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Yorodumi- PDB-8fwg: Structure of neck and portal vertex of Agrobacterium phage Milano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fwg | ||||||
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Title | Structure of neck and portal vertex of Agrobacterium phage Milano, C5 symmetry | ||||||
Components |
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Keywords | VIRUS / Myophage / redox trigger | ||||||
Function / homology | Bacterial Ig domain / Phage capsid / Phage capsid family / Virion-associated protein / Virion-associated protein / Major capsid protein / Virion-associated protein / Head-to-tail connector complex protein Function and homology information | ||||||
Biological species | Agrobacterium phage Milano (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||
Authors | Sonani, R.R. / Wang, F. / Esteves, N.C. / Kelly, R.J. / Sebastian, A. / Kreutzberger, M.A.B. / Leiman, P.G. / Scharf, B.E. / Egelman, E.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Neck and capsid architecture of the robust Agrobacterium phage Milano. Authors: Ravi R Sonani / Nathaniel C Esteves / Abigail A Horton / Rebecca J Kelly / Amanda L Sebastian / Fengbin Wang / Mark A B Kreutzberger / Petr G Leiman / Birgit E Scharf / Edward H Egelman / Abstract: Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is ...Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of the Agrobacterium phage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fwg.cif.gz | 4.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8fwg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/8fwg ftp://data.pdbj.org/pub/pdb/validation_reports/fw/8fwg | HTTPS FTP |
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-Related structure data
Related structure data | 29504MC 8fwbC 8fwcC 8fweC 8fwmC 8fxpC 8fxrC 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
-Linking protein ... , 2 types, 30 molecules a1b1d1e1a2b2d2e2a5b5d5e5a6b6d6e6a7b7d7e7cdefgf1f2f5f6f7
#1: Protein/peptide | Mass: 3942.762 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) #2: Protein | Mass: 22913.605 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFR0 |
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-Protein , 4 types, 135 molecules g1h1k1n1o1r1g2h2k2n2o2r2g5h5k5n5o5r5g6h6k6n6o6r6g7h7k7n7o7r7...
#3: Protein | Mass: 52037.324 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFS6 #4: Protein | Mass: 14548.290 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MFS0 #5: Protein | Mass: 24490.402 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MGH3 #6: Protein | Mass: 22255.439 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Agrobacterium phage Milano (virus) / References: UniProt: A0A482MHL8 |
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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: Agrobacterium phage Milano / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Agrobacterium phage Milano (virus) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Agrobacterium fabrum str. C58 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10086 / Symmetry type: POINT | ||||||||||||||||||||||||
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