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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 DUF1983 / Domain of unknown function DUF3672 / Domain of unknown function (DUF1983) / Fibronectin type III protein ...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 / 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: To Be Published
Title: Cryo-EM structure of lambda tail with LamB
Authors: Ge, X.F. / Wang, J.W.
History
DepositionDec 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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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
Water0
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 / Iron–sulfur cluster


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

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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