[English] 日本語
Yorodumi
- EMDB-1572: The T4 packaging motor, T4 procapsid with large terminase gp17 bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1572
TitleThe T4 packaging motor, T4 procapsid with large terminase gp17 bound
Map dataThe T4 packaging motor, T4 procapsid with large terminase gp17 bound.
Sample
  • Sample: T4 procapsid with gp17 bound
  • Virus: Enterobacteria phage T4 (virus)
Keywordsprocapsid / DNA packaging motor / large terminase
Function / homology
Function and homology information


viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity ...viral terminase, large subunit / DNA nuclease activity / viral genome packaging / viral procapsid maturation / viral DNA genome packaging / nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Terminase, large subunit, gp17-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 34.0 Å
AuthorsSun S / Kondabagil K / Draper B / Alam TI / Bowman VD / Zhang Z / Hegde S / Fokine A / Rossmann MG / Rao VB
CitationJournal: Cell / Year: 2008
Title: The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
Authors: Siyang Sun / Kiran Kondabagil / Bonnie Draper / Tanfis I Alam / Valorie D Bowman / Zhihong Zhang / Shylaja Hegde / Andrei Fokine / Michael G Rossmann / Venigalla B Rao /
Abstract: Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The ...Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which provides energy for compacting DNA, and a C-terminal nuclease domain, which terminates packaging. We show that another function of the C-terminal domain is to translocate the genome into the procapsid. The two domains are in close contact in the crystal structure, representing a "tensed state." A cryo-electron microscopy reconstruction of the T4 procapsid complexed with gp17 shows that the packaging motor is a pentamer and that the domains within each monomer are spatially separated, representing a "relaxed state." These structures suggest a mechanism, supported by mutational and other data, in which electrostatic forces drive the DNA packaging by alternating between tensed and relaxed states. Similar mechanisms may occur in other molecular motors.
History
DepositionOct 23, 2008-
Header (metadata) releaseOct 23, 2008-
Map releaseMay 5, 2009-
UpdateMay 5, 2009-
Current statusMay 5, 2009Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.504156736
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3ezk
  • Surface level: 2.2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3ezk
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1572.gif

Downloads & links

-
Map

FileDownload / File: emd_1572.map.gz / Format: CCP4 / Size: 54.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe T4 packaging motor, T4 procapsid with large terminase gp17 bound.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.48 Å/pix.
x 244 pix.
= 1581.12 Å		6.48 Å/pix.
x 244 pix.
= 1581.12 Å		6.48 Å/pix.
x 244 pix.
= 1581.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8 / Movie #1: 2.5041567
Minimum - Maximum-7.66036 - 9.93487
Average (Standard dev.)-0.00000000385206 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-122-122-122
Dimensions244244244
Spacing244244244
CellA=B=C: 1581.12 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.486.486.48
M x/y/z244244244
origin x/y/z0.0000.0000.000
length x/y/z1581.1201581.1201581.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-122-122-122
NC/NR/NS244244244
D min/max/mean-7.6609.935-0.000

-
Supplemental data

-
Sample components

-
Entire : T4 procapsid with gp17 bound

EntireName: T4 procapsid with gp17 bound
Components
  • Sample: T4 procapsid with gp17 bound
  • Virus: Enterobacteria phage T4 (virus)

-
Supramolecule #1000: T4 procapsid with gp17 bound

SupramoleculeName: T4 procapsid with gp17 bound / type: sample / ID: 1000 / Number unique components: 2

-
Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: bacteriophage T4 / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: bacteriophage T4
Host (natural)Organism: E. coli (E. coli) / synonym: BACTERIA(EUBACTERIA)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Details: 50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-mercaptoethanol
GridDetails: quantifoil copper grid 2um holes
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: in-house, gravity driven plunger
Method: 3.5ul of sample hand blotted approx. 1sec

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 97 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.25 µm / Number real images: 108 / Average electron dose: 20 e/Å2 / Bits/pixel: 8

-
Image processing

CTF correctionDetails: phase flipping for each micrograph
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider / Number images used: 1716

-
Atomic model buiding 1

Initial modelPDB ID:

3cpe

SoftwareName: EMFIT
DetailsProtocol: Rigid Body. The N- and C-terminal domains of gp17 were separately fitted into their corresponding cryoEM densities
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3ezk:
Bacteriophage T4 gp17 motor assembly based on crystal structures and cryo-EM reconstructions

+
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