+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6324 | |||||||||
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Title | Electron cryo-microscopy of T4 portal protein | |||||||||
Map data | Reconstruction of T4 portal protein gp20 | |||||||||
Sample |
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Keywords | T4 portal protein | |||||||||
Function / homology | Portal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral portal complex / viral genome packaging / viral release from host cell / host cell plasma membrane / membrane / Portal protein Function and homology information | |||||||||
Biological species | Enterobacteria phage T4 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Sun L / Zhang X / Gao S / Rao PA / Padilla-Sanchez V / Chen Z / Sun S / Xiang Y / Sriram S / Rao VB / Rossmann MG | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. Authors: Lei Sun / Xinzheng Zhang / Song Gao / Prashant A Rao / Victor Padilla-Sanchez / Zhenguo Chen / Siyang Sun / Ye Xiang / Sriram Subramaniam / Venigalla B Rao / Michael G Rossmann / Abstract: The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage ...The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6324.map.gz | 12.3 MB | EMDB map data format | |
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Header (meta data) | emd-6324-v30.xml emd-6324.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | 400_6324.gif 80_6324.gif | 83.2 KB 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6324 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6324 | HTTPS FTP |
-Validation report
Summary document | emd_6324_validation.pdf.gz | 340.4 KB | Display | EMDB validaton report |
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Full document | emd_6324_full_validation.pdf.gz | 340 KB | Display | |
Data in XML | emd_6324_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6324 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6324 | HTTPS FTP |
-Related structure data
Related structure data | 3ja7MC 6323C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6324.map.gz / Format: CCP4 / Size: 75 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of T4 portal protein gp20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : T4 portal protein gp20
Entire | Name: T4 portal protein gp20 |
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Components |
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-Supramolecule #1000: T4 portal protein gp20
Supramolecule | Name: T4 portal protein gp20 / type: sample / ID: 1000 / Oligomeric state: dodecamer / Number unique components: 1 |
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Molecular weight | Experimental: 660 KDa |
-Macromolecule #1: T4 Portal protein gp20
Macromolecule | Name: T4 Portal protein gp20 / type: protein_or_peptide / ID: 1 / Name.synonym: connector / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes |
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Source (natural) | Organism: Enterobacteria phage T4 (virus) / synonym: phage T4 |
Molecular weight | Experimental: 660 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3) pLysS / Recombinant plasmid: pCDFDuet-1 |
Sequence | UniProtKB: Portal protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.8 / Details: 20 mM Tris, 400 mM NaCl, 5 mM EDTA |
Grid | Details: Quantifoil R1.2/1.3 holey carbon on 200 mesh copper |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 7 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80 K / Max: 105 K / Average: 100 K |
Specialist optics | Energy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV |
Date | Jul 10, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 839 / Average electron dose: 2 e/Å2 Details: Every image is the average of 11 frames recorded by the direct electron detector. Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder: Liquid nitrogen-cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using an automatic selection program. |
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CTF correction | Details: each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 98000 |
Final two d classification | Number classes: 15 |