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- PDB-6e9z: DHF119 filament -

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Database: PDB / ID: 6e9z
TitleDHF119 filament
ComponentsDHF119 filament
KeywordsPROTEIN FIBRIL / Protein design / filament
Specimen sourcesynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.4 Å resolution
AuthorsLynch, E.M. / Shen, H. / Fallas, J.A. / Kollman, J.M. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Aug 1, 2018 / Release: Nov 21, 2018

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Deposited unit
B: DHF119 filament
A: DHF119 filament
C: DHF119 filament
F: DHF119 filament
D: DHF119 filament
H: DHF119 filament
G: DHF119 filament
E: DHF119 filament
I: DHF119 filament

Theoretical massNumber of molelcules
Total (without water)226,0829

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)11080
ΔGint (kcal/M)1
Surface area (Å2)95720
Helical symmetryCircular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 3 / Rise per n subunits: 14.3312 / Rotation per n subunits: 43.5023


#1: Protein/peptide
DHF119 filament

Mass: 25120.242 Da / Num. of mol.: 9 / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

Experimental details


EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

Sample preparation

ComponentName: DHF119 filament / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 90 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


EM software
2EPUimage acquisition
7PHENIXmodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11RELIONinitial Euler assignment
12RELIONfinal Euler assignment
14RELION3D reconstruction
Helical symmertyAngular rotation/subunit: 43.5023 / Axial rise/subunit: 14.3312 / Axial symmetry: C3
3D reconstructionResolution: 3.4 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 63067 / Symmetry type: HELICAL
Atomic model buildingRef protocol: FLEXIBLE FIT

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