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- EMDB-8318: Mutant E. coli GroEL (C-terminal truncated) bound with PepQ -

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Basic information

Entry
Database: EMDB / ID: 8318
TitleMutant E. coli GroEL (C-terminal truncated) bound with PepQ
Map datamutant E. coli GroEL (C-terminal truncated) bound with PepQ
SampleTetradecamer complex of C-terminal truncated mutant E. coli GroEL bound with PepQ:
GroEL / PepQ
Function / homologyGroEL-like equatorial domain superfamily / Creatinase/Aminopeptidase P/Spt16, N-terminal / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / Xaa-Pro dipeptidase / Chaperonin Cpn60, conserved site / Chaperonin Cpn60/TCP-1 family / Chaperonin Cpn60 / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Peptidase M24 ...GroEL-like equatorial domain superfamily / Creatinase/Aminopeptidase P/Spt16, N-terminal / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / Xaa-Pro dipeptidase / Chaperonin Cpn60, conserved site / Chaperonin Cpn60/TCP-1 family / Chaperonin Cpn60 / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Peptidase M24 / Creatinase/aminopeptidase-like / TCP-1/cpn60 chaperonin family / Aminopeptidase P and proline dipeptidase signature. / Chaperonins cpn60 signature. / Metallopeptidase family M24 / phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / metallodipeptidase activity / GroEL-GroES complex / dipeptidase activity / 'de novo' protein folding / peptide catabolic process / chaperone cofactor-dependent protein refolding / virion assembly / protein folding / response to radiation / unfolded protein binding / response to heat / manganese ion binding / protein refolding / ATPase activity / cell cycle / cell division / magnesium ion binding / membrane / ATP binding / identical protein binding / cytosol / 60 kDa chaperonin / Xaa-Pro dipeptidase
Function and homology information
SourceEscherichia coli (E. coli) / Escherichia (bacteria)
Methodsingle particle reconstruction / cryo EM / 8.3 Å resolution
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
DateDeposition: Aug 10, 2016 / Header (metadata) release: Oct 5, 2016 / Map release: Jul 12, 2017 / Last update: Jul 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8318.map.gz (map file in CCP4 format, 2049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
3.7 Å/pix.
= 296. Å
80 pix
3.7 Å/pix.
= 296. Å
80 pix
3.7 Å/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
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.19831309 - 0.47725803
Average (Standard dev.)0.0053920974 (0.030527208)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin0.00.00.0
Limit79.079.079.0
Spacing808080
CellA=B=C: 296.0 Å
α=β=γ: 90.0 deg.

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-0.1980.4770.005

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Supplemental data

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Sample components

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Entire Tetradecamer complex of C-terminal truncated mutant E. coli GroEL...

EntireName: Tetradecamer complex of C-terminal truncated mutant E. coli GroEL bound with PepQ
Number of components: 3

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Component #1: protein, Tetradecamer complex of C-terminal truncated mutant E. c...

ProteinName: Tetradecamer complex of C-terminal truncated mutant E. coli GroEL bound with PepQ
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Vector: pET21a

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Component #2: protein, GroEL

ProteinName: GroEL / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, PepQ

ProteinName: PepQ / Recombinant expression: No
SourceSpecies: Escherichia (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 19 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 26392
3D reconstructionResolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF

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