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- PDB-7pbx: Cryo-EM structure of the GroEL-GroES complex with ADP bound to bo... -

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Basic information

Entry
Database: PDB / ID: 7pbx
TitleCryo-EM structure of the GroEL-GroES complex with ADP bound to both rings ("tight" conformation).
Components
  • 10 kDa chaperonin
  • 60 kDa chaperonin
KeywordsCHAPERONE / cryo-EM / chaperonin / GroEL / GroEL-GroES
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein-folding chaperone binding / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / 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 / GroES-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsPichkur, E.B. / Stanishneva-Konovalova, T.B.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20055 Russian Federation
CitationJournal: Sci Rep / Year: 2021
Title: Novel cryo-EM structure of an ADP-bound GroEL-GroES complex.
Authors: Sofia S Kudryavtseva / Evgeny B Pichkur / Igor A Yaroshevich / Aleksandra A Mamchur / Irina S Panina / Andrei V Moiseenko / Olga S Sokolova / Vladimir I Muronetz / Tatiana B Stanishneva-Konovalova /
Abstract: The GroEL-GroES chaperonin complex is a bacterial protein folding system, functioning in an ATP-dependent manner. Upon ATP binding and hydrolysis, it undergoes multiple stages linked to substrate ...The GroEL-GroES chaperonin complex is a bacterial protein folding system, functioning in an ATP-dependent manner. Upon ATP binding and hydrolysis, it undergoes multiple stages linked to substrate protein binding, folding and release. Structural methods helped to reveal several conformational states and provide more information about the chaperonin functional cycle. Here, using cryo-EM we resolved two nucleotide-bound structures of the bullet-shaped GroEL-GroES complex at 3.4 Å resolution. The main difference between them is the relative orientation of their apical domains. Both structures contain nucleotides in cis and trans GroEL rings; in contrast to previously reported bullet-shaped complexes where nucleotides were only present in the cis ring. Our results suggest that the bound nucleotides correspond to ADP, and that such a state appears at low ATP:ADP ratios.
History
DepositionAug 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
Ac: 60 kDa chaperonin
Ad: 60 kDa chaperonin
Af: 10 kDa chaperonin
Ai: 60 kDa chaperonin
Aj: 60 kDa chaperonin
Al: 10 kDa chaperonin
Ao: 60 kDa chaperonin
Ap: 60 kDa chaperonin
Ar: 10 kDa chaperonin
Au: 60 kDa chaperonin
Av: 60 kDa chaperonin
Ax: 10 kDa chaperonin
Ba: 60 kDa chaperonin
Bb: 60 kDa chaperonin
Bd: 10 kDa chaperonin
Bg: 60 kDa chaperonin
Bh: 60 kDa chaperonin
Bj: 10 kDa chaperonin
Bm: 60 kDa chaperonin
Bn: 60 kDa chaperonin
Bp: 10 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)852,20949
Polymers845,88821
Non-polymers6,32128
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area77830 Å2
ΔGint-610 kcal/mol
Surface area311370 Å2
MethodPISA

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Components

#1: Protein
60 kDa chaperonin / GroEL protein / Protein Cpn60


Mass: 55220.105 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: GroEL from Escherichia coli str. K-12 substr. W3110
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: groL, groEL, mopA, b4143, JW4103
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
References: UniProt: P0A6F5
#2: Protein
10 kDa chaperonin / GroES protein / Protein Cpn10


Mass: 10400.938 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: GroES from Escherichia coli str. K-12 substr. W3110
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: groS, groES, mopB, b4142, JW4102
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
References: UniProt: P0A6F9
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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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: ADP-bound GroEL-GroES complex / Type: COMPLEX / Entity ID: #2 / Source: RECOMBINANT
Molecular weightValue: 0.882 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli str. K-12 substr. W3110 (bacteria)
Source (recombinant)Organism: Escherichia coli str. K-12 substr. W3110 (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4.5 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 100 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPU1.9image acquisition
7ISOLDEmodel fitting
9PHENIXmodel refinement
13cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41000 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1SX4

1sx4

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