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- PDB-6hdd: OBP chaperonin in the nucleotide-free state -

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Basic information

Entry
Database: PDB / ID: 6hdd
TitleOBP chaperonin in the nucleotide-free state
ComponentsPutative chaperonin GroEL
KeywordsCHAPERONE / chaperonin / nucleotide-free
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding
Similarity search - Function
Chaperonin Cpn60/GroEL / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Putative chaperonin GroEL
Similarity search - Component
Biological speciesPseudomonas phage OBP (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsSemenyuk, P.I. / Stanishneva-Konovalova, T.B. / Sokolova, O.S.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-04-00605 Russian Federation
Russian Foundation for Basic Research18-04-01281 Russian Federation
CitationJournal: J Struct Biol / Year: 2020
Title: Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin.
Authors: Tatiana B Stanishneva-Konovalova / Pavel I Semenyuk / Lidia P Kurochkina / Evgeny B Pichkur / Alexander L Vasilyev / Mikhail V Kovalchuk / Mikhail P Kirpichnikov / Olga S Sokolova /
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 ...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.
History
DepositionAug 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Putative chaperonin GroEL
B: Putative chaperonin GroEL
C: Putative chaperonin GroEL
D: Putative chaperonin GroEL
E: Putative chaperonin GroEL
F: Putative chaperonin GroEL
G: Putative chaperonin GroEL


Theoretical massNumber of molelcules
Total (without water)400,8187
Polymers400,8187
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21050 Å2
ΔGint-99 kcal/mol
Surface area162960 Å2
MethodPISA

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Components

#1: Protein
Putative chaperonin GroEL


Mass: 57259.703 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage OBP (virus) / Gene: OBP_246 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9I9H9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: OBP chaperonin in the nucleotide-free state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.42 MDa / Experimental value: YES
Source (natural)Organism: Pseudomonas phage OBP (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 100 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127180 / Symmetry type: POINT

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