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- EMDB-37853: Cryo-EM structure of H. thermoluteolus GroEL-GroES2 football complex -
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Open data
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Basic information
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Title | Cryo-EM structure of H. thermoluteolus GroEL-GroES2 football complex | |||||||||
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![]() | Chaperone / Chaperonin / ATPase / protein folding | |||||||||
Function / homology | ![]() mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / GroEL-GroES complex / chaperonin ATPase / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production ...mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / GroEL-GroES complex / chaperonin ATPase / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of T cell activation / unfolded protein binding / protein-folding chaperone binding / protein refolding / response to heat / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
![]() | Liao Z / Gopalasingam CC / Kameya M / Gerle C / Shigematsu H / Ishii M / Arakawa T / Fushinobu S | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 239.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.6 KB 25.6 KB | Display Display | ![]() |
Images | ![]() | 70.5 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() ![]() | 450.7 MB 396.3 MB 442.1 MB 442.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wucMC ![]() 8wu4C ![]() 8wuwC ![]() 8wuxC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Output sharpened map by NU-refinement of cryoSPARC
File | emd_37853_additional_1.map | ||||||||||||
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Annotation | Output sharpened map by NU-refinement of cryoSPARC | ||||||||||||
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-Additional map: Map sharpened using deepEMhancer
File | emd_37853_additional_2.map | ||||||||||||
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Annotation | Map sharpened using deepEMhancer | ||||||||||||
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
File | emd_37853_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+
Entire | Name: H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+ |
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Components |
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-Supramolecule #1: H. thermoluteolus GroEL-GroES2 football complex bound with ADP-Mg2+
Supramolecule | Name: 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) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 73 kDa/nm |
-Supramolecule #2: H. thermoluteolus GroEL
Supramolecule | Name: H. thermoluteolus GroEL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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-Supramolecule #3: H. thermoluteolus GroES
Supramolecule | Name: H. thermoluteolus GroES / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Chaperonin GroEL
Macromolecule | Name: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: chaperonin ATPase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.08134 KDa |
Sequence | String: 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 |
-Macromolecule #2: Co-chaperonin GroES
Macromolecule | Name: Co-chaperonin GroES / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.224831 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KLRPLHDRVV VKRIEAERKT ASGIVIPDTA GEKPDQGEVL AVGDGKILDD GSKRPMAVKV GDKVLFGKYA GQTVKVEGEE LLVLREDDI MAVIE UniProtKB: Co-chaperonin GroES |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 14 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 14 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: 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 | |||||||||||||||||||||
Vitrification | Cryogen 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
Microscope | FEI TALOS ARCTICA |
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Image recording | Film 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 beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |