[English] 日本語
Yorodumi
- EMDB-34679: Cyanophage Pam3 portal-adaptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34679
TitleCyanophage Pam3 portal-adaptor
Map data
SampleCyanophage Pam3 != uncultured cyanophage

Cyanophage Pam3

  • Virus: uncultured cyanophage (environmental samples)
    • Protein or peptide: Pam3 portal protein
    • Protein or peptide: Pam3 adaptor protein
Biological speciesuncultured cyanophage (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsYang F / Jiang YL / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Fine structure and assembly pattern of a minimal myophage Pam3.
Authors: Feng Yang / Yong-Liang Jiang / Jun-Tao Zhang / Jie Zhu / Kang Du / Rong-Cheng Yu / Zi-Lu Wei / Wen-Wen Kong / Ning Cui / Wei-Fang Li / Yuxing Chen / Qiong Li / Cong-Zhao Zhou /
Abstract: The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail ...The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.
History
DepositionNov 6, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34679.png

Downloads & links

-
Map

FileDownload / File: emd_34679.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.013 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.042518854 - 0.07462497
Average (Standard dev.)0.00011686478 (±0.003919816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 303.9 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_34679_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34679_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cyanophage Pam3

EntireName: Cyanophage Pam3
Components
  • Virus: uncultured cyanophage (environmental samples)
    • Protein or peptide: Pam3 portal protein
    • Protein or peptide: Pam3 adaptor protein

-
Supramolecule #1: uncultured cyanophage

SupramoleculeName: uncultured cyanophage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 215796 / Sci species name: uncultured cyanophage / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudanabaena mucicola (bacteria)

-
Macromolecule #1: Pam3 portal protein

MacromoleculeName: Pam3 portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 69.800445 KDa
SequenceString: MSDKLPTADS LRSMISGLGD PLRDKNASTF HWDRQLDDRQ LLYAYRNSWV ARKAVTIPAL DAVRKWRDWQ ADQKDISRIE ATEKRLGLQ QKLLQCKTLA RLWGGAAIVI GVKDQDMATP FEPETVNKDD LVYLTVMSRR ELSPEELEQD PLDEFYARPK R YQVSNGRN ...String:
MSDKLPTADS LRSMISGLGD PLRDKNASTF HWDRQLDDRQ LLYAYRNSWV ARKAVTIPAL DAVRKWRDWQ ADQKDISRIE ATEKRLGLQ QKLLQCKTLA RLWGGAAIVI GVKDQDMATP FEPETVNKDD LVYLTVMSRR ELSPEELEQD PLDEFYARPK R YQVSNGRN LSFVHPSRIV HQVGETHPDP MLATGVNVGW GDSTLQALYD AMMNSDNTQA NIASLVFEAN VDVIGLPDFM EN MSSEVYR QKLLDRFTLA AAGKGINKTL MLDAEEVFTA HSRSFANLDK IMEQFILFVA GAADIPLTRF LGQSPAGMSS TGQ HDMKNY HDRIQSIQTL DLQPSMYRLD EAIIRSSLGA RPEELFYIWS PLEQMSEKER AEIGKLHAET VNVIAGTGLF MQEE LREVF GNQLVETGLY PGLGDLLAQN GNELPEWDLE QRSAEASTKT AEAAALAAET ASRQPARAVT DATPRPLYMR RDVVN GDEI LRHYREQGVE GLYAAEELHV TIAYSKKPLD WMKLGEPWSA KLEVAPGGPR VHELFGDDSS VLVLCFAASE LNWRAQ QVI DAGGSSDHGE YQSHISLSLQ GRPEQIETLR PYQGRIVLGP ELFEQIEEGD WREKVKTD

-
Macromolecule #2: Pam3 adaptor protein

MacromoleculeName: Pam3 adaptor protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 13.871434 KDa
SequenceString:
MNPIPAASDL KTRYPEFTGV SDAVVNAIIA EVNGMVDDGW EVSDQKPAVL ALAAHMLSRE GYPGRATNPN SFDPTNRPIL SRKVGDVST TFGRTDGGAA EGGANSYNYS STVYGQTFLR LLRLNAPAVG LV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 126613

+
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