[English] 日本語
Yorodumi
- PDB-1pdl: Fitting of gp5 in the cryoEM reconstruction of the bacteriophage ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pdl
TitleFitting of gp5 in the cryoEM reconstruction of the bacteriophage T4 baseplate
ComponentsTail-associated lysozyme
KeywordsHYDROLASE
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral tail assembly / virus tail, baseplate / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / viral tail assembly / virus tail, baseplate / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / identical protein binding
Similarity search - Function
Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Pre-baseplate central spike protein Gp5
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsKostyuchenko, V.A. / Leiman, P.G. / Chipman, P.R. / Kanamaru, S. / van Raaij, M.J. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G.
Citation
Journal: Nat Struct Biol / Year: 2003
Title: Three-dimensional structure of bacteriophage T4 baseplate.
Authors: Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three- ...The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three-dimensional structure of the baseplate-tail tube complex determined to a resolution of 12 A by cryoelectron microscopy. The baseplate has a six-fold symmetric, dome-like structure approximately 520 A in diameter and approximately 270 A long, assembled around a central hub. A 940 A-long and 96 A-diameter tail tube, coaxial with the hub, is connected to the top of the baseplate. At the center of the dome is a needle-like structure that was previously identified as a cell puncturing device. We have identified the locations of six proteins with known atomic structures, and established the position and shape of several other baseplate proteins. The baseplate structure suggests a mechanism of baseplate triggering and structural transition during the initial stages of T4 infection.
#1: Journal: Nature / Year: 2002
Title: Structure of the cell-puncturing device of bacteriophage T4
Authors: Kanamaru, S. / Leiman, P.G. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Arisaka, F. / Rossmann, M.G.
History
DepositionMay 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 14, 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
Remark 999SEQUENCE COORDINATES FOR CA ATOMS ONLY SUBMITTED.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY ...BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY COMPONENTS COM_ID: 1 NAME:GP5 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1048
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tail-associated lysozyme
B: Tail-associated lysozyme
C: Tail-associated lysozyme


Theoretical massNumber of molelcules
Total (without water)189,5513
Polymers189,5513
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

-
Components

#1: Protein Tail-associated lysozyme / Protein Gp5 / Coordinate model: Cα atoms only


Mass: 63183.723 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / References: UniProt: P16009, lysozyme

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsParent-ID
1Bacteriophage T4 baseplate- tail tube assemblyVIRUSBaseplate-tail tube assemblies were produced from bacteriophage T4 double amber (18-,23-) mutant0
2gp5trimer1
Buffer solutionName: water / pH: 7 / Details: water
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon
VitrificationCryogen name: ETHANE / Details: ethane vitrification
Crystal grow
*PLUS
Method: electron microscopy

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 70 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

-
Processing

EM software
IDNameVersionCategory
1SITUS COLORES2model fitting
2SPIDER3D reconstruction
CTF correctionDetails: CTF was corrected for each particle image individually
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: model based projection matching / Resolution: 12 Å / Num. of particles: 945 / Nominal pixel size: 3.11 Å / Actual pixel size: 2.98 Å / Magnification calibration: TMV images
Details: a modified version of SPIDER program was used for the reconstruction
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Correlation Coefficient maximization / Details: REFINEMENT PROTOCOL--Laplacian filtered real space
Atomic model buildingPDB-ID: 1K28
Accession code: 1K28 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 0 0 1662

+
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