4A8A | pdb_00004a8a

Asymmetric cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozyme


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Newly Folded Substrates Inside the Molecular Cage of the Htra Chaperone Degq

Malet, H.Canellas, F.Sawa, J.Yan, J.Thalassinos, K.Ehrmann, M.Clausen, T.Saibil, H.R.

(2012) Nat Struct Mol Biol 19: 152

  • DOI: https://doi.org/10.1038/nsmb.2210
  • Primary Citation Related Structures: 
    4A8A, 4A8B, 4A8C, 4A8D, 4A9G

  • PubMed Abstract: 

    The HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA proteins are well characterized, their chaperone activity remains poorly understood. Here we describe cryo-EM structures of Escherichia coli DegQ in its 12- and 24-mer states in complex with model substrates, providing a structural model of HtrA chaperone action. Up to six lysozyme substrates bind inside the DegQ 12-mer cage and are visualized in a close-to-native state. An asymmetric reconstruction reveals the binding of a well-ordered lysozyme to four DegQ protomers. DegQ PDZ domains are located adjacent to substrate density and their presence is required for chaperone activity. The substrate-interacting regions appear conserved in 12- and 24-mer cages, suggesting a common mechanism of chaperone function.


  • Organizational Affiliation
    • Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, London, UK.

Macromolecule Content 

  • Total Structure Weight: 560.84 kDa 
  • Atom Count: 4,749 
  • Modeled Residue Count: 4,749 
  • Deposited Residue Count: 5,361 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
436Escherichia coli K-12Mutation(s): 1 
EC: 3.4.21.107
UniProt
Find proteins for P39099 (Escherichia coli (strain K12))
Explore P39099 
Go to UniProtKB:  P39099
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39099
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LYSOZYME C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMAGIC5
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Other
  • Version 1.2: 2012-02-15
    Changes: Other
  • Version 1.3: 2017-08-23
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Refinement description