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- PDB-6e9v: DHF79 filament -

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Basic information

Entry
Database: PDB / ID: 6e9v
TitleDHF79 filament
ComponentsDHF79 filament
KeywordsPROTEIN FIBRIL / Protein design / filament
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.9 Å
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 ...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.
History
DepositionAug 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
Q: DHF79 filament
A: DHF79 filament
B: DHF79 filament
C: DHF79 filament
D: DHF79 filament
E: DHF79 filament
F: DHF79 filament
G: DHF79 filament
H: DHF79 filament
I: DHF79 filament
J: DHF79 filament
K: DHF79 filament
L: DHF79 filament
M: DHF79 filament
N: DHF79 filament
O: DHF79 filament
P: DHF79 filament
R: DHF79 filament
S: DHF79 filament
T: DHF79 filament
U: DHF79 filament
V: DHF79 filament
W: DHF79 filament
X: DHF79 filament
Y: DHF79 filament
Z: DHF79 filament


Theoretical massNumber of molelcules
Total (without water)600,91026
Polymers600,91026
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28540 Å2
ΔGint-243 kcal/mol
Surface area270910 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 26 / Rise per n subunits: 5.07952 Å / Rotation per n subunits: 77.6764 °)

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Components

#1: Protein ...
DHF79 filament


Mass: 23111.928 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: DHF79 filament / Type: COMPLEX / Entity ID: all / 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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 77.6764 ° / Axial rise/subunit: 5.07952 Å / Axial symmetry: C1
3D reconstructionResolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32583 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT

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