane-integrated anchor protein colocalizes with the endoplasmic reticulum (ER), supporting the hypothesis that the biogenesis of the inner membrane is associated with the ER. Additionally, immunofluorescence assays indicate minor capsid proteins (mCPs) could form various building blocks with major capsid proteins (MCPs) before the formation of a viral factory (VF). These results expand our understanding of the capsid assembly of NCVs and provide more targets for vaccine and drug design to fight iridovirid infections.
History
DepositionNov 20, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34815.png

Downloads & links

-
Map

FileDownload / File: emd_34815.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a composite density map generated by combining the density maps of five blocks with the accession codes EMD-34227, EMD-34230, EMD-34235, EMD-34229, and EMD-34236, respectively.
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.07132883 - 0.10519954
Average (Standard dev.)0.00022278047 (±0.0026708446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions771790569
Spacing790771569
CellA: 1106.0 Å / B: 1079.4 Å / C: 796.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Singapore grouper iridovirus

EntireName: Singapore grouper iridovirus
Components
  • Virus: Singapore grouper iridovirus
    • Protein or peptide: Major capsid protein
    • Protein or peptide: VP38
    • Protein or peptide: VP137
    • Protein or peptide: VP88
    • Protein or peptide: VP59
    • Protein or peptide: VP139
    • Protein or peptide: Penton protein (VP14)

-
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: STRAIN / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 123 / 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

-
Macromolecule #2: VP38

MacromoleculeName: VP38 / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Singapore grouper iridovirus
Molecular weightTheoretical: 19.070715 KDa
SequenceString:
MIHNYAILIV TAAVVVWYYY KLYVVDKNGK KSLVRTRKHR NLESAARRDP ILKTYSKQDG TRSRKPKSTK KEPHWMDPQL MGSQTTQYS RNRGYGDPIR GDLPIVPDDG GWFATRANPA HHLHTGALSM IGGDASDCGS TAVQQLIKKY EDKGCNNNGL N VMSSHYGG VM

-
Macromolecule #3: VP137

MacromoleculeName: VP137 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Singapore grouper iridovirus
Molecular weightTheoretical: 49.777852 KDa
SequenceString: MDCATYATRK DKGWELNENR CVWAASVKPT SGAIMTNVGV HGKSGNAVLM TPKRRPHAQN HAGYKIKYCK QVPLIPLHGG DYILNHWET RGVDRMRIPG IQHAPPPPAP SGMQNAYSTH PDAYRTPLLA DSHALSRMPV VQVHGPQVAP KNSHFTVAPE K HGPVEDMN ...String:
MDCATYATRK DKGWELNENR CVWAASVKPT SGAIMTNVGV HGKSGNAVLM TPKRRPHAQN HAGYKIKYCK QVPLIPLHGG DYILNHWET RGVDRMRIPG IQHAPPPPAP SGMQNAYSTH PDAYRTPLLA DSHALSRMPV VQVHGPQVAP KNSHFTVAPE K HGPVEDMN AIINALPTKV DAVKLEYSAS KTNRTNKRPG DGGAPPPKNL SKCHQNKLKT FARTANSGAN PFRPATAAPQ GL SKQPVRK PFASARNANS GANPFRPPLA HQGLSKAHVV KTAVSVANRS AGAEPFVTRN DPRALAMELA NNKTISVTLG LRH WKTVSA APPEKMSKSG VCKIATNVYN RDGGANPFLV KYEPDSLAVC PMETVEIAAV PSKRPWEGSA NPRRPEQISF GMSD KPKFV NDKIGIVLRG PTLAPTLDRT ATHTVTRPRA LGSFHSTAGP AKHAASIMAE CKDESR

-
Macromolecule #4: VP88

MacromoleculeName: VP88 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Singapore grouper iridovirus
Molecular weightTheoretical: 54.052152 KDa
SequenceString: MGAAQSVNGV KIVTNAYAEI MTDLAVDQDI TADQTQVFSI DNVSGDVYVE GTVMTEKLVI NLASLMKAVT NQSSQDELID NIAQQAQAA VSGLNFAQFA FVTNNIDRLI TACVKLSVDM RVSCTAKVEM TQSFSVSSVM GDVRVKDVRM EEFSDVISTC A LNAAITNA ...String:
MGAAQSVNGV KIVTNAYAEI MTDLAVDQDI TADQTQVFSI DNVSGDVYVE GTVMTEKLVI NLASLMKAVT NQSSQDELID NIAQQAQAA VSGLNFAQFA FVTNNIDRLI TACVKLSVDM RVSCTAKVEM TQSFSVSSVM GDVRVKDVRM EEFSDVISTC A LNAAITNA QLSDIVSQIK QRGDATATGL NPMAILAAVV LAIIGLPLGA GFLAGRRVVG PLMMVTGMVG GGALAMGYVP EP IKLTGFA PEPDLTAVVP VAVENGLTLK AAISKLTGDP QYGAVYWQNY KVTGTTAVKL NQTVSYYAPP NFDPVTWTAS EPA QKQPSF RVFPTLFQGQ GLPKISYRLA YGTVALTQGP ERGDVYLDST TGNYYVLKDG WKLNGTIPGA IKDRPEAWGI VDPN ETTAL TGSERYTWVD PYTRVQGTLW YKPKDSHEWV KERQDPVPIN VPLTETPSDF NVWVYKDATA KKIVGWVSAG AGAAG AGLT ASAYFMPSTA VDAKAEVGEA AK

-
Macromolecule #5: VP59

MacromoleculeName: VP59 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Singapore grouper iridovirus
Molecular weightTheoretical: 16.343806 KDa
SequenceString:
MDSQGFWAIL AFTPVLMILS LKGEGLLAMV GLLVLTVTLL ASREKNDRPR LSCRGKIGRK VSGFENAGHV RDSHHVIYKR PPVNEYCAE TREDNSLYVP EYCGQNWKNG VLSGMGTHHD AYRNLAVNMM TLRRESAVSA GWAHSYL

-
Macromolecule #6: VP139

MacromoleculeName: VP139 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Singapore grouper iridovirus
Molecular weightTheoretical: 11.354337 KDa
SequenceString:
MNAYQNDKLH LCAPRPDLVR AAMSAMVRET GCTPNVNIRE MAISAGVMLT KIRANPGMLR YGMTATQTVI YNLKELFAAH AARGVVFKT PAIHPAHPSQ WKGF

-
Macromolecule #7: Penton protein (VP14)

MacromoleculeName: Penton protein (VP14) / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Singapore grouper iridovirus
Molecular weightTheoretical: 15.872862 KDa
SequenceString:
MYRGFSLKLP NNYRSGQVTT EHRLPASNSH ARWPVEVSFY SAVLHVPAKH QHKFPPVLEL KLHNMTTGSM AAHRGSGHHF TFMFHAQSS PTEAVYSCVP VPIVFSDYQS NVIASVDMGE HDTAEKLHFY GSIRNCDNGC TY

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37161

+
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