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- EMDB-37850: Cryo-EM structure of native H. thermoluteolus TH-1 GroEL -

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Basic information

Entry
Database: EMDB / ID: EMD-37850
TitleCryo-EM structure of native H. thermoluteolus TH-1 GroEL
Map data
Sample
  • Complex: Native H. thermoluteolus GroEL
    • Protein or peptide: Chaperonin GroEL
KeywordsChaperone / Chaperonin / ATPase / protein folding
Function / homology
Function and homology information


chaperonin ATPase / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHydrogenophilus thermoluteolus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiao Z / Gopalasingam CC / Kameya M / Gerle C / Shigematsu H / Ishii M / Arakawa T / Fushinobu S
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H00322 Japan
Japan Science and TechnologyJPMJSP2108 Japan
CitationJournal: Structure / Year: 2024
Title: Structural insights into thermophilic chaperonin complexes.
Authors: Zengwei Liao / Chai C Gopalasingam / Masafumi Kameya / Christoph Gerle / Hideki Shigematsu / Masaharu Ishii / Takatoshi Arakawa / Shinya Fushinobu /
Abstract: Group I chaperonins are dual heptamer protein complexes that play significant roles in protein homeostasis. The structure and function of the Escherichia coli chaperonin are well characterized. ...Group I chaperonins are dual heptamer protein complexes that play significant roles in protein homeostasis. The structure and function of the Escherichia coli chaperonin are well characterized. However, the dynamic properties of chaperonins, such as large ATPase-dependent conformational changes by binding of lid-like co-chaperonin GroES, have made structural analyses challenging, and our understanding of these changes during the turnover of chaperonin complex formation is limited. In this study, we used single-particle cryogenic electron microscopy to investigate the structures of GroES-bound chaperonin complexes from the thermophilic hydrogen-oxidizing bacteria Hydrogenophilus thermoluteolus and Hydrogenobacter thermophilus in the presence of ATP and AMP-PNP. We captured the structure of an intermediate state chaperonin complex, designated as an asymmetric football-shaped complex, and performed analyses to decipher the dynamic structural variations. Our structural analyses of inter- and intra-subunit communications revealed a unique mechanism of complex formation through the binding of a second GroES to a bullet-shaped complex.
History
DepositionOct 20, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37850.png

Downloads & links

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Map

FileDownload / File: emd_37850.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.0643
Minimum - Maximum-0.09370753 - 0.25629598
Average (Standard dev.)0.0015147317 (±0.013711513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37850_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Output sharpened map from NU-refinement of cryoSPARC

Fileemd_37850_additional_1.map
AnnotationOutput sharpened map from NU-refinement of cryoSPARC
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_37850_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37850_half_map_2.map
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Sample components

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Entire : Native H. thermoluteolus GroEL

EntireName: Native H. thermoluteolus GroEL
Components
  • Complex: Native H. thermoluteolus GroEL
    • Protein or peptide: Chaperonin GroEL

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Supramolecule #1: Native H. thermoluteolus GroEL

SupramoleculeName: Native H. thermoluteolus GroEL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hydrogenophilus thermoluteolus (bacteria) / Strain: TH-1
Molecular weightTheoretical: 809 kDa/nm

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Macromolecule #1: Chaperonin GroEL

MacromoleculeName: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: chaperonin ATPase
Source (natural)Organism: Hydrogenophilus thermoluteolus (bacteria) / Strain: TH-1
Molecular weightTheoretical: 55.83707 KDa
SequenceString: AAKEVKFHDS ARERLVAGVN LLANAVKTTL GPKGRNVVIE RSFGAPIVTK DGVTVAKEIE LKDKFENMGA QMVKEVASKT ADVAGDGTT TATVLAQAIV REGMKYVAAG MNPMDLKRGI DKAVTAIVEE LKAISKPCST TKEIAQVGTI SANADSSIGE I IAQAMDKV ...String:
AAKEVKFHDS ARERLVAGVN LLANAVKTTL GPKGRNVVIE RSFGAPIVTK DGVTVAKEIE LKDKFENMGA QMVKEVASKT ADVAGDGTT TATVLAQAIV REGMKYVAAG MNPMDLKRGI DKAVTAIVEE LKAISKPCST TKEIAQVGTI SANADSSIGE I IAQAMDKV GKEGVITVED GKSLENELEV VEGMQFDRGY LSPYFINNPD KQVAVLDNPY ILLHDKKISN IRDLLPVLEQ VA KAGRPLL IIAEDVEGEA LATLVVNNLR GILKTCAVKA PGFGDRRKAM LQDIAILTGG TVISEEVGLS LEKATLEDLG QAK RVEVAK EHTTIIDGAG DPAKIQARVK EIRVQIEEAT SDYDREKLQE RVAKLAGGVA VIKVGAATEV EMKEKKARVE DALH ATRAA VEEGIVPGGG VALLRAREAA VAKGLKGDNP DQEAGIKIVL RAVEQPLREI VANAGEEPSV IVAKVLEGKG NYGYN AATG EFGDMIEMGV LDPTKVTRSA LQNAASVAGL MLTTECMIAE AP

UniProtKB: Chaperonin GroEL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4S4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMKClPotassium chloride
5.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: OTHER / Details: PIB-10, hard mode
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 10, blot time 15 s.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3418 / Average exposure time: 4.95 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 40366

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial fitting was done using UCSF ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8wu4:
Cryo-EM structure of native H. thermoluteolus TH-1 GroEL

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