+Open data
-Basic information
Entry | Database: PDB / ID: 8iyl | ||||||
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Title | Tail tip conformation 2 of phage lambda tail | ||||||
Components |
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Keywords | VIRAL 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 | ||||||
Biological species | Escherichia phage lambda (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Wang, J.W. / Wang, C. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iyl.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8iyl.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8iyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iyl_validation.pdf.gz | 612.2 KB | Display | wwPDB validaton report |
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Full document | 8iyl_full_validation.pdf.gz | 664.2 KB | Display | |
Data in XML | 8iyl_validation.xml.gz | 167.9 KB | Display | |
Data in CIF | 8iyl_validation.cif.gz | 267.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/8iyl ftp://data.pdbj.org/pub/pdb/validation_reports/iy/8iyl | HTTPS FTP |
-Related structure data
Related structure data | 35825MC 8iydC 8iykC 8jvmC 8kgeC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Tail tip protein ... , 2 types, 9 molecules MmDFXZLGd
#1: Protein | 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 #3: Protein | 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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-Protein , 4 types, 33 molecules JEYHKeINfVvBbAaCcOPQRSTUWghijk...
#2: Protein | 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 #4: Protein | 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 #5: Protein | 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 #6: Protein | 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 |
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-Non-polymers , 1 types, 3 molecules
#7: Chemical |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tail tip conformation 2 of phage lambda tail / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia phage lambda (virus) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54547 / Symmetry type: POINT | ||||||||||||||||||||||||
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