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Yorodumi- EMDB-17565: CryoEM structure of a GroEL14-GroES14 cage with two encapsulated ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17565 | |||||||||
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Title | CryoEM structure of a GroEL14-GroES14 cage with two encapsulated disordered MetK substrates in the presence of ADP-BeFx | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Chaperonin / Folding cage / proteostasis / heat shock / ATPase / CHAPERONE | |||||||||
Function / homology | Function and homology information methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine cycle / S-adenosylmethionine biosynthetic process / GroEL-GroES complex / virion assembly / potassium ion binding / chaperone cofactor-dependent protein refolding / protein folding chaperone / unfolded protein binding ...methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine cycle / S-adenosylmethionine biosynthetic process / GroEL-GroES complex / virion assembly / potassium ion binding / chaperone cofactor-dependent protein refolding / protein folding chaperone / unfolded protein binding / protein folding / one-carbon metabolic process / protein-folding chaperone binding / response to heat / magnesium ion binding / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli BL21(DE3) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
Authors | Wagner J / Beck F / Bracher A / Caravajal AI / 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_17565.map.gz | 197.8 MB | EMDB map data format | |
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Header (meta data) | emd-17565-v30.xml emd-17565.xml | 22.9 KB 22.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17565_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_17565.png | 63.9 KB | ||
Masks | emd_17565_msk_1.map | 209.3 MB | Mask map | |
Filedesc metadata | emd-17565.cif.gz | 5.6 KB | ||
Others | emd_17565_half_map_1.map.gz emd_17565_half_map_2.map.gz | 194.5 MB 194.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17565 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17565 | HTTPS FTP |
-Validation report
Summary document | emd_17565_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17565_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17565_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | emd_17565_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17565 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17565 | HTTPS FTP |
-Related structure data
Related structure data | 8p4mC 8p4nC 8p4oC 8p4pC 8p4rC 8qxsC 8qxtC 8qxuC 8qxvC 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_17565.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17565_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17565_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17565_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GroEL14-GroES14-MetK
Entire | Name: GroEL14-GroES14-MetK |
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Components |
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-Supramolecule #1: GroEL14-GroES14-MetK
Supramolecule | Name: GroEL14-GroES14-MetK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: with bound ADP-BeF3 Mg2+ K+ |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 1.03 MDa |
-Macromolecule #1: GroEL
Macromolecule | Name: GroEL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAKHLFTSES VSEGHPDKIA DQISDAVLDA ILEQDPKARV ACETYVKTGM VLVGGEITTS AWVDIEEIT RNTVREIGYV HSDMGFDANS CAVLSAIGKQ SPDINQGVDR ADPLEQGAGD Q GLMFGYAT NETDVLMPAP ITYAHRLVQR QAEVRKNGTL PWLRPDAKSQ ...String: MAKHLFTSES VSEGHPDKIA DQISDAVLDA ILEQDPKARV ACETYVKTGM VLVGGEITTS AWVDIEEIT RNTVREIGYV HSDMGFDANS CAVLSAIGKQ SPDINQGVDR ADPLEQGAGD Q GLMFGYAT NETDVLMPAP ITYAHRLVQR QAEVRKNGTL PWLRPDAKSQ VTFQYDDGKI VG IDAVVLS TQHSEEIDQK SLQEAVMEEI IKPILPAEWL TSATKFFINP TGRFVIGGPM GDC GLTGRK IIVDTYGGMA RHGGGAFSGK DPSKVDRSAA YAARYVAKNI VAAGLADRCE IQVS YAIGV AEPTSIMVET FGTEKVPSEQ LTLLVREFFD LRPYGLIQML DLLHPIYKET AAYGH FGRE HFPWEKTDKA QLLRDAAGLK UniProtKB: S-adenosylmethionine synthase |
-Macromolecule #2: GroES
Macromolecule | Name: GroES / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MNIRPLHDRV IVKRKEVETK SAGGIVLTGS AAAKSTRGEV LAVGNGRILE NGEVKPLDVK VGDIVIFND GYGVKSEKID NEEVLIMSES DILAIVEA UniProtKB: Co-chaperonin GroES |
-Macromolecule #3: MetK
Macromolecule | Name: MetK / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAKHLFTSES VSEGHPDKIA DQISDAVLDA ILEQDPKARV ACETYVKTGM VLVGGEITTS AWVDIEEIT RNTVREIGYV HSDMGFDANS CAVLSAIGKQ SPDINQGVDR ADPLEQGAGD Q GLMFGYAT NETDVLMPAP ITYAHRLVQR QAEVRKNGTL PWLRPDAKSQ ...String: MAKHLFTSES VSEGHPDKIA DQISDAVLDA ILEQDPKARV ACETYVKTGM VLVGGEITTS AWVDIEEIT RNTVREIGYV HSDMGFDANS CAVLSAIGKQ SPDINQGVDR ADPLEQGAGD Q GLMFGYAT NETDVLMPAP ITYAHRLVQR QAEVRKNGTL PWLRPDAKSQ VTFQYDDGKI VG IDAVVLS TQHSEEIDQK SLQEAVMEEI IKPILPAEWL TSATKFFINP TGRFVIGGPM GDC GLTGRK IIVDTYGGMA RHGGGAFSGK DPSKVDRSAA YAARYVAKNI VAAGLADRCE IQVS YAIGV AEPTSIMVET FGTEKVPSEQ LTLLVREFFD LRPYGLIQML DLLHPIYKET AAYGH FGRE HFPWEKTDKA QLLRDAAGLK UniProtKB: S-adenosylmethionine synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10.3 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 5.9 mM n-octyl-beta-D-glucopyranoside were added before vitrification. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |