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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | GroEL with bound GroTAC peptide | |||||||||
![]() | GroEL with bound GroTAC peptide EM map | |||||||||
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![]() | GroEL / GroTAC / PROTAC / degrader / complex / CHAPERONE | |||||||||
Function / homology | ![]() 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 / isomerase activity / ATP-dependent protein folding chaperone / response to radiation ...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 / 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 / protein folding / positive regulation of T cell activation / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.45 Å | |||||||||
![]() | Wroblewski K / Izert-Nowakowska MA / Goral TK / Klimecka MM / Kmiecik S / Gorna MW | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 566.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24 KB 24 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.8 KB | Display | ![]() |
Images | ![]() | 139.7 KB | ||
Masks | ![]() | 600.7 MB | ![]() | |
Filedesc metadata | ![]() | 7.2 KB | ||
Others | ![]() ![]() ![]() | 290.6 MB 556.6 MB 556.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 36.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s32MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | GroEL with bound GroTAC peptide EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.5878 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_19687_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: GroEL with bound GroTAC peptide EM half map B
File | emd_19687_half_map_1.map | ||||||||||||
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Annotation | GroEL with bound GroTAC peptide EM half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: GroEL with bound GroTAC peptide EM half map A
File | emd_19687_half_map_2.map | ||||||||||||
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Annotation | GroEL with bound GroTAC peptide EM half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : A complex of GroEL with GroTAC peptide
Entire | Name: A complex of GroEL with GroTAC peptide |
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Components |
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-Supramolecule #1: A complex of GroEL with GroTAC peptide
Supramolecule | Name: A complex of GroEL with GroTAC peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 4 kDa/nm |
-Supramolecule #2: GroEL
Supramolecule | Name: GroEL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: GroTAC
Supramolecule | Name: GroTAC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Chaperonin GroEL
Macromolecule | Name: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: chaperonin ATPase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 57.391711 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: GroTAC
Macromolecule | Name: GroTAC / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.176783 KDa |
Sequence | String: CYRGGRPALR VVK(UNK)(UNK)(UNK)SWMT TPWGFHLP |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
Details: ATP was added to the sample immediately before disposing on a grid | |||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film 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 beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | Chain - 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). |
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Details | The 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). |
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: 0.88 |
Output model | ![]() PDB-8s32: |