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- PDB-8iyd: Tail cap of phage lambda tail -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8iyd
TitleTail cap of phage lambda tail
Components
  • Tail tube protein
  • Tail tube terminator protein
KeywordsVIRAL PROTEIN / Bacteriophage / caudovirales / siphoviridae / tail complex / delivery device / macromolecular assembly / phage lambda / cryo-EM
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 / host cell cytoplasm
Similarity search - Function
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
Tail tube terminator protein / Tail tube protein
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang, J.W. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Structure / Year: 2024
Title: Architecture of the bacteriophage lambda tail.
Authors: Chang Wang / Jinsong Duan / Zhiwei Gu / Xiaofei Ge / Jianwei Zeng / Jiawei Wang /
Abstract: Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host ...Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host recognition and delivery of viral DNA from the head shell to the cytoplasm of the infected cell. Here, we present a high-resolution structure of the tail complex of bacteriophage lambda determined by cryoelectron microscopy. Most component proteins of the lambda tail were determined at the atomic scale. The structure sheds light on the molecular organization of the extensively studied tail of bacteriophage lambda.
History
DepositionApr 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail tube protein
B: Tail tube protein
C: Tail tube protein
U: Tail tube terminator protein
a: Tail tube protein
b: Tail tube protein
c: Tail tube protein
u: Tail tube terminator protein
V: Tail tube protein
v: Tail tube protein
D: Tail tube protein
E: Tail tube protein
F: Tail tube protein
G: Tail tube terminator protein
H: Tail tube protein
I: Tail tube protein
J: Tail tube protein
K: Tail tube terminator protein
L: Tail tube protein
M: Tail tube protein
N: Tail tube protein
O: Tail tube protein
P: Tail tube protein
Q: Tail tube terminator protein
R: Tail tube protein
S: Tail tube protein
T: Tail tube protein
W: Tail tube terminator protein
X: Tail tube protein
Y: Tail tube protein


Theoretical massNumber of molelcules
Total (without water)707,91730
Polymers707,91730
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 25831.779 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: V, lambdap13 / Production host: Escherichia coli (E. coli) / 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 genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: U, lambdap12 / Production host: Escherichia coli (E. coli) / References: UniProt: P03732

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Tail cap of phage lambda tail / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage Lambda (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15959 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00850340
ELECTRON MICROSCOPYf_angle_d0.9668766
ELECTRON MICROSCOPYf_dihedral_angle_d6.2136999
ELECTRON MICROSCOPYf_chiral_restr0.0518085
ELECTRON MICROSCOPYf_plane_restr0.0078859

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