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- EMDB-17535: Cryo-EM structure of a C7-symmetrical GroEL14-GroES7 complex in p... -

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Basic information

Entry
Database: EMDB / ID: EMD-17535
TitleCryo-EM structure of a C7-symmetrical GroEL14-GroES7 complex in presence of ADP-BeFx
Map data
Sample
  • Complex: GroEL14-GroES7
    • Protein or peptide: GroEL
    • Protein or peptide: GroES
KeywordsChaperonin / Folding cage / proteostasis / heat shock / ATPase / CHAPERONE
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone ...GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / positive regulation of T cell activation / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / 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 / GroES-like superfamily
Similarity search - Domain/homology
Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsWagner J / Beck F / Bracher A / Caravajal AI / Wan W / Bohn S / Koerner R / Baumeister W / Fernandez-Busnadiego R / Hartl FU
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2024
Title: Visualizing chaperonin function in situ by cryo-electron tomography
Authors: Wagner J / Caravajal AI / Beck F / Bracher A / Wan W / Bohn S / Koerner R / Baumeister W / Fernandez-Busnadiego R / Hartl FU
History
DepositionMay 30, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17535.png

Downloads & links

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Map

FileDownload / File: emd_17535.map.gz / Format: CCP4 / Size: 437.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 486 pix.
= 408.24 Å		0.84 Å/pix.
x 486 pix.
= 408.24 Å		0.84 Å/pix.
x 486 pix.
= 408.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.623
Minimum - Maximum-2.14071 - 7.3425484
Average (Standard dev.)0.0045393384 (±0.13335074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions486486486
Spacing486486486
CellA=B=C: 408.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17535_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_17535_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17535_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : GroEL14-GroES7

EntireName: GroEL14-GroES7
Components
  • Complex: GroEL14-GroES7
    • Protein or peptide: GroEL
    • Protein or peptide: GroES

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Supramolecule #1: GroEL14-GroES7

SupramoleculeName: GroEL14-GroES7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: with bound ADP-BeF3 Mg2+ K+
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 950 KDa

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG KLIAEAMDKV ...String:
AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG KLIAEAMDKV GKEGVITVED G TGLQDELD VVEGMQFDRG YLSPYFINKP ETGAVELESP FILLADKKIS NIREMLPVLE AV AKAGKPL LIIAEDVEGE ALATLVVNTM RGIVKVAAVK APGFGDRRKA MLQDIATLTG GTV ISEEIG MELEKATLED LGQAKRVVIN KDTTTIIDGV GEEAAIQGRV AQIRQQIEEA TSDY DREKL QERVAKLAGG VAVIKVGAAT EVEMKEKKAR VEDALHATRA AVEEGVVAGG GVALI RVAS KLADLRGQNE DQNVGIKVAL RAMEAPLRQI VLNCGEEPSV VANTVKGGDG NYGYNA ATE EYGNMIDMGI LDPTKVTRSA LQYAASVAGL MITTECMVTD LPKNDAADLG AAGGMGG MG GMGGMM

UniProtKB: Chaperonin GroEL

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Macromolecule #2: GroES

MacromoleculeName: GroES / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MNIRPLHDRV IVKRKEVETK SAGGIVLTGS AAAKSTRGEV LAVGNGRILE NGEVKPLDVK VGDIVIFND GYGVKSEKID NEEVLIMSES DILAIVEA

UniProtKB: Co-chaperonin GroES

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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

Concentration0.95 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC7H15NO4SMOPS
200.0 mMKClPotassium chloride
10.0 mMMgCl2Magnesium chloride
5.0 mMC4H10O2S2Dithiothreitol
30.0 mMNaFSodium fluoride
5.0 mMBeSO4Beryllium sulfate
1.0 mMC10H16N5O13P3Adenosine triphosphate
GridSupport film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 5.9 mM n-octyl-beta-D-glucopyranoside were added before vitrification.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 293975
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1sx3

source_name: PDB, initial_model_type: experimental model

5opx

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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