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Yorodumi- EMDB-17426: In situ structure average of GroEL14-GroES14 complexes in Escheri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17426 | |||||||||
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Title | In situ structure average of GroEL14-GroES14 complexes in Escherichia coli cytosol obtained by cryo electron tomography | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Chaperonin / Folding cage / proteostasis / heat shock / ATPase / CHAPERONE | |||||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production ...GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / positive regulation of T cell activation / protein-folding chaperone binding / response to heat / protein refolding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli BL21(DE3) (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 11.9 Å | |||||||||
Authors | Wagner J / Caravajal AI / Beck F / Bracher A / Wan W / Bohn S / Koerner R / Baumeister W / Fernandez-Busnadiego R / Hartl FU | |||||||||
Funding support | 1 items
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Citation | Journal: Nature / Year: 2024 Title: Visualizing chaperonin function in situ by cryo-electron tomography Authors: Wagner J / Caravajal AI / Beck F / Bracher A / Wan W / Bohn S / Koerner R / Baumeister W / Fernandez-Busnadiego R / Hartl FU | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17426.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-17426-v30.xml emd-17426.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17426_fsc.xml | 4.5 KB | Display | FSC data file |
Images | emd_17426.png | 53.8 KB | ||
Masks | emd_17426_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-17426.cif.gz | 6.1 KB | ||
Others | emd_17426_half_map_1.map.gz emd_17426_half_map_2.map.gz | 7.4 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17426 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17426 | HTTPS FTP |
-Validation report
Summary document | emd_17426_validation.pdf.gz | 947.5 KB | Display | EMDB validaton report |
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Full document | emd_17426_full_validation.pdf.gz | 947.1 KB | Display | |
Data in XML | emd_17426_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_17426_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17426 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17426 | HTTPS FTP |
-Related structure data
Related structure data | 8p4rMC 8p4mC 8p4nC 8p4oC 8p4pC 8qxsC 8qxtC 8qxuC 8qxvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17426.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.52 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17426_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17426_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17426_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GroEL14-GroES14 complex
Entire | Name: GroEL14-GroES14 complex |
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Components |
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-Supramolecule #1: GroEL14-GroES14 complex
Supramolecule | Name: GroEL14-GroES14 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: Chaperonin GroEL
Macromolecule | Name: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 57.260504 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV ...String: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREIE LEDKFENMGA QMVKEVASKA NDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVEE LKALSVPCSD SKAIAQVGTI SANSDETVGK L IAEAMDKV GKEGVITVED GTGLQDELDV VEGMQFDRGY LSPYFINKPE TGAVELESPF ILLADKKISN IREMLPVLEA VA KAGKPLL IIAEDVEGEA LATLVVNTMR GIVKVAAVKA PGFGDRRKAM LQDIATLTGG TVISEEIGME LEKATLEDLG QAK RVVINK DTTTIIDGVG EEAAIQGRVA QIRQQIEEAT SDYDREKLQE RVAKLAGGVA VIKVGAATEV EMKEKKARVE DALH ATRAA VEEGVVAGGG VALIRVASKL ADLRGQNEDQ NVGIKVALRA MEAPLRQIVL NCGEEPSVVA NTVKGGDGNY GYNAA TEEY GNMIDMGILD PTKVTRSALQ YAASVAGLMI TTECMVTDLP KNDAADLGAA GGMGGMGGMG GMM 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: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 10.400938 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MNIRPLHDRV IVKRKEVETK SAGGIVLTGS AAAKSTRGEV LAVGNGRILE NGEVKPLDVK VGDIVIFNDG YGVKSEKIDN EEVLIMSES DILAIVEA UniProtKB: Co-chaperonin GroES |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 14 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-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 |
-Macromolecule #5: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 14 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 406 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
Details | Vitrified E. coli Bl21 (DE3) cells |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |