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Yorodumi- PDB-6vy1: Cryo-EM structure of filamentous PFD from Methanocaldococcus jann... -
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-Basic information
Entry | Database: PDB / ID: 6vy1 | ||||||||||||
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Title | Cryo-EM structure of filamentous PFD from Methanocaldococcus jannaschii | ||||||||||||
Components | Prefoldin subunit alpha 2 | ||||||||||||
Keywords | PROTEIN FIBRIL / helical symmetry / nanowire / prefoldin | ||||||||||||
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) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6 Å | ||||||||||||
Authors | Wang, F. / Chen, Y.X. / Ing, N.L. / Hochbaum, A.I. / Clark, D.S. / Glover, D.J. / Egelman, E.H. | ||||||||||||
Funding support | United States, 3items
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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
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6vy1.cif.gz | 288.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vy1.ent.gz | 239.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vy1_validation.pdf.gz | 719.7 KB | Display | wwPDB validaton report |
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Full document | 6vy1_full_validation.pdf.gz | 720.4 KB | Display | |
Data in XML | 6vy1_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 6vy1_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/6vy1 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/6vy1 | HTTPS FTP |
-Related structure data
Related structure data | 21455MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 16410.641 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) 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 Gene: pfdA2, MJ0648 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58064 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Methanocaldococcus jannaschii gamma-prefoldin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Methanocaldococcus jannaschii (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_2919: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Helical symmerty | Angular rotation/subunit: -48.93 ° / Axial rise/subunit: 18.27 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 6 Å / Resolution method: OTHER / Num. of particles: 32227 / Details: d99, model:map FSC and map:map FSC / Symmetry type: HELICAL |
Atomic model building | PDB-ID: 2ZDI Accession code: 2ZDI / Source name: PDB / Type: experimental model |