+Open data
-Basic information
Entry | Database: PDB / ID: 6lt4 | ||||||||||||
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Title | AAA+ ATPase, ClpL from Streptococcus pneumoniae: ATPrS-bound | ||||||||||||
Components | ATP-dependent Clp protease, ATP-binding subunit | ||||||||||||
Keywords | CHAPERONE / AAA+ ATPase / ClpL / Streptococcus pneumoniae | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Streptococcus pneumoniae serotype 2 | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||||||||
Authors | Kim, G. / Lee, S.G. / Han, S. / Jung, J. / Jeong, H.S. / Hyun, J.K. / Rhee, D.K. / Kim, H.M. / Lee, S. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: FASEB J / Year: 2020 Title: ClpL is a functionally active tetradecameric AAA+ chaperone, distinct from hexameric/dodecameric ones. Authors: Gyuhee Kim / Seong-Gyu Lee / Seungsu Han / Jaeeun Jung / Hyeong Seop Jeong / Jae-Kyung Hyun / Dong-Kwon Rhee / Ho Min Kim / Sangho Lee / Abstract: AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly ...AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly modulated by their hexameric/dodecameric quaternary structures. Here we report the structural and biochemical characterizations of a tetradecameric AAA+ chaperone, ClpL from Streptococcus pneumoniae. ClpL exists as a tetradecamer in solution in the presence of ATP. The cryo-EM structure of ClpL at 4.5 Å resolution reveals a striking tetradecameric arrangement. Solution structures of ClpL derived from small-angle X-ray scattering data suggest that the tetradecameric ClpL could assume a spiral conformation found in active hexameric/dodecameric AAA+ chaperone structures. Vertical positioning of the middle domain accounts for the head-to-head arrangement of two heptameric rings. Biochemical activity assays with site-directed mutagenesis confirmed the critical roles of residues both in the integrity of the tetradecameric arrangement and activities of ClpL. Non-conserved Q321 and R670 are crucial in the heptameric ring assembly of ClpL. These results establish that ClpL is a functionally active tetradecamer, clearly distinct from hexameric/dodecameric AAA+ chaperones. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lt4.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6lt4.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6lt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lt4_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6lt4_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6lt4_validation.xml.gz | 258.8 KB | Display | |
Data in CIF | 6lt4_validation.cif.gz | 372.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6lt4 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6lt4 | HTTPS FTP |
-Related structure data
Related structure data | 0967MC 0965C 6lsyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 77599.094 Da / Num. of mol.: 14 / Mutation: E193A/E526A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria) Gene: clpL, SPD_0308 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZMB9 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-AGS / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: AAA+ ATPase, chaperone / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 1.1 MDa / Experimental value: YES |
Source (natural) | Organism: Streptococcus pneumoniae (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DARK FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: phenix.real_space_refine / Version: 1.18.2_3874 / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49797 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 118.27 Å2 | ||||||||||||||||||||||||
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