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- PDB-8ub3: DpHF7 filament -

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Basic information

Entry
Database: PDB / ID: 8ub3
TitleDpHF7 filament
ComponentsDpHF7 filament
KeywordsDE NOVO PROTEIN / Filament / pH / designed
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLynch, E.M. / Farrell, D. / Shen, H. / Kollman, J.M. / DiMaio, F. / Baker, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149542 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118396 United States
National Institutes of Health/Office of the DirectorS10OD032290 United States
CitationJournal: Nat Nanotechnol / Year: 2024
Title: De novo design of pH-responsive self-assembling helical protein filaments.
Authors: Hao Shen / Eric M Lynch / Susrut Akkineni / Joseph L Watson / Justin Decarreau / Neville P Bethel / Issa Benna / William Sheffler / Daniel Farrell / Frank DiMaio / Emmanuel Derivery / James ...Authors: Hao Shen / Eric M Lynch / Susrut Akkineni / Joseph L Watson / Justin Decarreau / Neville P Bethel / Issa Benna / William Sheffler / Daniel Farrell / Frank DiMaio / Emmanuel Derivery / James J De Yoreo / Justin Kollman / David Baker /
Abstract: Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures ...Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.
History
DepositionSep 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DpHF7 filament
B: DpHF7 filament
C: DpHF7 filament
D: DpHF7 filament
E: DpHF7 filament
F: DpHF7 filament
G: DpHF7 filament
H: DpHF7 filament
J: DpHF7 filament
K: DpHF7 filament
L: DpHF7 filament
M: DpHF7 filament
Q: DpHF7 filament
U: DpHF7 filament
c: DpHF7 filament
k: DpHF7 filament
s: DpHF7 filament
w: DpHF7 filament
4: DpHF7 filament
Z: DpHF7 filament


Theoretical massNumber of molelcules
Total (without water)532,81320
Polymers532,81320
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
DpHF7 filament


Mass: 26640.637 Da / Num. of mol.: 20
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: DpHF7 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
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
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 50

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4cryoSPARCCTF correction
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13Rosettamodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -43.1 ° / Axial rise/subunit: 24 Å / Axial symmetry: D2
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56749 / Symmetry type: HELICAL
Atomic model buildingType: in silico model

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