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- EMDB-37853: Cryo-EM structure of H. thermoluteolus GroEL-GroES2 football complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37853
TitleCryo-EM structure of H. thermoluteolus GroEL-GroES2 football complex
Map data
Sample
  • Complex: H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+
    • Complex: H. thermoluteolus GroEL
      • Protein or peptide: Chaperonin GroEL
    • Complex: H. thermoluteolus GroES
      • Protein or peptide: Co-chaperonin GroES
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsChaperone / Chaperonin / ATPase / protein folding
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding ...GroEL-GroES complex / chaperonin ATPase / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / ATP binding / metal ion binding / cytoplasm
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
Co-chaperonin GroES / Chaperonin GroEL
Similarity search - Component
Biological speciesHydrogenophilus thermoluteolus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 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-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37853.png

Downloads & links

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Map

FileDownload / File: emd_37853.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 500 pix.
= 420. Å		0.84 Å/pix.
x 500 pix.
= 420. Å		0.84 Å/pix.
x 500 pix.
= 420. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.1874531 - 0.6780452
Average (Standard dev.)-0.00027881007 (±0.014757009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37853_msk_1.map
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AxesZYX

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

Fileemd_37853_additional_1.map
AnnotationOutput sharpened map by NU-refinement of cryoSPARC
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Additional map: Map sharpened using deepEMhancer

Fileemd_37853_additional_2.map
AnnotationMap sharpened using deepEMhancer
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Half map: #1

Fileemd_37853_half_map_1.map
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Half map: #2

Fileemd_37853_half_map_2.map
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Sample components

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Entire : H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+

EntireName: H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+
Components
  • Complex: H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+
    • Complex: H. thermoluteolus GroEL
      • Protein or peptide: Chaperonin GroEL
    • Complex: H. thermoluteolus GroES
      • Protein or peptide: Co-chaperonin GroES
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+

SupramoleculeName: H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: 6.76 mg/mL native GroEL was mixed with 3.7 mg/mL recombinant GroES followed by addition of 2 mM ATP in imaging buffer supplemented by detergents (0.1% 3-((3-cholamidopropyl) dimethylammonio)- ...Details: 6.76 mg/mL native GroEL was mixed with 3.7 mg/mL recombinant GroES followed by addition of 2 mM ATP in imaging buffer supplemented by detergents (0.1% 3-((3-cholamidopropyl) dimethylammonio)-1-propanesulfonate (CHAPS), 0.05% n-Octyl-beta-D-glucopyranoside)
Source (natural)Organism: Hydrogenophilus thermoluteolus (bacteria) / Strain: TH-1
Molecular weightTheoretical: 73 kDa/nm

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Supramolecule #2: H. thermoluteolus GroEL

SupramoleculeName: H. thermoluteolus GroEL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: H. thermoluteolus GroES

SupramoleculeName: H. thermoluteolus GroES / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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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: 56.08134 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 APKD

UniProtKB: Chaperonin GroEL

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Macromolecule #2: Co-chaperonin GroES

MacromoleculeName: Co-chaperonin GroES / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Hydrogenophilus thermoluteolus (bacteria) / Strain: TH-1
Molecular weightTheoretical: 10.224831 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
KLRPLHDRVV VKRIEAERKT ASGIVIPDTA GEKPDQGEVL AVGDGKILDD GSKRPMAVKV GDKVLFGKYA GQTVKVEGEE LLVLREDDI MAVIE

UniProtKB: Co-chaperonin GroES

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 14 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 14 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMKClPotassium chloride
5.0 mMMgCl2Magnesium chloride
2.0 mMAdenosine triphosphate
0.1 %3-((3-cholamidopropyl) dimethylammonio)-1-propanesulfonate
0.05 %n-Octyl-beta-D-glucopyranoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER / Details: Grids were freshly treated using Gatan Solarus II
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0, blot time 8 s.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 1233 / Average exposure time: 4.95 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 103957
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: RELION (ver. 4)

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