+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31560 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of apo BsClpP at pH 6.5 | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
| |||||||||||||||||||||
Function / homology | Function and homology information endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / identical protein binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||
Authors | Kim L / Lee B-G / Kim MK / Kwon DH / Kim H / Brotz-Oesterhelt H / Roh S-H / Song HK | |||||||||||||||||||||
Funding support | Korea, Republic Of, 6 items
| |||||||||||||||||||||
Citation | Journal: EMBO J / Year: 2022 Title: Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis. Authors: Leehyeon Kim / Byung-Gil Lee / Minki Kim / Min Kyung Kim / Do Hoon Kwon / Hyunmin Kim / Heike Brötz-Oesterhelt / Soung-Hun Roh / Hyun Kyu Song / Abstract: The ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. ...The ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause the dysregulation and activation of ClpP without ATPases and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed its structural details, conformational changes, and activation mechanism. Although product release through side exit pores has been proposed, the detailed driving force for product release remains elusive. Herein, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures of BsClpP revealed various conformational states under different pH conditions. To understand the conformational change required for product release, we investigated the relationship between substrate hydrolysis and the pH-lowering process. The production of hydrolyzed peptides from acidic and basic substrates by proteinase K and BsClpP lowered the pH values. Our data, together with those of previous findings, provide insight into the molecular mechanism of product release by the ClpP self-compartmentalizing protease. | |||||||||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_31560.map.gz | 117.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-31560-v30.xml emd-31560.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
Images | emd_31560.png | 118.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31560 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31560 | HTTPS FTP |
-Related structure data
Related structure data | 7feqMC 7fepC 7ferC 7fesC 7p80C 7p81C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_31560.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.675 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : Cryo-EM structure of apo BsClpP at pH 6.5
Entire | Name: Cryo-EM structure of apo BsClpP at pH 6.5 |
---|---|
Components |
|
-Supramolecule #1: Cryo-EM structure of apo BsClpP at pH 6.5
Supramolecule | Name: Cryo-EM structure of apo BsClpP at pH 6.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Bacillus subtilis (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: ATP-dependent Clp protease proteolytic subunit
Macromolecule | Name: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: endopeptidase Clp |
---|---|
Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 22.404664 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: NLIPTVIEQT NRGERAYDIY SRLLKDRIIM LGSAIDDNVA NSIVSQLLFL AAEDPEKEIS LYINSPGGSI TAGMAIYDTM QFIKPKVST ICIGMAASMG AFLLAAGEKG KRYALPNSEV MIHQPLGGAQ GQATEIEIAA KRILLLRDKL NKVLAERTGQ P LEVIERDT ...String: NLIPTVIEQT NRGERAYDIY SRLLKDRIIM LGSAIDDNVA NSIVSQLLFL AAEDPEKEIS LYINSPGGSI TAGMAIYDTM QFIKPKVST ICIGMAASMG AFLLAAGEKG KRYALPNSEV MIHQPLGGAQ GQATEIEIAA KRILLLRDKL NKVLAERTGQ P LEVIERDT DRDNFKSAEE ALEYGLIDKI LTHTEDKKHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 Component:
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 108389 |
---|---|
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 78413 |