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- PDB-8uao: DpHF18 filament -

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Basic information

Entry
Database: PDB / ID: 8uao
TitleDpHF18 filament
ComponentsDpHF18
KeywordsDE NOVO PROTEIN / Filament / pH / designed
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLynch, E.M. / Shen, H. / Kollman, J.M. / 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 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DpHF18
B: DpHF18
C: DpHF18
N: DpHF18
D: DpHF18
O: DpHF18
E: DpHF18
P: DpHF18
F: DpHF18
Q: DpHF18
G: DpHF18
R: DpHF18
H: DpHF18
S: DpHF18
I: DpHF18
T: DpHF18
J: DpHF18
U: DpHF18
K: DpHF18
V: DpHF18
L: DpHF18
W: DpHF18
M: DpHF18
X: DpHF18


Theoretical massNumber of molelcules
Total (without water)631,62224
Polymers631,62224
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
DpHF18


Mass: 26317.572 Da / Num. of mol.: 24
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: DpHF18 / 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 FIELD / 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
7UCSF Chimeramodel fitting
9ISOLDEmodel refinement
10PHENIXmodel refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 59.3 ° / Axial rise/subunit: 16.7 Å / Axial symmetry: D1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71194 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingType: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00542072
ELECTRON MICROSCOPYf_angle_d0.70956976
ELECTRON MICROSCOPYf_dihedral_angle_d37.2465712
ELECTRON MICROSCOPYf_chiral_restr0.0357536
ELECTRON MICROSCOPYf_plane_restr0.0097176

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