[English] 日本語
Yorodumi
- EMDB-6492: Electron cryo-microscopy of bacteriophage EL chaperonin in the AT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6492
TitleElectron cryo-microscopy of bacteriophage EL chaperonin in the ATP-bound conformation
Map dataPhi-EL chaperonin in the ATP-bound conformation
Sample
  • Sample: Bacteriphage phi-EL encoded chaperonin in the ATP-bound conformation
  • Protein or peptide: phi-EL chaperonin
Keywordschaperonin / phi-EL / protein folding / ATP conformation
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Chaperone tailless complex polypeptide 1 (TCP-1) / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Putative GroEL-like chaperonine protein
Similarity search - Component
Biological speciesPseudomonas phage EL (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsMolugu SK / Hildenbrand ZL / Morgan DG / Sherman MB / He L / Georgopoulos C / Sernova NV / Kurochkina LP / Mesyanzhinov VV / Miroshnikov KA / Bernal RA
CitationJournal: Structure / Year: 2016
Title: Ring Separation Highlights the Protein-Folding Mechanism Used by the Phage EL-Encoded Chaperonin.
Authors: Sudheer K Molugu / Zacariah L Hildenbrand / David Gene Morgan / Michael B Sherman / Lilin He / Costa Georgopoulos / Natalia V Sernova / Lidia P Kurochkina / Vadim V Mesyanzhinov / Konstantin ...Authors: Sudheer K Molugu / Zacariah L Hildenbrand / David Gene Morgan / Michael B Sherman / Lilin He / Costa Georgopoulos / Natalia V Sernova / Lidia P Kurochkina / Vadim V Mesyanzhinov / Konstantin A Miroshnikov / Ricardo A Bernal /
Abstract: Chaperonins are ubiquitous, ATP-dependent protein-folding molecular machines that are essential for all forms of life. Bacteriophage φEL encodes its own chaperonin to presumably fold exceedingly ...Chaperonins are ubiquitous, ATP-dependent protein-folding molecular machines that are essential for all forms of life. Bacteriophage φEL encodes its own chaperonin to presumably fold exceedingly large viral proteins via profoundly different nucleotide-binding conformations. Our structural investigations indicate that ATP likely binds to both rings simultaneously and that a misfolded substrate acts as the trigger for ATP hydrolysis. More importantly, the φEL complex dissociates into two single rings resulting from an evolutionarily altered residue in the highly conserved ATP-binding pocket. Conformational changes also more than double the volume of the single-ring internal chamber such that larger viral proteins are accommodated. This is illustrated by the fact that φEL is capable of folding β-galactosidase, a 116-kDa protein. Collectively, the architecture and protein-folding mechanism of the φEL chaperonin are significantly different from those observed in group I and II chaperonins.
History
DepositionOct 21, 2015-
Header (metadata) releaseMar 30, 2016-
Map releaseMar 30, 2016-
UpdateApr 27, 2016-
Current statusApr 27, 2016Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6492.jpg

Downloads & links

-
Map

FileDownload / File: emd_6492.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhi-EL chaperonin in the ATP-bound conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 128 pix.
= 307.2 Å		2.4 Å/pix.
x 128 pix.
= 307.2 Å		2.4 Å/pix.
x 128 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.09223329 - 0.2510705
Average (Standard dev.)0.00487331 (±0.02107129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z307.200307.200307.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.0920.2510.005

-
Supplemental data

-
Sample components

-
Entire : Bacteriphage phi-EL encoded chaperonin in the ATP-bound conformation

EntireName: Bacteriphage phi-EL encoded chaperonin in the ATP-bound conformation
Components
  • Sample: Bacteriphage phi-EL encoded chaperonin in the ATP-bound conformation
  • Protein or peptide: phi-EL chaperonin

-
Supramolecule #1000: Bacteriphage phi-EL encoded chaperonin in the ATP-bound conformation

SupramoleculeName: Bacteriphage phi-EL encoded chaperonin in the ATP-bound conformation
type: sample / ID: 1000 / Oligomeric state: homotetradecamer / Number unique components: 1
Molecular weightTheoretical: 863.5354 KDa

-
Macromolecule #1: phi-EL chaperonin

MacromoleculeName: phi-EL chaperonin / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Oligomeric state: tetradecamer / Recombinant expression: Yes
Source (natural)Organism: Pseudomonas phage EL (virus) / synonym: Bacteriophage EL
Molecular weightTheoretical: 61.6811 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET22
SequenceUniProtKB: Putative GroEL-like chaperonine protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
Details: 50 mM HEPES, pH 7.5, 150 mM NaCl, 2 mM ATP, 2 mM MgCl2, 2 mM EDTA
GridDetails: Quantifoil R2/2 grids glow-discharged in air for 1 minute
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 2-3 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 88 K / Max: 103 K / Average: 100 K
DateAug 1, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12 µm / Number real images: 50 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2, RELION / Number images used: 40613

+
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