[English] 日本語
Yorodumi
- EMDB-2112: Maturation in action: CryoEM study of a viral capsid caught durin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2112
TitleMaturation in action: CryoEM study of a viral capsid caught during expansion. (The HK97 first expansion intermediate).
Map dataReconstruction of the phage HK97 first expansion intermediate harboring E-loop truncated coat subunits.
Sample
  • Sample: HK97 Expansion intermediate 1 (E-loop truncated mutant)
  • Protein or peptide: HK97 gp5
Keywordsvirus maturation / capsid / bacteriophage HK97 / quasi-equivalence / electron cryomicroscopy
Biological speciesEnterobacteria phage HK97 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsVeesler D / Quispe J / Grigorieff N / Potter CS / Carragher B / Johnson JE
CitationJournal: Structure / Year: 2012
Title: Maturation in action: CryoEM study of a viral capsid caught during expansion.
Authors: David Veesler / Joel Quispe / Nikolaus Grigorieff / Clinton S Potter / Bridget Carragher / John E Johnson /
Abstract: Bacteriophage HK97 maturation involves discrete intermediate particle forms, comparable to transitional states in protein folding, before reaching its mature form. The process starts by formation of ...Bacteriophage HK97 maturation involves discrete intermediate particle forms, comparable to transitional states in protein folding, before reaching its mature form. The process starts by formation of a metastable prohead, poised for exothermic expansion triggered by DNA packaging. During maturation, the capsid subunit transitions from a strained to a canonical tertiary conformation and this has been postulated to be the driving mechanism for initiating expansion via switching hexameric capsomer architecture from skewed to 6-fold symmetric. We report the subnanometer electron-cryomicroscopy reconstruction of the HK97 first expansion intermediate before any crosslink formation. This form displays 6-fold symmetric hexamers, but capsid subunit tertiary structures exhibit distortions comparable to the prohead forms. We propose that coat subunit strain release acts in synergy with the first crosslinks to drive forward maturation. Finally, we speculate that the energetic features of this transition may result from increased stability of intermediates during maturation via enhanced inter-subunit interactions.
History
DepositionJun 2, 2012-
Header (metadata) releaseJul 9, 2012-
Map releaseJul 9, 2012-
UpdateJul 9, 2012-
Current statusJul 9, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2112.png

Downloads & links

-
Map

FileDownload / File: emd_2112.map.gz / Format: CCP4 / Size: 162.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the phage HK97 first expansion intermediate harboring E-loop truncated coat subunits.
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour LevelBy AUTHOR: 4.8 / Movie #1: 4.8
Minimum - Maximum-9.005289080000001 - 17.709112170000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-176-176-176
Dimensions352352352
Spacing352352352
CellA=B=C: 985.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z985.600985.600985.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-176-176-176
NC/NR/NS352352352
D min/max/mean-9.00517.709-0.000

-
Supplemental data

-
Sample components

-
Entire : HK97 Expansion intermediate 1 (E-loop truncated mutant)

EntireName: HK97 Expansion intermediate 1 (E-loop truncated mutant)
Components
  • Sample: HK97 Expansion intermediate 1 (E-loop truncated mutant)
  • Protein or peptide: HK97 gp5

-
Supramolecule #1000: HK97 Expansion intermediate 1 (E-loop truncated mutant)

SupramoleculeName: HK97 Expansion intermediate 1 (E-loop truncated mutant)
type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightTheoretical: 12.5 MDa

-
Macromolecule #1: HK97 gp5

MacromoleculeName: HK97 gp5 / type: protein_or_peptide / ID: 1 / Details: The capsid harbor E-loop truncated coat subunits / Oligomeric state: icosahedral / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage HK97 (virus)
Molecular weightTheoretical: 12.5 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pT7-5Hd2.9

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration11 mg/mL
BufferpH: 7.5 / Details: 10mM Tris, 40mM NaCl
GridDetails: C-flat
VitrificationCryogen name: ETHANE / Chamber temperature: 94 K / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.6 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Liquid Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 50000 times magnification
DateOct 28, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 1714 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: whole micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Frealign / Details: The final map was calculated from a single dataset / Number images used: 17116

+
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