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- PDB-6xhi: Cryo-EM structure of octadecameric TF55 (beta-only) complex from ... -

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Basic information

Entry
Database: PDB / ID: 6xhi
TitleCryo-EM structure of octadecameric TF55 (beta-only) complex from S. solfataricus bound to ADP
ComponentsThermosome subunit beta
KeywordsCHAPERONE / Chaperonin / Complex
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Thermosome, archaeal / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily ...Thermosome, archaeal / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / 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
ADENOSINE-5'-DIPHOSPHATE / Thermosome subunit beta
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsZeng, Y.C. / Sobti, M. / Stewart, A.G.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1159347 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1146403 Australia
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2021
Title: Structural analysis of the Sulfolobus solfataricus TF55β chaperonin by cryo-electron microscopy.
Authors: Yi Cheng Zeng / Meghna Sobti / Alastair G Stewart /
Abstract: Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. ...Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, structures of the β-only complex of S. solfataricus TF55 (TF55β) were determined to 3.6-4.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle.
History
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Assembly

Deposited unit
A: Thermosome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4632
Polymers60,0361
Non-polymers4271
Water00
1
A: Thermosome subunit beta
hetero molecules
x 18


Theoretical massNumber of molelcules
Total (without water)1,088,33636
Polymers1,080,64618
Non-polymers7,69018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation17
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D9 (2x9 fold dihedral))

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Components

#1: Protein Thermosome subunit beta / Chaperonin subunit beta / Thermophilic factor 55 beta / TF55-beta / Thermosome subunit 2


Mass: 60035.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / References: UniProt: Q9V2T8
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN

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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 Octadecameric TF55 beta-subunit chaperonin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 1.08 MDa / Experimental value: NO
Source (natural)Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris.HCl1
22 mMMagnesium chlorideMgCl21
31 mMEDTA1
4100 mMSodium chlorideNaCl1
SpecimenConc.: 12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: 3.5 uL drop with 5 s blotting

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 61 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2321

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC2.12.0particle selectionBlob picker
2EPUimage acquisition
4cryoSPARC2.12.0CTF correctionPatch CTF correction
7Cootmodel fitting
10cryoSPARC2.12.0initial Euler assignment
11cryoSPARC2.12.0final Euler assignment
13cryoSPARC2.12.03D reconstruction
20PHENIXmodel refinementReal-space refine
21ISOLDEmodel refinementMDFF
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 395079
SymmetryPoint symmetry: D9 (2x9 fold dihedral)
3D reconstructionResolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43528 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 4XCD

4xcd


Pdb chain-ID: A / Accession code: 4XCD / Source name: PDB / Type: experimental model

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