+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19687 | |||||||||
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Title | GroEL with bound GroTAC peptide | |||||||||
Map data | GroEL with bound GroTAC peptide EM map | |||||||||
Sample |
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Keywords | GroEL / GroTAC / PROTAC / degrader / complex / CHAPERONE | |||||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / 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 / chaperone cofactor-dependent protein refolding / 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 / membrane / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.45 Å | |||||||||
Authors | Wroblewski K / Izert-Nowakowska MA / Goral TK / Klimecka MM / Kmiecik S / Gorna MW | |||||||||
Funding support | Poland, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19687.map.gz | 566.9 MB | EMDB map data format | |
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Header (meta data) | emd-19687-v30.xml emd-19687.xml | 24 KB 24 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19687_fsc.xml | 17.8 KB | Display | FSC data file |
Images | emd_19687.png | 139.7 KB | ||
Masks | emd_19687_msk_1.map | 600.7 MB | Mask map | |
Filedesc metadata | emd-19687.cif.gz | 7.2 KB | ||
Others | emd_19687_additional_1.map.gz emd_19687_half_map_1.map.gz emd_19687_half_map_2.map.gz | 290.6 MB 556.6 MB 556.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19687 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19687 | HTTPS FTP |
-Related structure data
Related structure data | 8s32MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19687.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_19687_msk_1.map | ||||||||||||
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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 |
-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: Escherichia coli (E. coli) |
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: Escherichia coli (E. coli) |
-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: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 57.391711 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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 |
-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: |