[English] 日本語
Yorodumi
- PDB-3j4a: Structure of gp8 connector protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j4a
TitleStructure of gp8 connector protein
ComponentsHead-to-tail joining protein
KeywordsVIRAL PROTEIN / Bacteriophage / DNA translocation / connector
Function / homologyPortal 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 speciesEnterobacteria phage T7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsCuervo, A. / Pulido-Cid, M. / Chagoyen, M. / Arranz, R. / Gonzalez-Garcia, V.A. / Garcia-Doval, C. / Caston, J.R. / Valpuesta, J.M. / van Raaij, M.J. / Martin-Benito, J. / Carrascosa, J.L.
CitationJournal: J Biol Chem / Year: 2013
Title: Structural characterization of the bacteriophage T7 tail machinery.
Authors: Ana Cuervo / Mar Pulido-Cid / Mónica Chagoyen / Rocío Arranz / Verónica A González-García / Carmela Garcia-Doval / José R Castón / José M Valpuesta / Mark J van Raaij / Jaime Martín- ...Authors: Ana Cuervo / Mar Pulido-Cid / Mónica Chagoyen / Rocío Arranz / Verónica A González-García / Carmela Garcia-Doval / José R Castón / José M Valpuesta / Mark J van Raaij / Jaime Martín-Benito / José L Carrascosa /
Abstract: Most bacterial viruses need a specialized machinery, called "tail," to inject their genomes inside the bacterial cytoplasm without disrupting the cellular integrity. Bacteriophage T7 is a well ...Most bacterial viruses need a specialized machinery, called "tail," to inject their genomes inside the bacterial cytoplasm without disrupting the cellular integrity. Bacteriophage T7 is a well characterized member of the Podoviridae family infecting Escherichia coli, and it has a short noncontractile tail that assembles sequentially on the viral head after DNA packaging. The T7 tail is a complex of around 2.7 MDa composed of at least four proteins as follows: the connector (gene product 8, gp8), the tail tubular proteins gp11 and gp12, and the fibers (gp17). Using cryo-electron microscopy and single particle image reconstruction techniques, we have determined the precise topology of the tail proteins by comparing the structure of the T7 tail extracted from viruses and a complex formed by recombinant gp8, gp11, and gp12 proteins. Furthermore, the order of assembly of the structural components within the complex was deduced from interaction assays with cloned and purified tail proteins. The existence of common folds among similar tail proteins allowed us to obtain pseudo-atomic threaded models of gp8 (connector) and gp11 (gatekeeper) proteins, which were docked into the corresponding cryo-EM volumes of the tail complex. This pseudo-atomic model of the connector-gatekeeper interaction revealed the existence of a common molecular architecture among viruses belonging to the three tailed bacteriophage families, strongly suggesting that a common molecular mechanism has been favored during evolution to coordinate the transition between DNA packaging and tail assembly.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5690
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Head-to-tail joining protein
J: Head-to-tail joining protein
K: Head-to-tail joining protein
L: Head-to-tail joining protein
B: Head-to-tail joining protein
C: Head-to-tail joining protein
D: Head-to-tail joining protein
E: Head-to-tail joining protein
F: Head-to-tail joining protein
G: Head-to-tail joining protein
H: Head-to-tail joining protein
I: Head-to-tail joining protein


Theoretical massNumber of molelcules
Total (without water)666,55112
Polymers666,55112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Head-to-tail joining protein / gp8 / connector protein / Coordinate model: Cα atoms only


Mass: 55545.922 Da / Num. of mol.: 12 / Fragment: UNP residues 1-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Gene: 8 / Plasmid: pRSET-B / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P03728

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: T7 tail complex formed by proteins gp8, gp11 and gp12 / Type: VIRUS / Details: gp8 (12mer), gp11(12mer), gp12 (6mer)
Molecular weightValue: 1.5 MDa / Experimental value: NO
Details of virusHost category: BACTERIA / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionName: 50 mM Tris-HCl, 10 mM MgCl2, 100 mM NaCl / pH: 7.8 / Details: 50 mM Tris-HCl, 10 mM MgCl2, 100 mM NaCl
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: R2/2 Quantifoil coated with a thin carbon layer
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE
Details: Samples were applied to grids for 1 minute, blotted and plunged into liquid ethane (LEICA EM CPC).
Method: Samples were applied to grids for 1 minute, blotted and plunged into liquid ethane.

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Nov 8, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 108696 X / Calibrated magnification: 108696 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 113 K / Temperature (min): 91 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
Image scansNum. digital images: 264
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2EMAN3D reconstruction
3SPIDER3D reconstruction
4Xmipp3D reconstruction
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionMethod: Cross-common lines / Resolution: 12 Å / Resolution method: FSC / Num. of particles: 1820 / Nominal pixel size: 2.75 Å / Actual pixel size: 2.75 Å / Details: (Single particle--Applied symmetry: C6) / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Volumetric correlation
Details: REFINEMENT PROTOCOL--rigid body DETAILS--One monomer was manually fitted and then the oligomer was generated using SITUS program
Atomic model buildingPDB-ID: 3LJ5

3lj5


Pdb chain-ID: L / Accession code: 3LJ5 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 0 0 0 5964

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more