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- EMDB-9021: DHF119 filament -

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Basic information

Entry
Database: EMDB / ID: 9021
TitleDHF119 filament
Map dataDHF119 filament
SampleDHF119 filament:
Sourcesynthetic construct (others)
Methodhelical reconstruction / cryo EM / 3.4 Å resolution
AuthorsLynch EM / Shen H / Fallas JA / Kollman JM / Baker D
CitationJournal: Science / Year: 2018
Title: De novo design of self-assembling helical protein filaments.
Authors: Hao Shen / Jorge A Fallas / Eric Lynch / William Sheffler / Bradley Parry / Nicholas Jannetty / Justin Decarreau / Michael Wagenbach / Juan Jesus Vicente / Jiajun Chen / Lei Wang / Quinton Dowling / Gustav Oberdorfer / Lance Stewart / Linda Wordeman / James De Yoreo / Christine Jacobs-Wagner / Justin Kollman / David Baker
Abstract: We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale ...We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo-electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.
Validation ReportPDB-ID: 6e9z

SummaryFull reportAbout validation report
DateDeposition: Aug 1, 2018 / Header (metadata) release: Oct 17, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6e9z
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6e9z
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9021.map.gz (map file in CCP4 format, 70305 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
260 pix
1.05 Å/pix.
= 273. Å
260 pix
1.05 Å/pix.
= 273. Å
260 pix
1.05 Å/pix.
= 273. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:0.055 (by author), 0.055 (movie #1):
Minimum - Maximum-0.12345359 - 0.27188686
Average (Standard dev.)0.0012909784 (0.009797667)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions260260260
Origin-130.0-130.0-130.0
Limit129.0129.0129.0
Spacing260260260
CellA=B=C: 273.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z273.000273.000273.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS-130-130-130
NC/NR/NS260260260
D min/max/mean-0.1230.2720.001

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Supplemental data

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Sample components

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Entire DHF119 filament

EntireName: DHF119 filament / Number of components: 2

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Component #1: protein, DHF119 filament

ProteinName: DHF119 filament / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, DHF119 filament

ProteinName: DHF119 filament / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 25.120242 kDa
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C3 (3 fold cyclic) / Delta z: 14.3312 Å / Delta phi: 43.5023 deg.
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 9 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Output model

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