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- PDB-8k35: Structure of the bacteriophage lambda tail tip complex -

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Basic information

Entry
Database: PDB / ID: 8k35
TitleStructure of the bacteriophage lambda tail tip complex
Components
  • (Tail tip protein ...) x 2
  • Tail tip assembly protein I
  • Tail tube protein
  • Tape measure protein
  • Tip attachment protein J
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 / 4 iron, 4 sulfur cluster binding / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / virion attachment to host cell / metal ion binding
Similarity search - Function
Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Phage minor tail protein L / Phage minor tail protein ...Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Phage minor tail protein L / Phage minor tail protein / Bacteriophage lambda tail assembly protein I / Domain of unknown function DUF1983 / Domain of unknown function DUF3672 / Domain of unknown function (DUF1983) / Fibronectin type III protein / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Tip attachment protein J / Putative phage tail protein / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Beta-grasp domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Tail tip assembly protein I / Tail tube protein / Tape measure protein / Tail tip protein M / Tail tip protein L / Tip attachment protein J
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Tip attachment protein J
A: Tip attachment protein J
B: Tip attachment protein J
J: Tail tip protein L
G: Tail tip protein L
N: Tail tip protein L
H: Tail tip protein M
O: Tail tip protein M
C: Tail tip protein M
E: Tail tip protein M
D: Tail tip protein M
F: Tail tip protein M
x: Tail tip assembly protein I
K: Tail tip assembly protein I
Q: Tail tip assembly protein I
L: Tail tube protein
R: Tail tube protein
T: Tail tube protein
U: Tail tube protein
V: Tail tube protein
W: Tail tube protein
P: Tape measure protein
M: Tape measure protein
S: Tape measure protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,028,79427
Polymers1,027,73924
Non-polymers1,0553
Water00
1


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

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Components

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Protein , 4 types, 15 molecules IABxKQLRTUVWPMS

#1: Protein Tip attachment protein J / Central tail fiber / Host specificity protein J


Mass: 124550.625 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03749
#4: Protein Tail tip assembly protein I


Mass: 23146.590 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03730
#5: 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
#6: Protein Tape measure protein / TMP / Gene product H / gpH / Minor tail protein H


Mass: 92393.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03736

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Tail tip protein ... , 2 types, 9 molecules JGNHOCEDF

#2: Protein Tail tip protein L


Mass: 25730.578 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03738
#3: Protein
Tail tip protein M


Mass: 12547.373 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03737

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Non-polymers , 1 types, 3 molecules

#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestN

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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: Escherichia phage Lambda / Type: VIRUS / Entity ID: #1-#6 / 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

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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: 2200 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54385 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00441238
ELECTRON MICROSCOPYf_angle_d0.50456052
ELECTRON MICROSCOPYf_dihedral_angle_d4.6735637
ELECTRON MICROSCOPYf_chiral_restr0.0436198
ELECTRON MICROSCOPYf_plane_restr0.0047284

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