[English] 日本語
Yorodumi
- EMDB-31431: Cyanophage A-1(L) capsid asymmetric unit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31431
TitleCyanophage A-1(L) capsid asymmetric unit
Map dataThe whole capsid structure of cyanophage A-1(L)
Sample
  • Virus: Nostoc phage A1 (virus)
    • Protein or peptide: Putative major capsid protein
KeywordsMajor capsid proteins / VIRUS
Function / homologyPutative major capsid protein
Function and homology information
Biological speciesNostoc phage A1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsCui N / Li Q
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: J Virol / Year: 2021
Title: Capsid Structure of Cyanophage A-1(L).
Authors: Ning Cui / Feng Yang / Jun-Tao Zhang / Hui Sun / Yu Chen / Rong-Cheng Yu / Zhi-Peng Chen / Yong-Liang Jiang / Shu-Jing Han / Xudong Xu / Qiong Li / Cong-Zhao Zhou /
Abstract: A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a ...A-1(L) is a freshwater cyanophage with a contractile tail that specifically infects sp. PCC 7120, one of the model strains for molecular studies of cyanobacteria. Although isolated for half a century, its structure remains unknown, which limits our understanding on the interplay between A-1(L) and its host. Here we report the 3.35 Å cryo-EM structure of A-1(L) capsid, representing the first near-atomic resolution structure of a phage capsid with a T number of 9. The major capsid gp4 proteins assemble into 91 capsomers, including 80 hexons: 20 at the center of the facet and 60 at the facet edge, in addition to 11 identical pentons. These capsomers further assemble into the icosahedral capsid, via gradually increasing curvatures. Different from the previously reported capsids of known-structure, A-1(L) adopts a noncovalent chainmail structure of capsid stabilized by two kinds of mortise-and-tenon inter-capsomer interactions: a three-layered interface at the pseudo 3-fold axis combined with the complementarity in shape and electrostatic potential around the 2-fold axis. This unique capsomer construction enables A-1(L) to possess a rigid capsid, which is solely composed of the major capsid proteins with an HK97 fold. Cyanobacteria are the most abundant photosynthetic bacteria, contributing significantly to the biomass production, O generation, and CO consumption on our planet. Their community structure and homeostasis in natural aquatic ecosystems are largely regulated by the corresponding cyanophages. In this study, we solved the structure of cyanophage A-1(L) capsid at near-atomic resolution and revealed a unique capsid construction. This capsid structure provides the molecular details for better understanding the assembly of A-1(L), and a structural platform for future investigation and application of A-1(L) in combination with its host sp. PCC 7120. As the first isolated freshwater cyanophage that infects the genetically tractable model cyanobacterium, A-1(L) should become an ideal template for the genetic engineering and synthetic biology studies.
History
DepositionJun 15, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7f38
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7f38
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31431.png

Downloads & links

-
Map

FileDownload / File: emd_31431.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe whole capsid structure of cyanophage A-1(L)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 800 pix.
= 976. Å		1.22 Å/pix.
x 800 pix.
= 976. Å		1.22 Å/pix.
x 800 pix.
= 976. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.020961551 - 0.0469604
Average (Standard dev.)0.0002773424 (±0.0026696678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 976.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.221.221.22
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z976.000976.000976.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-0.0210.0470.000

-
Supplemental data

-
Sample components

-
Entire : Nostoc phage A1

EntireName: Nostoc phage A1 (virus)
Components
  • Virus: Nostoc phage A1 (virus)
    • Protein or peptide: Putative major capsid protein

-
Supramolecule #1: Nostoc phage A1

SupramoleculeName: Nostoc phage A1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1775256 / Sci species name: Nostoc phage A1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

-
Macromolecule #1: Putative major capsid protein

MacromoleculeName: Putative major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Nostoc phage A1 (virus)
Molecular weightTheoretical: 39.524617 KDa
Recombinant expressionOrganism: Nostoc phage A1 (virus)
SequenceString: MPLTNLTPTE LLANKAVDYL ANSFLVETPM LGLLANRVIN QKQKAIEWGA KVAQGVVGGR TRTGALANDT QGTIKGASLS VPDYYIKHQ FDVGKDEIVN SDATGKISAV RDPVGTAIAD AFDVLSKKIN SVLYTASGVA DATNYGIFGL DAAAGTTVAN S ATGTYAGI ...String:
MPLTNLTPTE LLANKAVDYL ANSFLVETPM LGLLANRVIN QKQKAIEWGA KVAQGVVGGR TRTGALANDT QGTIKGASLS VPDYYIKHQ FDVGKDEIVN SDATGKISAV RDPVGTAIAD AFDVLSKKIN SVLYTASGVA DATNYGIFGL DAAAGTTVAN S ATGTYAGI SKVTFPRWRS IIQGGAVPGT NEALTIARMT AMLRARRTAG VTYKGNQNQR LVILTSDNIE NDVLRPLYGT VV DNQNVDF TRLDKDLLPY VNYMVKGIPV VSDIDCPANK MYLLNLDKLA IYSFDQSDAD QSNGKITYIP LRYVDETGDT PSE STLWVR LADVSDEHPD LLKFELSVAL QLVAFDLIDS ISVIRDITQ

UniProtKB: Putative major capsid protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32687
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
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