[English] 日本語
Yorodumi
- PDB-8k37: Structure of the bacteriophage lambda neck -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k37
TitleStructure of the bacteriophage lambda neck
Components
  • Head-tail connector protein FII
  • Tail tube protein
  • Tail tube terminator protein
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / virion assembly / virion component / host cell cytoplasm
Similarity search - Function
Bacteriophage tail attachment protein FII / Phage Head-Tail Attachment / : / Minor tail protein U-like / GpU-like superfamily / Phage minor tail protein U / Phage tail protein-like superfamily / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) ...Bacteriophage tail attachment protein FII / Phage Head-Tail Attachment / : / Minor tail protein U-like / GpU-like superfamily / Phage minor tail protein U / Phage tail protein-like superfamily / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Head-tail connector protein FII / Tail tube terminator protein / Tail tube protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsXiao, H. / Tan, L. / Cheng, L.P. / Liu, H.R.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: PLoS Biol / Year: 2023
Title: Structure of the siphophage neck-Tail complex suggests that conserved tail tip proteins facilitate receptor binding and tail assembly.
Authors: Hao Xiao / Le Tan / Zhixue Tan / Yewei Zhang / Wenyuan Chen / Xiaowu Li / Jingdong Song / Lingpeng Cheng / Hongrong Liu /
Abstract: Siphophages have a long, flexible, and noncontractile tail that connects to the capsid through a neck. The phage tail is essential for host cell recognition and virus-host cell interactions; ...Siphophages have a long, flexible, and noncontractile tail that connects to the capsid through a neck. The phage tail is essential for host cell recognition and virus-host cell interactions; moreover, it serves as a channel for genome delivery during infection. However, the in situ high-resolution structure of the neck-tail complex of siphophages remains unknown. Here, we present the structure of the siphophage lambda "wild type," the most widely used, laboratory-adapted fiberless mutant. The neck-tail complex comprises a channel formed by stacked 12-fold and hexameric rings and a 3-fold symmetrical tip. The interactions among DNA and a total of 246 tail protein molecules forming the tail and neck have been characterized. Structural comparisons of the tail tips, the most diversified region across the lambda and other long-tailed phages or tail-like machines, suggest that their tail tip contains conserved domains, which facilitate tail assembly, receptor binding, cell adsorption, and DNA retaining/releasing. These domains are distributed in different tail tip proteins in different phages or tail-like machines. The side tail fibers are not required for the phage particle to orient itself vertically to the surface of the host cell during attachment.
History
DepositionJul 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Tail tube protein
H: Tail tube protein
I: Tail tube protein
J: Tail tube protein
K: Tail tube protein
L: Tail tube protein
A: Tail tube terminator protein
B: Tail tube terminator protein
C: Tail tube terminator protein
D: Tail tube terminator protein
E: Tail tube terminator protein
F: Tail tube terminator protein
M: Head-tail connector protein FII
N: Head-tail connector protein FII
O: Head-tail connector protein FII
P: Head-tail connector protein FII
Q: Head-tail connector protein FII
R: Head-tail connector protein FII


Theoretical massNumber of molelcules
Total (without water)319,59618
Polymers319,59618
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Tail tube protein / TTP / Gene product V / gpV / Major tail protein V


Mass: 25831.779 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03733
#2: Protein
Tail tube terminator protein / TrP / Gene product U / gpU / Minor tail protein U / Tail sheath-stabilizing protein / Tail-to-head ...TrP / Gene product U / gpU / Minor tail protein U / Tail sheath-stabilizing protein / Tail-to-head joining protein / THJP


Mass: 14659.124 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03732
#3: Protein
Head-tail connector protein FII / Head-tail joining protein / Minor capsid protein FII


Mass: 12775.037 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03714

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Escherichia phage Lambda / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage Lambda (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75098 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00618954
ELECTRON MICROSCOPYf_angle_d0.63725812
ELECTRON MICROSCOPYf_dihedral_angle_d4.9932610
ELECTRON MICROSCOPYf_chiral_restr0.0462808
ELECTRON MICROSCOPYf_plane_restr0.0043408

+
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