+Open data
-Basic information
Entry | Database: PDB / ID: 7eeq | ||||||
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Title | Cyanophage Pam1 tail machine | ||||||
Components |
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Keywords | VIRAL PROTEIN / Needle head proteins and tailspike head-binding proteins | ||||||
Biological species | unidentified (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å | ||||||
Authors | Zhang, J.T. / Jiang, Y.L. / Zhou, C.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Structure / Year: 2022 Title: Structure and assembly pattern of a freshwater short-tailed cyanophage Pam1. Authors: Jun-Tao Zhang / Feng Yang / Kang Du / Wei-Fang Li / Yuxing Chen / Yong-Liang Jiang / Qiong Li / Cong-Zhao Zhou / Abstract: Despite previous structural analyses of bacteriophages, quite little is known about the structures and assembly patterns of cyanophages. Using cryo-EM combined with crystallography, we solve the near- ...Despite previous structural analyses of bacteriophages, quite little is known about the structures and assembly patterns of cyanophages. Using cryo-EM combined with crystallography, we solve the near-atomic-resolution structure of a freshwater short-tailed cyanophage, Pam1, which comprises a 400-Å-long tail and an icosahedral capsid of 650 Å in diameter. The outer capsid surface is reinforced by trimeric cement proteins with a β-sandwich fold, which structurally resemble the distal motif of Pam1's tailspike, suggesting its potential role in host recognition. At the portal vertex, the dodecameric portal and connected adaptor, followed by a hexameric needle head, form a DNA ejection channel, which is sealed by a trimeric needle. Moreover, we identify a right-handed rifling pattern that might help DNA to revolve along the wall of the ejection channel. Our study reveals the precise assembly pattern of a cyanophage and lays the foundation to support its practical biotechnological and environmental applications. | ||||||
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 | 7eeq.cif.gz | 717.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eeq.ent.gz | 609.7 KB | Display | PDB format |
PDBx/mmJSON format | 7eeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eeq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7eeq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7eeq_validation.xml.gz | 99.6 KB | Display | |
Data in CIF | 7eeq_validation.cif.gz | 155 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/7eeq ftp://data.pdbj.org/pub/pdb/validation_reports/ee/7eeq | HTTPS FTP |
-Related structure data
Related structure data | 31080MC 7eeaC 7eelC 7eepC 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: 48534.621 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) unidentified (others) #2: Protein | Mass: 10782.913 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) unidentified (others) Source details | The source organism is a short-tailed cyanophage which was separated and sequenced by the author. | |
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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: Pam1 / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: unidentified (others) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
Particle selection | Num. of particles selected: 20704 | ||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20700 / Symmetry type: POINT |