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- EMDB-21455: Cryo-EM structure of filamentous PFD from Methanocaldococcus jann... -

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Basic information

Entry
Database: EMDB / ID: EMD-21455
TitleCryo-EM structure of filamentous PFD from Methanocaldococcus jannaschii
Map dataCryo-EM structure of filamentous PFD
Sample
  • Complex: Methanocaldococcus jannaschii gamma-prefoldin
    • Protein or peptide: Prefoldin subunit alpha 2
Keywordshelical symmetry / nanowire / prefoldin / PROTEIN FIBRIL
Function / homologyPrefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / prefoldin complex / Prefoldin / unfolded protein binding / protein folding / cytoplasm / Prefoldin subunit alpha 2
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea) / Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsWang F / Chen YX
Funding support United States, 3 items
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, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseMay 13, 2020-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vy1
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vy1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21455.png

Downloads & links

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Map

FileDownload / File: emd_21455.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of filamentous PFD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 384 pix.
= 418.56 Å		1.09 Å/pix.
x 384 pix.
= 418.56 Å		1.09 Å/pix.
x 384 pix.
= 418.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.04107503 - 0.118998244
Average (Standard dev.)0.00022461686 (±0.0033181484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 418.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z418.560418.560418.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-0.0410.1190.000

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Supplemental data

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Sample components

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Entire : Methanocaldococcus jannaschii gamma-prefoldin

EntireName: Methanocaldococcus jannaschii gamma-prefoldin
Components
  • Complex: Methanocaldococcus jannaschii gamma-prefoldin
    • Protein or peptide: Prefoldin subunit alpha 2

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Supramolecule #1: Methanocaldococcus jannaschii gamma-prefoldin

SupramoleculeName: Methanocaldococcus jannaschii gamma-prefoldin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

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Macromolecule #1: Prefoldin subunit alpha 2

MacromoleculeName: Prefoldin subunit alpha 2 / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
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 weightTheoretical: 16.410641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVNEVIDINE AVRAYIAQIE GLRAEIGRLD ATIATLRQSL ATLKSLKTLG EGKTVLVPVG SIAQVEMKVE KMDKVVVSVG QNISAELEY EEALKYIEDE IKKLLTFRLV LEQAIAELYA KIEDLIAEAQ QTSEEEKAEE EENEEKAE

UniProtKB: Prefoldin subunit alpha 2

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied 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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

2zdi


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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