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- EMDB-19687: GroEL with bound GroTAC peptide -

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Basic information

Entry
Database: EMDB / ID: EMD-19687
TitleGroEL with bound GroTAC peptide
Map dataGroEL with bound GroTAC peptide EM map
Sample
  • Complex: A complex of GroEL with GroTAC peptide
    • Complex: GroEL
      • Protein or peptide: Chaperonin GroEL
    • Complex: GroTAC
      • Protein or peptide: GroTAC
KeywordsGroEL / GroTAC / PROTAC / degrader / complex / CHAPERONE
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 (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsWroblewski K / Izert-Nowakowska MA / Goral TK / Klimecka MM / Kmiecik S / Gorna MW
Funding support Poland, 2 items
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-5EC1 Poland
Polish National Science Centre2020/39/B/NZ2/01301 Poland
CitationJournal: To Be Published
Title: Depletion of essential GroEL protein in Escherichia coli using Clp-Interacting Peptidic Protein Erasers (CLIPPERs)
Authors: Izert-Nowakowska MA / Klimecka MM / Antosiewicz A / Wroblewski K / Bandyra KJ / Goral TK / Kmiecik S / Serwa RA / Gorna MW
History
DepositionFeb 19, 2024-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19687.png

Downloads & links

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Map

FileDownload / File: emd_19687.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGroEL with bound GroTAC peptide EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.59 Å/pix.
x 540 pix.
= 317.412 Å		0.59 Å/pix.
x 540 pix.
= 317.412 Å		0.59 Å/pix.
x 540 pix.
= 317.412 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.059
Minimum - Maximum-0.3979776 - 0.9389116
Average (Standard dev.)-0.0010603229 (±0.02579084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 317.41202 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19687_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_19687_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GroEL with bound GroTAC peptide EM half map B

Fileemd_19687_half_map_1.map
AnnotationGroEL with bound GroTAC peptide EM half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GroEL with bound GroTAC peptide EM half map A

Fileemd_19687_half_map_2.map
AnnotationGroEL with bound GroTAC peptide EM half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A complex of GroEL with GroTAC peptide

EntireName: A complex of GroEL with GroTAC peptide
Components
  • Complex: A complex of GroEL with GroTAC peptide
    • Complex: GroEL
      • Protein or peptide: Chaperonin GroEL
    • Complex: GroTAC
      • Protein or peptide: GroTAC

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Supramolecule #1: A complex of GroEL with GroTAC peptide

SupramoleculeName: A complex of GroEL with GroTAC peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 4 kDa/nm

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Supramolecule #2: GroEL

SupramoleculeName: GroEL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: GroTAC

SupramoleculeName: GroTAC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Chaperonin GroEL

MacromoleculeName: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: chaperonin ATPase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 57.391711 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGT TTATVLAQAI ITEGLKAVAA GMNPMDLKRG IDKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG K LIAEAMDK ...String:
MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGT TTATVLAQAI ITEGLKAVAA GMNPMDLKRG IDKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG K LIAEAMDK VGKEGVITVE DGTGLQDELD VVEGMQFDRG YLSPYFINKP ETGAVELESP FILLADKKIS NIREMLPVLE AV AKAGKPL LIIAEDVEGE ALATLVVNTM RGIVKVAAVK APGFGDRRKA MLQDIATLTG GTVISEEIGM ELEKATLEDL GQA KRVVIN KDTTTIIDGV GEEAAIQGRV AQIRQQIEEA TSDYDREKLQ ERVAKLAGGV AVIKVGAATE VEMKEKKARV EDAL HATRA AVEEGVVAGG GVALIRVASK LADLRGQNED QNVGIKVALR AMEAPLRQIV LNCGEEPSVV ANTVKGGDGN YGYNA ATEE YGNMIDMGIL DPTKVTRSAL QYAASVAGLM ITTECMVTDL PKNDAADLGA AGGMGGMGGM GGMM

UniProtKB: Chaperonin GroEL

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Macromolecule #2: GroTAC

MacromoleculeName: GroTAC / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.176783 KDa
SequenceString:
CYRGGRPALR VVK(UNK)(UNK)(UNK)SWMT TPWGFHLP

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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

Concentration4 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMHEPES pH 8.0
200.0 mMpotassium chlorideKCl
5.0 mMmagnesium chlorideMgCl2
1.0 mMATP

Details: ATP was added to the sample immediately before disposing on a grid
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 4672 / Average exposure time: 16.67 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 240000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 350383
Startup modelType of model: NONE
Final reconstructionNumber classes used: 40 / Applied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 203031
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final 3D classificationNumber classes: 40 / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model
Details: The CA model was obtained by ModelAngelo (1.09) and then subsequently rebuilt to full-atom by cg2all (1.5).
DetailsThe C-alpha model was obtained by two rounds of ab initio modeling using machine learning-based ModelAngelo 1.09 software. The incorrectly assigned GroEL residues were then manually corrected. The C-alpha trace of the GroTAC peptide was initially constructed by ModelAngelo, with residue identities suggested through a comparison to the 1MNF PDB structure. The reconstruction to full-atom was performed using cg2all 1.5 software. The first stage of refinement was done in Coot (0.9.8.5). The final refinement stage involved two rounds of phenix.real_space_refine (Phenix 1.21.5207).
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: 0.88
Output model

PDB-8s32:
GroEL with bound GroTAC peptide

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