+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15940 | |||||||||
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Title | CryoEM structure of GroEL-ADP.BeF3-Rubisco. | |||||||||
Map data | CryoEM reconstruction of GroEL-ADP.BeFx-Rubisco. | |||||||||
Sample |
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Keywords | GroEL / nucleotide / Rubisco / Chameleon / 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) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Gardner S / Saibil HR | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structural basis of substrate progression through the bacterial chaperonin cycle. Authors: Scott Gardner / Michele C Darrow / Natalya Lukoyanova / Konstantinos Thalassinos / Helen R Saibil / Abstract: The bacterial chaperonin GroEL-GroES promotes protein folding through ATP-regulated cycles of substrate protein binding, encapsulation, and release. Here, we have used cryoEM to determine structures ...The bacterial chaperonin GroEL-GroES promotes protein folding through ATP-regulated cycles of substrate protein binding, encapsulation, and release. Here, we have used cryoEM to determine structures of GroEL, GroEL-ADP·BeF, and GroEL-ADP·AlF-GroES all complexed with the model substrate Rubisco. Our structures provide a series of snapshots that show how the conformation and interactions of non-native Rubisco change as it proceeds through the GroEL-GroES reaction cycle. We observe specific charged and hydrophobic GroEL residues forming strong initial contacts with non-native Rubisco. Binding of ATP or ADP·BeF to GroEL-Rubisco results in the formation of an intermediate GroEL complex displaying striking asymmetry in the ATP/ADP·BeF-bound ring. In this ring, four GroEL subunits bind Rubisco and the other three are in the GroES-accepting conformation, suggesting how GroEL can recruit GroES without releasing bound substrate. Our cryoEM structures of stalled GroEL-ADP·AlF-Rubisco-GroES complexes show Rubisco folding intermediates interacting with GroEL-GroES via different sets of residues. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15940.map.gz | 187.3 MB | EMDB map data format | |
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Header (meta data) | emd-15940-v30.xml emd-15940.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15940_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_15940.png | 100.4 KB | ||
Masks | emd_15940_msk_1.map | 343 MB | Mask map | |
Filedesc metadata | emd-15940.cif.gz | 6 KB | ||
Others | emd_15940_half_map_1.map.gz emd_15940_half_map_2.map.gz | 274 MB 273.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15940 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15940 | HTTPS FTP |
-Related structure data
Related structure data | 8ba8MC 8ba7C 8ba9C 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_15940.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM reconstruction of GroEL-ADP.BeFx-Rubisco. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2194 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15940_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: CryoEM reconstruction of GroEL-ADP.BeFx-Rubisco.
File | emd_15940_half_map_1.map | ||||||||||||
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Annotation | CryoEM reconstruction of GroEL-ADP.BeFx-Rubisco. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM reconstruction of GroEL-ADP.BeFx-Rubisco.
File | emd_15940_half_map_2.map | ||||||||||||
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Annotation | CryoEM reconstruction of GroEL-ADP.BeFx-Rubisco. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GroEL-ADP.BeFx-Rubisco
Entire | Name: GroEL-ADP.BeFx-Rubisco |
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Components |
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-Supramolecule #1: GroEL-ADP.BeFx-Rubisco
Supramolecule | Name: GroEL-ADP.BeFx-Rubisco / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 802 KDa |
-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 K-12 (bacteria) / Strain: K-12 |
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: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 2 / Number of copies: 7 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 14 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 14 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 14 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 7 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.7 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: SPOTITON Details: The grid was prepared using a chameleon (SPT Labtech).. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4000000000000001 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Average electron dose: 40.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |