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- EMDB-8317: Wild-type E. coli GroEL -

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Basic information

Entry
Database: EMDB / ID: EMD-8317
TitleWild-type E. coli GroEL
Map datawild-type E. coli GroEL
Sample
  • Complex: Tetradecamer complex of wild-type E. coli GroEL
    • Protein or peptide: GroEL
Function / homology
Function and homology information


phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / metallodipeptidase activity / GroEL-GroES complex / dipeptidase activity / chaperonin ATPase / virion assembly / peptide catabolic process / chaperone cofactor-dependent protein refolding ...phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / metallodipeptidase activity / GroEL-GroES complex / dipeptidase activity / chaperonin ATPase / virion assembly / peptide catabolic process / chaperone cofactor-dependent protein refolding / aminopeptidase activity / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / manganese ion binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / protein homodimerization activity / proteolysis / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
: / Xaa-Pro dipeptidase, N-terminal domain / Xaa-Pro dipeptidase / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatinase/Aminopeptidase P/Spt16, N-terminal / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / Peptidase M24 ...: / Xaa-Pro dipeptidase, N-terminal domain / Xaa-Pro dipeptidase / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatinase/Aminopeptidase P/Spt16, N-terminal / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / 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
Chaperonin GroEL / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsJiang M / Zhang J
CitationJournal: Nat Commun / Year: 2017
Title: GroEL actively stimulates folding of the endogenous substrate protein PepQ.
Authors: Jeremy Weaver / Mengqiu Jiang / Andrew Roth / Jason Puchalla / Junjie Zhang / Hays S Rye /
Abstract: Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key ...Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key predictions of both passive and active models of GroELS-stimulated folding, using the endogenous E. coli metalloprotease PepQ. While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate that slow spontaneous folding of PepQ is not caused by aggregation. Fluorescence measurements suggest that, when folding inside the GroEL-GroES cavity, PepQ populates conformations not observed during spontaneous folding in free solution. Using cryo-electron microscopy, we show that the GroEL C-termini make physical contact with the PepQ folding intermediate and help retain it deep within the GroEL cavity, resulting in reduced compactness of the PepQ monomer. Our findings strongly support an active model of chaperonin-mediated protein folding, where partial unfolding of misfolded intermediates plays a key role.
History
DepositionAug 11, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseJul 12, 2017-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8317.png

Downloads & links

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Map

FileDownload / File: emd_8317.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationwild-type E. coli GroEL
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 80 pix.
= 296. Å		3.7 Å/pix.
x 80 pix.
= 296. Å		3.7 Å/pix.
x 80 pix.
= 296. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.3739938 - 0.5943923
Average (Standard dev.)0.005215778 (±0.036247626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.73.73.7
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z296.000296.000296.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-41
NX/NY/NZ737384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.3740.5940.005

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Supplemental data

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Sample components

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Entire : Tetradecamer complex of wild-type E. coli GroEL

EntireName: Tetradecamer complex of wild-type E. coli GroEL
Components
  • Complex: Tetradecamer complex of wild-type E. coli GroEL
    • Protein or peptide: GroEL

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Supramolecule #1: Tetradecamer complex of wild-type E. coli GroEL

SupramoleculeName: Tetradecamer complex of wild-type E. coli GroEL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: 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 (E. coli)
SequenceString: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK LIAEAMDKVG ...String:
MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK LIAEAMDKVG KEGVITVEDG TGLQDELDVV EGMQFDRGYL SPYFINKPET GAVELESPFI LLADKKISNI REMLPVLEAV AKAGKPLLII AEDVEGEALA TAVVNTIRGI VKVAAVKAPG FGDRRKAMLQ DIATLTGGTV ISEEIGMELE KATLEDLGQA KRVVINKDTT TIIDGVGEEA AIQGRVAQIR QQIEEATSD YDREKLQERV AKLAGGVAVI KVGAATEVEM KEKKARVEDA LHATRAAVEE GVVAGGGVAL IRVASKLADL RGQNEDQNVG IKVALRAMEA PLRQIVLNCG EEPSVVANTV KGGDGNYGYN AATEEYGNMI DMGILDPTKV TRSALQYAAS VAGLMITTEC MVTDLPKNDA ADLGAAGGMG GMGGMGGMM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 19.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4hel

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81442

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