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- PDB-6vy1: Cryo-EM structure of filamentous PFD from Methanocaldococcus jann... -

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Basic information

Entry
Database: PDB / ID: 6vy1
TitleCryo-EM structure of filamentous PFD from Methanocaldococcus jannaschii
ComponentsPrefoldin subunit alpha 2
KeywordsPROTEIN 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
Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin
Similarity search - Domain/homology
Prefoldin subunit alpha 2
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6 Å
AuthorsWang, F. / Chen, Y.X. / Ing, N.L. / Hochbaum, A.I. / Clark, D.S. / Glover, D.J. / Egelman, E.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
Department of Defense (DOD, United States)FA9550-17-1-0451 United States
Department of Defense (DOD, United States)FA9550-14-1-0350 United States
CitationJournal: 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
DepositionFeb 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: Prefoldin subunit alpha 2
B: Prefoldin subunit alpha 2
C: Prefoldin subunit alpha 2
D: Prefoldin subunit alpha 2
E: Prefoldin subunit alpha 2
F: Prefoldin subunit alpha 2
G: Prefoldin subunit alpha 2
a: Prefoldin subunit alpha 2
b: Prefoldin subunit alpha 2
c: Prefoldin subunit alpha 2
d: Prefoldin subunit alpha 2
e: Prefoldin subunit alpha 2
f: Prefoldin subunit alpha 2
g: Prefoldin subunit alpha 2


Theoretical massNumber of molelcules
Total (without water)229,74914
Polymers229,74914
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Prefoldin subunit alpha 2 / GimC subunit alpha 2


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Methanocaldococcus jannaschii gamma-prefoldin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -48.93 ° / Axial rise/subunit: 18.27 Å / Axial symmetry: C1
3D reconstructionResolution: 6 Å / Resolution method: OTHER / Num. of particles: 32227 / Details: d99, model:map FSC and map:map FSC / Symmetry type: HELICAL
Atomic model buildingPDB-ID: 2ZDI

2zdi


Accession code: 2ZDI / Source name: PDB / Type: experimental model

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