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- EMDB-42075: DpHF7 filament -

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Basic information

Entry
Database: EMDB / ID: EMD-42075
TitleDpHF7 filament
Map dataDpHF7 filament
Sample
  • Complex: DpHF7
    • Protein or peptide: DpHF7 filament
KeywordsFilament / pH / designed / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLynch EM / Farrell D / Shen H / Kollman JM / DiMaio F / Baker D
Funding support United States, 3 items
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, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42075.png

Downloads & links

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Map

FileDownload / File: emd_42075.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDpHF7 filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.95
Minimum - Maximum-7.3613644 - 14.377176
Average (Standard dev.)0.000040938234 (±0.40346402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_42075_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_42075_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DpHF7

EntireName: DpHF7
Components
  • Complex: DpHF7
    • Protein or peptide: DpHF7 filament

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Supramolecule #1: DpHF7

SupramoleculeName: DpHF7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DpHF7 filament

MacromoleculeName: DpHF7 filament / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.640637 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSEVEILKA LLELKKSTAE LKRATASLRA ITEELKKNPS EDALVEHNRA IVEHNAIIVE NNRIIAAVLM LIVVAVGMTQ EIKKALEEL VASTAELKRA TASLRAITEE LKKNPSEDAL VEHNRAIVEH NAIIVENNRI IAAVLELIVR ALNLTDAEVI K ALIELRLS ...String:
MGSEVEILKA LLELKKSTAE LKRATASLRA ITEELKKNPS EDALVEHNRA IVEHNAIIVE NNRIIAAVLM LIVVAVGMTQ EIKKALEEL VASTAELKRA TASLRAITEE LKKNPSEDAL VEHNRAIVEH NAIIVENNRI IAAVLELIVR ALNLTDAEVI K ALIELRLS TLELVAATAS LREITEELKK NPSEDALVEH NRAIVEHNAI IVENNRIIAA VLELIVGGSG GSGGSGGSSL EH HHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 24.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -43.1 °
Applied symmetry - Helical parameters - Axial symmetry: D2 (2x2 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 56749
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Initial model type: in silico model
Output model

PDB-8ub3:
DpHF7 filament

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