[English] 日本語
Yorodumi
- EMDB-35795: top segment of the bacteriophage M13 mini variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35795
Titletop segment of the bacteriophage M13 mini variant
Map data
Sample
  • Complex: top segment of the bacteriophage M13 mini variant
    • Protein or peptide: Capsid protein G8P
    • Protein or peptide: Tail virion protein G9P
    • Protein or peptide: Tail virion protein G7P
KeywordsViral coat protein / M13 / VIRAL PROTEIN
Function / homology
Function and homology information


helical viral capsid / host cell membrane / virion component / host cell plasma membrane / membrane
Similarity search - Function
Tail virion protein G7P / Tail virion protein G7P / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P
Similarity search - Domain/homology
Tail virion protein G7P / Tail virion protein G9P / Capsid protein G8P
Similarity search - Component
Biological speciesInovirus M13
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsXiang Y / Jia Q
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of a bacteriophage M13 mini variant.
Authors: Qi Jia / Ye Xiang /
Abstract: Filamentous bacteriophages package their circular, single stranded DNA genome with the major coat protein pVIII and the minor coat proteins pIII, pVII, pVI, and pIX. Here, we report the cryo-EM ...Filamentous bacteriophages package their circular, single stranded DNA genome with the major coat protein pVIII and the minor coat proteins pIII, pVII, pVI, and pIX. Here, we report the cryo-EM structure of a ~500 Å long bacteriophage M13 mini variant. The distal ends of the mini phage are sealed by two cap-like complexes composed of the minor coat proteins. The top cap complex consists of pVII and pIX, both exhibiting a single helix structure. Arg33 of pVII and Glu29 of pIX, located on the inner surface of the cap, play a key role in recognizing the genome packaging signal. The bottom cap complex is formed by the hook-like structures of pIII and pVI, arranged in helix barrels. Most of the inner ssDNA genome adopts a double helix structure with a similar pitch to that of the A-form double-stranded DNA. These findings provide insights into the assembly of filamentous bacteriophages.
History
DepositionApr 1, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35795.png

Downloads & links

-
Map

FileDownload / File: emd_35795.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 240 pix.
= 232.8 Å		0.97 Å/pix.
x 240 pix.
= 232.8 Å		0.97 Å/pix.
x 240 pix.
= 232.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0168
Minimum - Maximum-0.038225047 - 0.0704167
Average (Standard dev.)0.00021709602 (±0.0026509145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 232.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_35795_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35795_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : top segment of the bacteriophage M13 mini variant

EntireName: top segment of the bacteriophage M13 mini variant
Components
  • Complex: top segment of the bacteriophage M13 mini variant
    • Protein or peptide: Capsid protein G8P
    • Protein or peptide: Tail virion protein G9P
    • Protein or peptide: Tail virion protein G7P

-
Supramolecule #1: top segment of the bacteriophage M13 mini variant

SupramoleculeName: top segment of the bacteriophage M13 mini variant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Inovirus M13

-
Macromolecule #1: Capsid protein G8P

MacromoleculeName: Capsid protein G8P / type: protein_or_peptide / ID: 1 / Number of copies: 25 / Enantiomer: LEVO
Source (natural)Organism: Inovirus M13
Molecular weightTheoretical: 5.243014 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AEGDDPAKAA FNSLQASATE YIGYAWAMVV VIVGATIGIK LFKKFTSKAS

UniProtKB: Capsid protein G8P

-
Macromolecule #2: Tail virion protein G9P

MacromoleculeName: Tail virion protein G9P / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Inovirus M13
Molecular weightTheoretical: 3.65527 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSVLVYSFAS FVLGWCLRSG ITYFTRLMET SS

UniProtKB: Tail virion protein G9P

-
Macromolecule #3: Tail virion protein G7P

MacromoleculeName: Tail virion protein G7P / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Inovirus M13
Molecular weightTheoretical: 3.603215 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEQVADFDTI YQAMIQISVV LCFALGIIAG GQR

UniProtKB: Tail virion protein G7P

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20910
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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