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- PDB-4ciu: Crystal structure of E. coli ClpB -

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Basic information

Entry
Database: PDB / ID: 4ciu
TitleCrystal structure of E. coli ClpB
ComponentsCHAPERONE PROTEIN CLPB
KeywordsCHAPERONE / AAA+ / ATPASE
Function / homology
Function and homology information


cellular response to heat / response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / : / Clp, repeat (R) domain ...Chaperonin ClpB / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperone protein ClpB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsKopp, J. / Sinning, I. / Bukau, B. / Kummer, E. / Mogk, A.
CitationJournal: 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
DepositionDec 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHAPERONE PROTEIN CLPB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6893
Polymers82,8341
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.329, 127.329, 119.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein CHAPERONE PROTEIN CLPB / HEAT SHOCK PROTEIN F84.1


Mass: 82834.430 Da / Num. of mol.: 1 / Fragment: RESIDUES 143-857 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PDS56-CLPB-DN-E279A/E432A/E678A
Production host: ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
Variant (production host): DELTACLPB / References: UniProt: P63284
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growTemperature: 291 K
Details: 1.5 M AMSO4, 0.4 % PEG 400, 0.1 M HEPES PH 7.5, 22 % GLYCEROL AT 291 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.5→81.2 Å / Num. obs: 14024 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 14.5 % / Biso Wilson estimate: 121 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.8
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.5→36.8 Å / SU ML: 0.4 / σ(F): 1.37 / Phase error: 28.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.247 695 5 %
Rwork0.224 --
obs0.2252 13970 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL PHENIX 1.8
Displacement parametersBiso mean: 91.1 Å2
Refinement stepCycle: LAST / Resolution: 3.5→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 54 0 5257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.770.29941310.25992633X-RAY DIFFRACTION100
3.77-4.1490.31621430.2462653X-RAY DIFFRACTION100
4.149-4.74820.24521430.22172648X-RAY DIFFRACTION100
4.7482-5.97810.25991410.24872656X-RAY DIFFRACTION100
5.9781-36.75870.2131370.20072685X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1382-2.39310.83741.983-0.10393.17890.1299-0.83-1.1070.0398-0.1240.95410.7516-0.99170.08750.7156-0.30790.03320.8577-0.09740.6773-3.762832.046411.6647
2-1.20422.02091.51921.96892.30423.31860.25970.1320.338-0.0009-0.107-0.28370.08280.4718-0.07040.57630.2108-0.08880.6217-0.09730.708529.068943.016511.2267
35.3481-4.36291.60475.97-2.41112.54160.46290.1978-0.9139-1.34840.00821.18190.128-0.4486-0.32640.6786-0.135-0.18330.36110.01310.440727.367811.2061-19.6137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 159 THROUGH 387 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 388 THROUGH 589 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 590 THROUGH 858 )

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