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- PDB-8xcg: Tail tip complex of bacteriophage lambda in the open state -

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Basic information

Entry
Database: PDB / ID: 8xcg
TitleTail tip complex of bacteriophage lambda in the open state
Components
  • Tail tip assembly protein I
  • Tail tip protein L
  • Tail tip protein M
  • Tip attachment protein J
KeywordsVIRUS / Bacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM
Function / homology
Function and homology information


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 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 DUF3672 / : / Tip attachment protein J, C-terminal receptor binding domain / Tip attachment protein J, Ig-like domain ...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 DUF3672 / : / Tip attachment protein J, C-terminal receptor binding domain / Tip attachment protein J, Ig-like domain / Tip attachment protein J second Ig-like domain / : / : / Tip attachment protein J,FNIII-A domain / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Tip attachment protein J / Putative phage tail protein / 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 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: 3.46 Å
AuthorsGe, X.F. / Wang, J.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural mechanism of bacteriophage lambda tail's interaction with the bacterial receptor.
Authors: Xiaofei Ge / Jiawei Wang /
Abstract: Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. ...Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. Although comprehensive studies on the interaction between bacteriophage lambda and its outer membrane receptor, LamB, have provided rich information about the system's biochemical properties, the precise molecular mechanism remains undetermined. This study revealed the high-resolution cryo-electron microscopy (cryo-EM) structures of the bacteriophage lambda tail complexed with its irreversible Shigella sonnei 3070 LamB receptor and the closed central tail fiber. These structures reveal the complex processes that trigger infection and demonstrate a substantial conformational change in the phage lambda tail tip upon LamB binding. Providing detailed structures of bacteriophage lambda infection initiation, this study contributes to the expanding knowledge of lambda-bacterial interaction, which holds significance in the fields of microbiology and therapeutic development.
History
DepositionDec 9, 2023Deposition site: PDBJ / Processing site: PDBJ
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Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Tail tip protein M
F: Tip attachment protein J
I: Tail tip assembly protein I
J: Tip attachment protein J
K: Tail tip protein M
L: Tail tip protein L
M: Tail tip protein M
N: Tail tip protein L
P: Tail tip assembly protein I
Y: Tail tip protein M
Z: Tip attachment protein J
e: Tail tip protein M
f: Tail tip protein L
h: Tail tip assembly protein I
m: Tail tip protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)596,62318
Polymers595,56815
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

#1: 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P03737
#2: Protein Tip attachment 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P03749
#3: 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P03730
#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
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
Has ligand of interestN
Has protein modificationY

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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: Bacteriophage lambda tail with LamB / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage Lambda (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
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: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 358235 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00526473
ELECTRON MICROSCOPYf_angle_d0.67935985
ELECTRON MICROSCOPYf_dihedral_angle_d5.393608
ELECTRON MICROSCOPYf_chiral_restr0.0473986
ELECTRON MICROSCOPYf_plane_restr0.0064686

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