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- EMDB-13762: GroEL - PrP complex -

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Basic information

Entry
Database: EMDB / ID: EMD-13762
TitleGroEL - PrP complex
Map data
SampleComplex of GroEL with Prion protein:
(GroEL) x 2 / (Prion proteinPRNP) x 2
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / unfolded protein binding / response to radiation / protein folding / response to heat / protein refolding / cell cycle ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / unfolded protein binding / response to radiation / protein folding / response to heat / protein refolding / cell cycle / cell division / magnesium ion binding / membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
Chaperonins cpn60 signature. / Chaperonin Cpn60, conserved site / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / TCP-1/cpn60 chaperonin family / GroEL-like apical domain superfamily / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria) / Ovis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsMoiseenko AV / Pichkur EB / Kudryavtseva SS / Stanishneva-Konovalova TB
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20055 Russian Federation
CitationJournal: Biomedicines / Year: 2021
Title: Structural and Computational Study of the GroEL-Prion Protein Complex.
Authors: Aleksandra A Mamchur / Andrei V Moiseenko / Irina S Panina / Igor A Yaroshevich / Sofia S Kudryavtseva / Evgeny B Pichkur / Olga S Sokolova / Vladimir I Muronetz / Tatiana B Stanishneva-Konovalova /
Abstract: The molecular chaperone GroEL is designed to promote protein folding and prevent aggregation. However, the interaction between GroEL and the prion protein, PrP, could lead to pathogenic ...The molecular chaperone GroEL is designed to promote protein folding and prevent aggregation. However, the interaction between GroEL and the prion protein, PrP, could lead to pathogenic transformation of the latter to the aggregation-prone PrP form. Here, the molecular basis of the interactions in the GroEL-PrP complex is studied with cryo-EM and molecular dynamics approaches. The obtained cryo-EM structure shows PrP to be bound to several subunits of GroEL at the level of their apical domains. According to MD simulations, the disordered N-domain of PrP forms much more intermolecular contacts with GroEL. Upon binding to the GroEL, the N-domain of PrP begins to form short helices, while the C-domain of PrP exhibits a tendency to unfold its α2-helix. In the absence of the nucleotides in the system, these processes are manifested at the hundred nanoseconds to microsecond timescale.
History
DepositionOct 20, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 8, 2021-
Current statusDec 8, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_13762.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 280 pix.
= 309.96 Å
1.11 Å/pix.
x 280 pix.
= 309.96 Å
1.11 Å/pix.
x 280 pix.
= 309.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.107 Å
Density
Contour LevelBy AUTHOR: 0.041 / Movie #1: 0.041
Minimum - Maximum-0.023144815 - 0.10889976
Average (Standard dev.)-0.0010228101 (±0.008039622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 309.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1071.1071.107
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z309.960309.960309.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0230.109-0.001

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Supplemental data

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Sample components

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Entire Complex of GroEL with Prion protein

EntireName: Complex of GroEL with Prion protein / Number of Components: 5

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Component #1: protein, Complex of GroEL with Prion protein

ProteinName: Complex of GroEL with Prion protein / Recombinant expression: No

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Component #2: protein, GroEL

ProteinName: GroEL / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #3: protein, Prion protein

ProteinName: Prion proteinPRNP / Recombinant expression: No
SourceSpecies: Ovis aries (sheep)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, GroEL

ProteinName: GroEL / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #5: protein, Prion protein

ProteinName: Prion proteinPRNP / Recombinant expression: No
SourceSpecies: Ovis aries (sheep)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277.5 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 100 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 0.05 mm / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 1621

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 82300
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution Method: FSC 0.143 CUT-OFF
Details: Final reconstruction was performed on C2-symmetry expanded dataset with the mask encapsulating one of the GroEL rings along with the PrP volume. The other ring density was subjected to particle subtraction.
FSC plot (resolution estimation)

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