+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4669 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Bacteriophage packaging protein | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||
Keywords | viral protein / DNA packaging | ||||||||||||||||||||||||
Function / homology | Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein Function and homology information | ||||||||||||||||||||||||
Biological species | Enterobacteria phage T7 (virus) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||||||||||||||
Authors | Fabrega-Ferrer M / Cuervo A | ||||||||||||||||||||||||
Funding support | Spain, 7 items
| ||||||||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism. Authors: Ana Cuervo / Montserrat Fàbrega-Ferrer / Cristina Machón / José Javier Conesa / Francisco J Fernández / Rosa Pérez-Luque / Mar Pérez-Ruiz / Joan Pous / M Cristina Vega / José L Carrascosa / Miquel Coll / Abstract: Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been ...Double-stranded DNA bacteriophages package their genome at high pressure inside a procapsid through the portal, an oligomeric ring protein located at a unique capsid vertex. Once the DNA has been packaged, the tail components assemble on the portal to render the mature infective virion. The tail tightly seals the ejection conduit until infection, when its interaction with the host membrane triggers the opening of the channel and the viral genome is delivered to the host cell. Using high-resolution cryo-electron microscopy and X-ray crystallography, here we describe various structures of the T7 bacteriophage portal and fiber-less tail complex, which suggest a possible mechanism for DNA retention and ejection: a portal closed conformation temporarily retains the genome before the tail is assembled, whereas an open portal is found in the tail. Moreover, a fold including a seven-bladed β-propeller domain is described for the nozzle tail protein. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4669.map.gz | 15.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4669-v30.xml emd-4669.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4669_fsc.xml | 5.5 KB | Display | FSC data file |
Images | emd_4669.png | 248.9 KB | ||
Filedesc metadata | emd-4669.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4669 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4669 | HTTPS FTP |
-Validation report
Summary document | emd_4669_validation.pdf.gz | 287.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4669_full_validation.pdf.gz | 286.4 KB | Display | |
Data in XML | emd_4669_validation.xml.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4669 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4669 | HTTPS FTP |
-Related structure data
Related structure data | 6qxmMC 4667C 4706C 6qwpC 6qx5C 6r21C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_4669.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Bacteriophage packaging protein
Entire | Name: Bacteriophage packaging protein |
---|---|
Components |
|
-Supramolecule #1: Bacteriophage packaging protein
Supramolecule | Name: Bacteriophage packaging protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Enterobacteria phage T7 (virus) |
-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Enterobacteria phage T7 (virus) |
Molecular weight | Theoretical: 60.458387 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAEKRTGLAE DGAKSVYERL KNDRAPYETR AQNCAQYTIP SLFPKDSDNA STDYQTPWQA VGARGLNNLA SKLMLALFPM QTWMRLTIS EYEAKQLLSD PDGLAKVDEG LSMVERIIMN YIESNSYRVT LFEALKQLVV AGNVLLYLPE PEGSNYNPMK L YRLSSYVV ...String: MAEKRTGLAE DGAKSVYERL KNDRAPYETR AQNCAQYTIP SLFPKDSDNA STDYQTPWQA VGARGLNNLA SKLMLALFPM QTWMRLTIS EYEAKQLLSD PDGLAKVDEG LSMVERIIMN YIESNSYRVT LFEALKQLVV AGNVLLYLPE PEGSNYNPMK L YRLSSYVV QRDAFGNVLQ MVTRDQIAFG ALPEDIRKAV EGQGGEKKAD ETIDVYTHIY LDEDSGEYLR YEEVEGMEVQ GS DGTYPKE ACPYIPIRMV RLDGESYGRS YIEEYLGDLR SLENLQEAIV KMSMISSKVI GLVNPAGITQ PRRLTKAQTG DFV TGRPED ISFLQLEKQA DFTVAKAVSD AIEARLSFAF MLNSAVQRTG ERVTAEEIRY VASELEDTLG GVYSILSQEL QLPL VRVLL KQLQATQQIP ELPKEAVEPT ISTGLEAIGR GQDLDKLERC VTAWAALAPM RDDPDINLAM IKLRIANAIG IDTSG ILLT EEQKQQKMAQ QSMQMGMDNG AAALAQGMAA QATASPEAMA AAADSVGLQP GIAAALEHHH HHH UniProtKB: Portal protein |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 39.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |