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Yorodumi- EMDB-0755: Recombinant Pyrococcus furiosus PbaA/PF0014 with 30 residue C-ter... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0755 | |||||||||
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Title | Recombinant Pyrococcus furiosus PbaA/PF0014 with 30 residue C-terminal truncation. | |||||||||
Map data | PbaA/PF0014 complex with 30 residue C-terminal truncation at 7.3A | |||||||||
Sample |
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Biological species | Pyrococcus furiosus (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.3 Å | |||||||||
Authors | Burton-Smith RN / Song C / Murata K | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: Sci Rep / Year: 2020 Title: Supramolecular tholos-like architecture constituted by archaeal proteins without functional annotation. Authors: Maho Yagi-Utsumi / Arunima Sikdar / Chihong Song / Jimin Park / Rintaro Inoue / Hiroki Watanabe / Raymond N Burton-Smith / Toshiya Kozai / Tatsuya Suzuki / Atsuji Kodama / Kentaro Ishii / ...Authors: Maho Yagi-Utsumi / Arunima Sikdar / Chihong Song / Jimin Park / Rintaro Inoue / Hiroki Watanabe / Raymond N Burton-Smith / Toshiya Kozai / Tatsuya Suzuki / Atsuji Kodama / Kentaro Ishii / Hirokazu Yagi / Tadashi Satoh / Susumu Uchiyama / Takayuki Uchihashi / Keehyoung Joo / Jooyoung Lee / Masaaki Sugiyama / Kazuyoshi Murata / Koichi Kato / Abstract: Euryarchaeal genomes encode proteasome-assembling chaperone homologs, PbaA and PbaB, although archaeal proteasome formation is a chaperone-independent process. Homotetrameric PbaB functions as a ...Euryarchaeal genomes encode proteasome-assembling chaperone homologs, PbaA and PbaB, although archaeal proteasome formation is a chaperone-independent process. Homotetrameric PbaB functions as a proteasome activator, while PbaA forms a homopentamer that does not interact with the proteasome. Notably, PbaA forms a complex with PF0014, an archaeal protein without functional annotation. In this study, based on our previous research on PbaA crystal structure, we performed an integrative analysis of the supramolecular structure of the PbaA/PF0014 complex using native mass spectrometry, solution scattering, high-speed atomic force microscopy, and electron microscopy. The results indicated that this highly thermostable complex constitutes ten PbaA and ten PF0014 molecules, which are assembled into a dumbbell-shaped structure. Two PbaA homopentameric rings correspond to the dumbbell plates, with their N-termini located outside of the plates and C-terminal segments left mobile. Furthermore, mutant PbaA lacking the mobile C-terminal segment retained the ability to form a complex with PF0014, allowing 3D modeling of the complex. The complex shows a five-column tholos-like architecture, in which each column comprises homodimeric PF0014, harboring a central cavity, which can potentially accommodate biomacromolecules including proteins. Our findings provide insight into the functional roles of Pba family proteins, offering a novel framework for designing functional protein cages. | |||||||||
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_0755.map.gz | 124.4 MB | EMDB map data format | |
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Header (meta data) | emd-0755-v30.xml emd-0755.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0755_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_0755.png | 61.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0755 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0755 | HTTPS FTP |
-Validation report
Summary document | emd_0755_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_0755_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_0755_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0755 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0755 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0755.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PbaA/PF0014 complex with 30 residue C-terminal truncation at 7.3A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.93 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 : Recombinant Pyrococcus furiosus PbaA/PF0014 with 30 residue C-ter...
Entire | Name: Recombinant Pyrococcus furiosus PbaA/PF0014 with 30 residue C-terminal truncation. |
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Components |
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-Supramolecule #1: Recombinant Pyrococcus furiosus PbaA/PF0014 with 30 residue C-ter...
Supramolecule | Name: Recombinant Pyrococcus furiosus PbaA/PF0014 with 30 residue C-terminal truncation. type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 370 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL 2100F |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
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