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Yorodumi- EMDB-17570: Conformer 4 of the (GroEL)14(GroES)14 complex with two encapsulat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17570 | |||||||||
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Title | Conformer 4 of the (GroEL)14(GroES)14 complex with two encapsulated, near-native and ordered 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 / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / potassium ion binding ...methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine cycle / S-adenosylmethionine biosynthetic process / GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / potassium ion binding / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / positive regulation of T cell activation / protein folding / one-carbon metabolic process / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / 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: 4.4 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_17570.map.gz | 23.9 MB | EMDB map data format | |
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Header (meta data) | emd-17570-v30.xml emd-17570.xml | 23 KB 23 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17570_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_17570.png | 54.5 KB | ||
Masks | emd_17570_msk_1.map | 209.3 MB | Mask map | |
Filedesc metadata | emd-17570.cif.gz | 6 KB | ||
Others | emd_17570_half_map_1.map.gz emd_17570_half_map_2.map.gz | 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17570 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17570 | HTTPS FTP |
-Validation report
Summary document | emd_17570_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_17570_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_17570_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_17570_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17570 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17570 | 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_17570.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_17570_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17570_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17570_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GroEL14-GroES14-MetK2
Entire | Name: GroEL14-GroES14-MetK2 |
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Components |
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-Supramolecule #1: GroEL14-GroES14-MetK2
Supramolecule | Name: GroEL14-GroES14-MetK2 / 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: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG KLIAEAMDKV ...String: AAKDVKFGND ARVKMLRGVN VLADAVKVTL GPKGRNVVLD KSFGAPTITK DGVSVAREI ELEDKFENMG AQMVKEVASK ANDAAGDGTT TATVLAQAII TEGLKAVAAG MNPMDLKRGI DKAVTAAVE ELKALSVPCS DSKAIAQVGT ISANSDETVG KLIAEAMDKV GKEGVITVED G TGLQDELD VVEGMQFDRG YLSPYFINKP ETGAVELESP FILLADKKIS NIREMLPVLE AV AKAGKPL LIIAEDVEGE ALATLVVNTM RGIVKVAAVK APGFGDRRKA MLQDIATLTG GTV ISEEIG MELEKATLED LGQAKRVVIN KDTTTIIDGV GEEAAIQGRV AQIRQQIEEA TSDY DREKL QERVAKLAGG VAVIKVGAAT EVEMKEKKAR VEDALHATRA AVEEGVVAGG GVALI RVAS KLADLRGQNE DQNVGIKVAL RAMEAPLRQI VLNCGEEPSV VANTVKGGDG NYGYNA ATE EYGNMIDMGI LDPTKVTRSA LQYAASVAGL MITTECMVTD LPKNDAADLG AAGGMGG MG GMGGMM UniProtKB: Chaperonin GroEL |
-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 |