[English] 日本語
Yorodumi
- PDB-1zku: Fitting of the gp9 structure in the EM density of bacteriophage T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zku
TitleFitting of the gp9 structure in the EM density of bacteriophage T4 extended tail
ComponentsBaseplate structural protein Gp9
KeywordsVIRAL PROTEIN / Structural protein
Function / homologyBaseplate structural protein Gp9 C-terminal domain superfamily / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / virus tail, baseplate / viral tail assembly / viral release from host cell / Baseplate protein gp9
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 Å
AuthorsKostyuchenko, V.A.
CitationJournal: Nat Struct Mol Biol / Year: 2005
Title: The tail structure of bacteriophage T4 and its mechanism of contraction.
Authors: Victor A Kostyuchenko / Paul R Chipman / Petr G Leiman / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail ...Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail assembly at 15-A resolution shows the hexagonal dome-shaped baseplate, the extended contractile sheath, the long tail fibers attached to the baseplate and the collar formed by six whiskers that interact with the long tail fibers. Comparison with the structure of the contracted tail shows that tail contraction is associated with a substantial rearrangement of the domains within the sheath protein and results in shortening of the sheath to about one-third of its original length. During contraction, the tail tube extends beneath the baseplate by about one-half of its total length and rotates by 345 degrees , allowing it to cross the host's periplasmic space.
History
DepositionMay 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 3, 2013Group: Database references
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Baseplate structural protein Gp9
B: Baseplate structural protein Gp9
C: Baseplate structural protein Gp9
D: Baseplate structural protein Gp9
E: Baseplate structural protein Gp9
F: Baseplate structural protein Gp9
G: Baseplate structural protein Gp9
H: Baseplate structural protein Gp9
I: Baseplate structural protein Gp9
J: Baseplate structural protein Gp9
K: Baseplate structural protein Gp9
L: Baseplate structural protein Gp9
M: Baseplate structural protein Gp9
N: Baseplate structural protein Gp9
O: Baseplate structural protein Gp9
P: Baseplate structural protein Gp9
Q: Baseplate structural protein Gp9
R: Baseplate structural protein Gp9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,73536
Polymers558,44518
Non-polymers4,28918
Water0
1


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

-
Components

#1: Protein
Baseplate structural protein Gp9 / Baseplate wedge protein 9


Mass: 31024.725 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 9 / References: UniProt: P10927
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: T4 / Type: VIRUS
Buffer solutionpH: 7 / Details: H2O
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: COPPER GRID
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jan 10, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3.2 nm / Nominal defocus min: 0.8 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingFilm or detector model: GENERIC FILM
Image scansNum. digital images: 75
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1SITUS COLORESmodel fitting
2XFITmodel fitting
3SPIDER3D reconstruction
CTF correctionDetails: EACH IMAGE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: REAL SPACE SIRT / Resolution: 15 Å / Num. of particles: 3029 / Nominal pixel size: 3.97 Å / Actual pixel size: 3.97 Å / Magnification calibration: 47000 / Details: EM MAP DEPOSITED AS EMD-1126 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: REFINEMENT PROTOCOL--MANUAL FITTING FOLLOWED BY REFINEMENT IN COLORES
Atomic model buildingPDB-ID: 1S2E

1s2e


Accession code: 1S2E / Source name: PDB / Type: experimental model
RefinementHighest resolution: 15 Å
Refinement stepCycle: LAST / Highest resolution: 15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39150 0 270 0 39420

+
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