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- EMDB-13762: GroEL - PrP complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-13762
TitleGroEL - PrP complex
Map dataC1 map of GroEL-PrP complex
Sample
  • Complex: Complex of GroEL with Prion protein
    • Complex: GroEL
      • Protein or peptide: GroEL
    • Complex: Prion protein
      • Protein or peptide: Prion protein
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / 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
Biological speciesEscherichia coli K-12 (bacteria) / Ovis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13762.png

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)
AnnotationC1 map of GroEL-PrP complex
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

Histogram

Histogram (log scale)
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
Components
  • Complex: Complex of GroEL with Prion protein
    • Complex: GroEL
      • Protein or peptide: GroEL
    • Complex: Prion protein
      • Protein or peptide: Prion protein

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Supramolecule #1: Complex of GroEL with Prion protein

SupramoleculeName: Complex of GroEL with Prion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: GroEL

SupramoleculeName: GroEL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Supramolecule #3: Prion protein

SupramoleculeName: Prion protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Ovis aries (sheep)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
SequenceString: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTTT ATVLAQAIIT EGLKAVAAGM NPMDLKRGID KAVTAAVEEL KALSVPCSDS KAIAQVGTIS ANSDETVGKL IAEAMDKVGK ...String:
AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTTT ATVLAQAIIT EGLKAVAAGM NPMDLKRGID KAVTAAVEEL KALSVPCSDS KAIAQVGTIS ANSDETVGKL IAEAMDKVGK EGVITVEDGT GLQDELDVVE GMQFDRGYLS PYFINKPETG AVELESPFIL LADKKISNIR EMLPVLEAVA KAGKPLLIIA EDVEGEALAT LVVNTMRGIV KVAAVKAPGF GDRRKAMLQD IATLTGGTVI SEEIGMELEK ATLEDLGQAK RVVINKDTTT IIDGVGEEAA IQGRVAQIRQ QIEEATSDYD REKLQERVAK LAGGVAVIKV GAATEVEMKE KKARVEDALH ATRAAVEEGV VAGGGVALIR VASKLADLRG QNEDQNVGIK VALRAMEAPL RQIVLNCGEE PSVVANTVKG GDGNYGYNAA TEEYGNMIDM GILDPTKVTR SALQYAASVA GLMITTECMV TDLPKNDAAD LGAAGGMGGM GGMGGMM

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Macromolecule #2: Prion protein

MacromoleculeName: Prion protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SKKRPKPGGG WNTGGSRYPG QGSPGGNRYP PQGGGGWGQP HGGGWGQPHG GGWGQPHGGG WGQPHGGGGW GQGGSHSQWN KPSKPKTNMK HVAGAAAAGA VVGGLGGYML GSAMSRPLIH FGNDYEDRYY RENMYRYPNQ VYYRPVDRYS NQNNFVHDCV NITVKQHTVT ...String:
SKKRPKPGGG WNTGGSRYPG QGSPGGNRYP PQGGGGWGQP HGGGWGQPHG GGWGQPHGGG WGQPHGGGGW GQGGSHSQWN KPSKPKTNMK HVAGAAAAGA VVGGLGGYML GSAMSRPLIH FGNDYEDRYY RENMYRYPNQ VYYRPVDRYS NQNNFVHDCV NITVKQHTVT TTTKGENFTE TDIKIMERVV EQMCITQYQR ESQAYYQRGA

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number real images: 1621 / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.05 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 154000
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: NONE / Details: Initial model generated in Relion with SGD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8)
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.
Number images used: 82300
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0.8)
Details: The classification 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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