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Yorodumi- EMDB-21455: Cryo-EM structure of filamentous PFD from Methanocaldococcus jann... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21455 | ||||||||||||
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Title | Cryo-EM structure of filamentous PFD from Methanocaldococcus jannaschii | ||||||||||||
Map data | Cryo-EM structure of filamentous PFD | ||||||||||||
Sample |
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Keywords | helical symmetry / nanowire / prefoldin / PROTEIN FIBRIL | ||||||||||||
Function / homology | Function and homology information prefoldin complex / unfolded protein binding / protein folding / regulation of DNA-templated transcription / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Methanocaldococcus jannaschii (archaea) / Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 6.0 Å | ||||||||||||
Authors | Wang F / Chen YX | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: ACS Nano / Year: 2020 Title: Structural Determination of a Filamentous Chaperone to Fabricate Electronically Conductive Metalloprotein Nanowires. Authors: Yun X Chen / Nicole L Ing / Fengbin Wang / Dawei Xu / Nancy B Sloan / Nga T Lam / Daniel L Winter / Edward H Egelman / Allon I Hochbaum / Douglas S Clark / Dominic J Glover / Abstract: The transfer of electrons through protein complexes is central to cellular respiration. Exploiting proteins for charge transfer in a controllable fashion has the potential to revolutionize the ...The transfer of electrons through protein complexes is central to cellular respiration. Exploiting proteins for charge transfer in a controllable fashion has the potential to revolutionize the integration of biological systems and electronic devices. Here we characterize the structure of an ultrastable protein filament and engineer the filament subunits to create electronically conductive nanowires under aqueous conditions. Cryoelectron microscopy was used to resolve the helical structure of gamma-prefoldin, a filamentous protein from a hyperthermophilic archaeon. Conjugation of tetra-heme c3-type cytochromes along the longitudinal axis of the filament created nanowires capable of long-range electron transfer. Electrochemical transport measurements indicated networks of the nanowires capable of conducting current between electrodes at the redox potential of the cytochromes. Functionalization of these highly engineerable nanowires with other molecules, such as redox enzymes, may be useful for bioelectronic applications. | ||||||||||||
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_21455.map.gz | 3.4 MB | EMDB map data format | |
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Header (meta data) | emd-21455-v30.xml emd-21455.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_21455.png | 86.8 KB | ||
Filedesc metadata | emd-21455.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21455 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21455 | HTTPS FTP |
-Related structure data
Related structure data | 6vy1MC 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_21455.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of filamentous PFD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 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 : Methanocaldococcus jannaschii gamma-prefoldin
Entire | Name: Methanocaldococcus jannaschii gamma-prefoldin |
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Components |
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-Supramolecule #1: Methanocaldococcus jannaschii gamma-prefoldin
Supramolecule | Name: Methanocaldococcus jannaschii gamma-prefoldin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Methanocaldococcus jannaschii (archaea) |
-Macromolecule #1: Prefoldin subunit alpha 2
Macromolecule | Name: Prefoldin subunit alpha 2 / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 |
Molecular weight | Theoretical: 16.410641 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MVNEVIDINE AVRAYIAQIE GLRAEIGRLD ATIATLRQSL ATLKSLKTLG EGKTVLVPVG SIAQVEMKVE KMDKVVVSVG QNISAELEY EEALKYIEDE IKKLLTFRLV LEQAIAELYA KIEDLIAEAQ QTSEEEKAEE EENEEKAE UniProtKB: Prefoldin subunit alpha 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 55.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: featureless cylinder |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 18.27 Å Applied symmetry - Helical parameters - Δ&Phi: -48.93 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Details: d99, model:map FSC and map:map FSC / Number images used: 32227 |