+Open data
-Basic information
Entry | Database: PDB / ID: 6uzc | ||||||
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Title | Portal vertex structure of bacteriophage T4 | ||||||
Components |
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Keywords | VIRUS / portal protein assembly / gp20 / gp23 / portal vertex | ||||||
Function / homology | Function and homology information symbiont genome ejection through host cell envelope, contractile tail mechanism / T=13 icosahedral viral capsid / viral portal complex / viral genome packaging / viral release from host cell / viral capsid / host cell plasma membrane / membrane Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Fang, Q. / Fokine, A. / Rao, V.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural morphing in a symmetry-mismatched viral vertex. Authors: Qianglin Fang / Wei-Chun Tang / Pan Tao / Marthandan Mahalingam / Andrei Fokine / Michael G Rossmann / Venigalla B Rao / Abstract: Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of ...Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of asymmetry, a 12-fold-symmetric dodecameric portal complex inserted into a 5-fold-symmetric capsid vertex, is found in numerous icosahedral viruses, including tailed bacteriophages, herpesviruses, and archaeal viruses. This vertex is critical for driving capsid assembly, DNA packaging, tail attachment, and genome ejection. Here, we report the near-atomic in situ structure of the symmetry-mismatched portal vertex from bacteriophage T4. Remarkably, the local structure of portal morphs to compensate for symmetry-mismatch, forming similar interactions in different capsid environments while maintaining strict symmetry in the rest of the structure. This creates a unique and unusually dynamic symmetry-mismatched vertex that is central to building an infectious virion. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6uzc.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6uzc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6uzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uzc_validation.pdf.gz | 964.1 KB | Display | wwPDB validaton report |
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Full document | 6uzc_full_validation.pdf.gz | 975.9 KB | Display | |
Data in XML | 6uzc_validation.xml.gz | 410.3 KB | Display | |
Data in CIF | 6uzc_validation.cif.gz | 673.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/6uzc ftp://data.pdbj.org/pub/pdb/validation_reports/uz/6uzc | HTTPS FTP |
-Related structure data
Related structure data | 20956MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 56074.242 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / References: UniProt: P04535 #2: Protein | Mass: 61117.082 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / References: UniProt: P13334 |
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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: Escherichia virus T4 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Escherichia virus T4 |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 23.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53608 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |