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Yorodumi- EMDB-22186: Cryo-EM structure of octadecameric TF55 (beta-only) complex from ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22186 | |||||||||
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Title | Cryo-EM structure of octadecameric TF55 (beta-only) complex from S. solfataricus bound to ADP | |||||||||
Map data | TF55 (beta-only) complex from S. solfataricus bound to ADP | |||||||||
Sample |
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Keywords | Chaperonin / Complex / CHAPERONE | |||||||||
Function / homology | Function and homology information ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.19 Å | |||||||||
Authors | Zeng YC / Sobti M | |||||||||
Funding support | Australia, 2 items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2021 Title: Structural analysis of the Sulfolobus solfataricus TF55β chaperonin by cryo-electron microscopy. Authors: Yi Cheng Zeng / Meghna Sobti / Alastair G Stewart / Abstract: Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. ...Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, structures of the β-only complex of S. solfataricus TF55 (TF55β) were determined to 3.6-4.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22186.map.gz | 306.3 MB | EMDB map data format | |
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Header (meta data) | emd-22186-v30.xml emd-22186.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22186_fsc.xml | 15.3 KB | Display | FSC data file |
Images | emd_22186.png | 74.4 KB | ||
Filedesc metadata | emd-22186.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22186 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22186 | HTTPS FTP |
-Validation report
Summary document | emd_22186_validation.pdf.gz | 559.9 KB | Display | EMDB validaton report |
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Full document | emd_22186_full_validation.pdf.gz | 559.5 KB | Display | |
Data in XML | emd_22186_validation.xml.gz | 15 KB | Display | |
Data in CIF | emd_22186_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22186 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22186 | HTTPS FTP |
-Related structure data
Related structure data | 6xhiMC 6xhjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22186.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TF55 (beta-only) complex from S. solfataricus bound to ADP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ADP-bound Octadecameric TF55 beta-subunit chaperonin
Entire | Name: ADP-bound Octadecameric TF55 beta-subunit chaperonin |
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Components |
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-Supramolecule #1: ADP-bound Octadecameric TF55 beta-subunit chaperonin
Supramolecule | Name: ADP-bound Octadecameric TF55 beta-subunit chaperonin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 |
Molecular weight | Theoretical: 1.08 MDa |
-Macromolecule #1: Thermosome subunit beta
Macromolecule | Name: Thermosome subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 |
Molecular weight | Theoretical: 60.035891 KDa |
Sequence | String: MATATVATTP EGIPVIILKE GSSRTYGKEA LRANIAAVKA IEEALKSTYG PRGMDKMLVD SLGDITITND GATILDKMDL QHPTGKLLV QIAKGQDEET ADGTKTAVIL AGELAKKAED LLYKEIHPTI IVSGYKKAEE IALKTIQEIA QPVTINDTDV L RKVALTSL ...String: MATATVATTP EGIPVIILKE GSSRTYGKEA LRANIAAVKA IEEALKSTYG PRGMDKMLVD SLGDITITND GATILDKMDL QHPTGKLLV QIAKGQDEET ADGTKTAVIL AGELAKKAED LLYKEIHPTI IVSGYKKAEE IALKTIQEIA QPVTINDTDV L RKVALTSL GSKAVAGARE YLADLVVKAV AQVAELRGDK WYVDLDNVQI VKKHGGSVND TQLVYGIVVD KEVVHPGMPK RI ENAKIAL LDASLEVEKP ELDAEIRIND PTQMHKFLEE EENILKEKVD KIAATGANVV ICQKGIDEVA QHYLAKKGIL AVR RAKKSD LEKLARATGG RVISNIDELT SQDLGYAALV EERKVGEDKM VFVEGAKNPK SVSILIRGGL ERVVDETERA LRDA LGTVA DVIRDGRAVA GGGAVEIEIA KRLRKYAPQV GGKEQLAIEA YANAIEGLIM ILAENAGLDP IDKLMQLRSL HENET NKWY GLNLFTGNPE DMWKLGVIEP ALVKMNAVKA ATEAVTLVLR IDDIVAAGKK SGSEPSGKKE KDKEEKSSED UniProtKB: Thermosome subunit beta |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 12 mg/mL | |||||||||||||||
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Buffer | pH: 8 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: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: 3.5 uL drop with 5 s blotting. |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2321 / Average exposure time: 61.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |