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- EMDB-6492: Electron cryo-microscopy of bacteriophage EL chaperonin in the AT... -

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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 / identical protein binding
Similarity search - Function
Chaperonin Cpn60/GroEL / Chaperone tailless complex polypeptide 1 (TCP-1) / 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

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6492.jpg

Downloads & links

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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
Voxel sizeX=Y=Z: 2.4 Å
Density
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

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Supplemental data

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Sample components

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
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
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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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

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