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Yorodumi- EMDB-17421: CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordere... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17421 | |||||||||
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Title | CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx | |||||||||
Map data | GroEL7-GroES7 cage with encapsulated ordered substrate MetK in presence of ADP-BeFx | |||||||||
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) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 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_17421.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-17421-v30.xml emd-17421.xml | 25.7 KB 25.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17421_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_17421.png | 101.9 KB | ||
Filedesc metadata | emd-17421.cif.gz | 7.1 KB | ||
Others | emd_17421_half_map_1.map.gz emd_17421_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17421 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17421 | HTTPS FTP |
-Validation report
Summary document | emd_17421_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_17421_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17421_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_17421_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17421 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17421 | HTTPS FTP |
-Related structure data
Related structure data | 8p4oMC 8p4mC 8p4nC 8p4pC 8p4rC 8qxsC 8qxtC 8qxuC 8qxvC C: citing same article (ref.) M: atomic model generated by this map |
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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_17421.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | GroEL7-GroES7 cage with encapsulated ordered substrate MetK in presence of ADP-BeFx | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17421_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17421_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: #1-#3 / 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: Chaperonin GroEL
Macromolecule | Name: Chaperonin GroEL / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO / EC number: chaperonin ATPase |
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Source (natural) | Organism: Escherichia coli (E. coli) |
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: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
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: S-adenosylmethionine synthase
Macromolecule | Name: S-adenosylmethionine synthase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: methionine adenosyltransferase |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 41.998508 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MAKHLFTSES VSEGHPDKIA DQISDAVLDA ILEQDPKARV ACETYVKTGM VLVGGEITTS AWVDIEEITR NTVREIGYVH SDMGFDANS CAVLSAIGKQ SPDINQGVDR ADPLEQGAGD QGLMFGYATN ETDVLMPAPI TYAHRLVQRQ AEVRKNGTLP W LRPDAKSQ ...String: MAKHLFTSES VSEGHPDKIA DQISDAVLDA ILEQDPKARV ACETYVKTGM VLVGGEITTS AWVDIEEITR NTVREIGYVH SDMGFDANS CAVLSAIGKQ SPDINQGVDR ADPLEQGAGD QGLMFGYATN ETDVLMPAPI TYAHRLVQRQ AEVRKNGTLP W LRPDAKSQ VTFQYDDGKI VGIDAVVLST QHSEEIDQKS LQEAVMEEII KPILPAEWLT SATKFFINPT GRFVIGGPMG DC GLTGRKI IVDTYGGMAR HGGGAFSGKD PSKVDRSAAY AARYVAKNIV AAGLADRCEI QVSYAIGVAE PTSIMVETFG TEK VPSEQL TLLVREFFDL RPYGLIQMLD LLHPIYKETA AYGHFGREHF PWEKTDKAQL LRDAAGLK UniProtKB: S-adenosylmethionine synthase |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 7 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #7: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 7 / Number of copies: 7 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 21 / 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 | 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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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||||||||||||||
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 |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL | ||||||
Output model | PDB-8p4o: |