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Yorodumi- PDB-4d2u: Negative-stain electron microscopy of E. coli ClpB (BAP form boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d2u | ||||||
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Title | Negative-stain electron microscopy of E. coli ClpB (BAP form bound to ClpP) | ||||||
Components | CHAPERONE PROTEIN CLPB | ||||||
Keywords | CHAPERONE / DISAGGREGASE / WILD TYPE / COILED-COIL DOMAIN | ||||||
Function / homology | Function and homology information cellular response to heat / response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 17 Å | ||||||
Authors | Carroni, M. / Kummer, E. / Oguchi, Y. / Clare, D.K. / Wendler, P. / Sinning, I. / Kopp, J. / Mogk, A. / Bukau, B. / Saibil, H.R. | ||||||
Citation | Journal: Elife / Year: 2014 Title: Head-to-tail interactions of the coiled-coil domains regulate ClpB activity and cooperation with Hsp70 in protein disaggregation. Authors: Marta Carroni / Eva Kummer / Yuki Oguchi / Petra Wendler / Daniel K Clare / Irmgard Sinning / Jürgen Kopp / Axel Mogk / Bernd Bukau / Helen R Saibil / Abstract: The hexameric AAA+ chaperone ClpB reactivates aggregated proteins in cooperation with the Hsp70 system. Essential for disaggregation, the ClpB middle domain (MD) is a coiled-coil propeller that binds ...The hexameric AAA+ chaperone ClpB reactivates aggregated proteins in cooperation with the Hsp70 system. Essential for disaggregation, the ClpB middle domain (MD) is a coiled-coil propeller that binds Hsp70. Although the ClpB subunit structure is known, positioning of the MD in the hexamer and its mechanism of action are unclear. We obtained electron microscopy (EM) structures of the BAP variant of ClpB that binds the protease ClpP, clearly revealing MD density on the surface of the ClpB ring. Mutant analysis and asymmetric reconstructions show that MDs adopt diverse positions in a single ClpB hexamer. Adjacent, horizontally oriented MDs form head-to-tail contacts and repress ClpB activity by preventing Hsp70 interaction. Tilting of the MD breaks this contact, allowing Hsp70 binding, and releasing the contact in adjacent subunits. Our data suggest a wavelike activation of ClpB subunits around the ring.DOI: http://dx.doi.org/10.7554/eLife.02481.001. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4d2u.cif.gz | 573.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d2u.ent.gz | 336.9 KB | Display | PDB format |
PDBx/mmJSON format | 4d2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d2u_validation.pdf.gz | 691.8 KB | Display | wwPDB validaton report |
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Full document | 4d2u_full_validation.pdf.gz | 697.5 KB | Display | |
Data in XML | 4d2u_validation.xml.gz | 92.7 KB | Display | |
Data in CIF | 4d2u_validation.cif.gz | 161.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/4d2u ftp://data.pdbj.org/pub/pdb/validation_reports/d2/4d2u | HTTPS FTP |
-Related structure data
Related structure data | 2557MC 2555C 2556C 2558C 2559C 2560C 2561C 2562C 2563C 4ciuC 4d2qC 4d2xC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 96835.086 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: THE PROTEIN IS ENGINEERED TO BIND TO CLPP. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PDS56 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC4100 / References: UniProt: P63284 |
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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: BAP FORM OF CLPB WITH ATPGS / Type: COMPLEX |
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Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO |
EM staining | Type: NEGATIVE / Material: uranyl acetate |
Specimen support | Details: CARBON |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Mar 7, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 68000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm / Cs: 2 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 220 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: PHASE FLIPPING ENTIRE FRAME | ||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||
3D reconstruction | Method: ANGULAR RECONSTITUTION AND PROJECTION MATCHING / Resolution: 17 Å / Num. of particles: 11568 Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2557. (DEPOSITION ID: 12240). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Details: METHOD--RIGID BODY | ||||||||||||
Refinement | Highest resolution: 17 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 17 Å
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