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- PDB-6e9y: DHF38 filament -

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Basic information

Entry
Database: PDB / ID: 6e9y
TitleDHF38 filament
ComponentsDHF38 filament
KeywordsPROTEIN FIBRIL / Protein design / filament
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.3 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
A: DHF38 filament
B: DHF38 filament
C: DHF38 filament
D: DHF38 filament
E: DHF38 filament
F: DHF38 filament
G: DHF38 filament
H: DHF38 filament
I: DHF38 filament
J: DHF38 filament
K: DHF38 filament
L: DHF38 filament
M: DHF38 filament
N: DHF38 filament
O: DHF38 filament


Theoretical massNumber of molelcules
Total (without water)375,99315
Polymers375,99315
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33440 Å2
ΔGint-135 kcal/mol
Surface area153880 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 15 / Rise per n subunits: 8.29531 Å / Rotation per n subunits: -88.17 °)

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Components

#1: Protein
DHF38 filament


Mass: 25066.168 Da / Num. of mol.: 15
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: DHF38 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: 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 FIELDBright-field microscopy
Image recordingElectron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
7PHENIXmodel fitting
9RELIONinitial Euler assignment
10FREALIGNfinal Euler assignment
12FREALIGN3D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -88.17 ° / Axial rise/subunit: 8.29531 Å / Axial symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112593 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT

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