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- PDB-8iyk: Tail tip conformation 1 of phage lambda tail -

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Basic information

Entry
Database: PDB / ID: 8iyk
TitleTail tip conformation 1 of phage lambda tail
Components
  • (Tail tip protein ...) x 2
  • Tail tip assembly protein I
  • Tail tube protein
  • Tape measure protein
  • Tip attachment protein J
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 / 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 lambda, Tail tip protein L / Bacteriophage tail tape measure, N-terminal / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Tape measure protein / Phage minor tail protein L / Phage minor tail protein / Prophage tail length tape measure protein / Bacteriophage lambda tail assembly protein I ...Bacteriophage tail tape measure, C-terminal / Bacteriophage lambda, Tail tip protein L / Bacteriophage tail tape measure, N-terminal / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Tape measure protein / Phage minor tail protein L / Phage minor tail protein / Prophage tail length tape measure protein / Bacteriophage lambda tail assembly protein I / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Domain of unknown function DUF1983 / Domain of unknown function DUF3672 / Domain of unknown function (DUF1983) / Fibronectin type III protein / Tip attachment protein J / Putative phage tail protein / 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 / 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: 2.95 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 5, 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
V: Tail tube protein
M: Tail tip protein M
J: Tip attachment protein J
v: Tail tube protein
m: Tail tip protein M
L: Tail tip protein L
H: Tape measure protein
I: Tail tip assembly protein I
B: Tail tube protein
b: Tail tube protein
A: Tail tube protein
a: Tail tube protein
C: Tail tube protein
c: Tail tube protein
D: Tail tube protein
E: Tail tip protein M
F: Tip attachment protein J
G: Tail tube protein
K: Tail tip protein M
N: Tail tip protein L
O: Tape measure protein
P: Tail tip assembly protein I
Q: Tail tube protein
R: Tail tube protein
S: Tail tube protein
T: Tail tube protein
U: Tail tube protein
W: Tail tube protein
X: Tail tube protein
Y: Tail tip protein M
Z: Tip attachment protein J
d: Tail tube protein
e: Tail tip protein M
f: Tail tip protein L
g: Tape measure protein
h: Tail tip assembly protein I
i: Tail tube protein
j: Tail tube protein
k: Tail tube protein
l: Tail tube protein
n: Tail tube protein
o: Tail tube protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,493,76645
Polymers1,492,71142
Non-polymers1,0553
Water0
1


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

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Components

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Protein , 4 types, 33 molecules VvBbAaCcDGQRSTUWXdijklnoJFZHOg...

#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
#3: 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 genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: J, lambdap21 / Production host: Escherichia coli (E. coli) / References: UniProt: P03749
#5: 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 genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: H, lambdap16 / Production host: Escherichia coli (E. coli) / References: UniProt: P03736
#6: Protein Tail tip assembly protein I


Mass: 23146.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: I, lambdap20 / Production host: Escherichia coli (E. coli) / References: UniProt: P03730

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

#2: Protein
Tail tip protein M


Mass: 12547.373 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: M, lambdap17 / Production host: Escherichia coli (E. coli) / References: UniProt: P03737
#4: Protein Tail tip protein L


Mass: 25730.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: L, lambdap18 / Production host: Escherichia coli (E. coli) / References: UniProt: P03738

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Non-polymers , 1 types, 3 molecules

#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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 tip conformation 1 of phage lambda tail / Type: COMPLEX / Entity ID: #1-#6 / 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 FIELDBright-field microscopy / 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: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57290 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00478954
ELECTRON MICROSCOPYf_angle_d0.671107580
ELECTRON MICROSCOPYf_dihedral_angle_d4.73610926
ELECTRON MICROSCOPYf_chiral_restr0.04512384
ELECTRON MICROSCOPYf_plane_restr0.00513893

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