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- EMDB-6494: Electron cryo-microscopy of bacteriophage EL chaperonin in the nu... -

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Basic information

Entry
Database: EMDB / ID: EMD-6494
TitleElectron cryo-microscopy of bacteriophage EL chaperonin in the nucleotide-free conformation
Map dataReconstruction of the phi-EL chaperonin in the nucleotide-free conformation.
Sample
  • Sample: Bacteriphage phi-EL encoded chaperonin in the nucleotide-free conformation
  • Protein or peptide: phi-EL chaperonin
Keywordschaperonin / phi-EL / protein folding / nucleotide free (apo) 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: 9.0 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: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6494.jpg

Downloads & links

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Map

FileDownload / File: emd_6494.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the phi-EL chaperonin in the nucleotide-free conformation.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 160 pix.
= 315.2 Å		1.97 Å/pix.
x 160 pix.
= 315.2 Å		1.97 Å/pix.
x 160 pix.
= 315.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-9.823476790000001 - 7.84446955
Average (Standard dev.)0.00177792 (±0.60859835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 315.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.971.971.97
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z315.200315.200315.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-9.8237.8440.002

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Supplemental data

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Sample components

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Entire : Bacteriphage phi-EL encoded chaperonin in the nucleotide-free con...

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

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Supramolecule #1000: Bacteriphage phi-EL encoded chaperonin in the nucleotide-free con...

SupramoleculeName: Bacteriphage phi-EL encoded chaperonin in the nucleotide-free 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 ADP, 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

MicroscopeJEOL 2200FS
TemperatureMin: 88 K / Max: 103 K / Average: 100 K
DateAug 1, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 12 µm / Number real images: 100 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 76142 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2, RELION / Number images used: 58477

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