+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8316 | |||||||||
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Title | Wild-type E. coli GroEL bound with PepQ | |||||||||
Map data | wild-type E. coli GroEL bound with PepQ | |||||||||
Sample |
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Function / homology | Function and homology information phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / GroEL-GroES complex / metallodipeptidase activity / dipeptidase activity / chaperonin ATPase / virion assembly / peptide catabolic process / chaperone cofactor-dependent protein refolding ...phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / GroEL-GroES complex / metallodipeptidase activity / dipeptidase activity / chaperonin ATPase / virion assembly / peptide catabolic process / chaperone cofactor-dependent protein refolding / aminopeptidase activity / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / manganese ion binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / protein homodimerization activity / proteolysis / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.3 Å | |||||||||
Authors | Jiang M / Zhang J | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: GroEL actively stimulates folding of the endogenous substrate protein PepQ. Authors: Jeremy Weaver / Mengqiu Jiang / Andrew Roth / Jason Puchalla / Junjie Zhang / Hays S Rye / Abstract: Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key ...Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key predictions of both passive and active models of GroELS-stimulated folding, using the endogenous E. coli metalloprotease PepQ. While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate that slow spontaneous folding of PepQ is not caused by aggregation. Fluorescence measurements suggest that, when folding inside the GroEL-GroES cavity, PepQ populates conformations not observed during spontaneous folding in free solution. Using cryo-electron microscopy, we show that the GroEL C-termini make physical contact with the PepQ folding intermediate and help retain it deep within the GroEL cavity, resulting in reduced compactness of the PepQ monomer. Our findings strongly support an active model of chaperonin-mediated protein folding, where partial unfolding of misfolded intermediates plays a key role. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8316.map.gz | 360.1 KB | EMDB map data format | |
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Header (meta data) | emd-8316-v30.xml emd-8316.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_8316.png | 225.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8316 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8316 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8316.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | wild-type E. coli GroEL bound with PepQ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tetradecamer complex of wild-type E. coli GroEL bound with PepQ
Entire | Name: Tetradecamer complex of wild-type E. coli GroEL bound with PepQ |
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Components |
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-Supramolecule #1: Tetradecamer complex of wild-type E. coli GroEL bound with PepQ
Supramolecule | Name: Tetradecamer complex of wild-type E. coli GroEL bound with PepQ type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Recombinant plasmid: pET21a |
-Macromolecule #1: GroEL
Macromolecule | Name: GroEL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Sequence | String: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK LIAEAMDKVG ...String: MAAKDVKFGN DARVKMLRGV NVLADAVKVT LGPKGRNVVL DKSFGAPTIT KDGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK LIAEAMDKVG KEGVITVEDG TGLQDELDVV EGMQFDRGYL SPYFINKPET GAVELESPFI LLADKKISNI REMLPVLEAV AKAGKPLLII AEDVEGEALA TAVVNTIRGI VKVAAVKAPG FGDRRKAMLQ DIATLTGGTV ISEEIGMELE KATLEDLGQA KRVVINKDTT TIIDGVGEEA AIQGRVAQIR QQIEEATSD YDREKLQERV AKLAGGVAVI KVGAATEVEM KEKKARVEDA LHATRAAVEE GVVAGGGVAL IRVASKLADL RGQNEDQNVG IKVALRAMEA PLRQIVLNCG EEPSVVANTV KGGDGNYGYN AATEEYGNMI DMGILDPTKV TRSALQYAAS VAGLMITTEC MVTDLPKNDA ADLGAAGGMG GMGGMGGMM |
-Macromolecule #2: PepQ
Macromolecule | Name: PepQ / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MESLASLYKN HIATLQERTR DALARFKLDA LLIHSGELFN VFLDDHPYPF KVNPQFKAWV PVTQVPNCWL LVDGVNKPKL WFYLPVDYWH NVEPLPTSFW TEDVEVIALP KADGIGSLLP AARGNIGYIG PVPERALQLG IEASNINPKG VIDYLHYYRS FKTEYELACM ...String: MESLASLYKN HIATLQERTR DALARFKLDA LLIHSGELFN VFLDDHPYPF KVNPQFKAWV PVTQVPNCWL LVDGVNKPKL WFYLPVDYWH NVEPLPTSFW TEDVEVIALP KADGIGSLLP AARGNIGYIG PVPERALQLG IEASNINPKG VIDYLHYYRS FKTEYELACM REAQKMAVNG HRAAEEAFRS GMSEFDINIA YLTATGHRDT DEPYSNIVAL NEHAAVLHYT KLDHQAPEEM RSFLLDAGAE YNGYAADLTR TWPAKSDNDY AQLVKDVNDE QLALIATMKA GVSYVDYHIQ FHQRIAKLLR KHQIITDMSE EAMVENDLTG PFMPHGIGHP LGLQVHDVAG FMQDDSGTHL AAPAKYPYLR CTRILQPGMV LTIEPGIYFI ESLLAPWREG QFSKHFNWQK IEALKPFGGI RIEDNVVIHE NNVENMTRDL KLA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 19.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: RANDOM ASSIGNMENT |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31905 |