6HDD

OBP chaperonin in the nucleotide-free state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin.

Stanishneva-Konovalova, T.B.Semenyuk, P.I.Kurochkina, L.P.Pichkur, E.B.Vasilyev, A.L.Kovalchuk, M.V.Kirpichnikov, M.P.Sokolova, O.S.

(2020) J Struct Biol 209: 107439-107439

  • DOI: 10.1016/j.jsb.2019.107439
  • Primary Citation of Related Structures:  
    6HDD

  • PubMed Abstract: 
  • Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants) ...

    Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both of these groups do not include recently discovered viral chaperonins. Here, we solved the symmetry-free cryo-EM structures of a single-ring chaperonin encoded by the gene 246 of bacteriophage OBP Pseudomonas fluorescens, in the nucleotide-free, ATPγS-, and ADP-bound states, with resolutions of 4.3 Å, 5.0 Å, and 6 Å, respectively. The structure of OBP chaperonin reveals a unique subunit arrangement, with three pairs of subunits and one unpaired subunit. Each pair combines subunits in two possible conformations, differing in nucleotide-binding affinity. The binding of nucleotides results in the increase of subunits' conformational variability. Due to its unique structural and functional features, OBP chaperonin can represent a new group.


    Organizational Affiliation

    Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1, Bld 12, Moscow 119991, Russia. Electronic address: sokolova@mail.bio.msu.ru.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative chaperonin GroEL
A, B, C, D, E, F, G
A, B, C, D, E, F, G
515Pseudomonas phage OBPMutation(s): 0 
Gene Names: OBP_246
UniProt
Find proteins for G9I9H9 (Pseudomonas phage OBP)
Explore G9I9H9 
Go to UniProtKB:  G9I9H9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9I9H9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation19-04-00605
Russian Foundation for Basic ResearchRussian Federation18-04-01281

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Database references
  • Version 1.2: 2020-03-11
    Changes: Database references