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- EMDB-42088: DpHF19 filament -

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Basic information

Entry
Database: EMDB / ID: EMD-42088
TitleDpHF19 filament
Map dataDpHF19 filament
Sample
  • Complex: DpHF19
    • Protein or peptide: DpHF19,Green fluorescent protein (Fragment)
KeywordsFilament / pH / designed / DE NOVO PROTEIN
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciessynthetic construct (others) / Aequorea victoria (jellyfish)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLynch EM / Shen H / Kollman JM / 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_42088.png

Downloads & links

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Map

FileDownload / File: emd_42088.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDpHF19 filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.16 Å/pix.
x 320 pix.
= 371.2 Å		1.16 Å/pix.
x 320 pix.
= 371.2 Å		1.16 Å/pix.
x 320 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-9.646986 - 16.662372999999999
Average (Standard dev.)0.00007683134 (±0.38877887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 371.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_42088_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_42088_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 : DpHF19

EntireName: DpHF19
Components
  • Complex: DpHF19
    • Protein or peptide: DpHF19,Green fluorescent protein (Fragment)

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Supramolecule #1: DpHF19

SupramoleculeName: DpHF19 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DpHF19,Green fluorescent protein (Fragment)

MacromoleculeName: DpHF19,Green fluorescent protein (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 54.425699 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSEEEIAKA LEELVASLAE LKRATLKLLD ITDKLKKNPS ESALVSHNKA IVEHNAIIVE NNRIIAAVLE LIVRAVGMTD EIDLALLKL KASTARLKVA TALLRMITEE LKKNPSEDAL VEHNRAIVNH NAIIVENNRI IAAVLELIVR ALNLTDEEVR K ALEELKAS ...String:
MGSEEEIAKA LEELVASLAE LKRATLKLLD ITDKLKKNPS ESALVSHNKA IVEHNAIIVE NNRIIAAVLE LIVRAVGMTD EIDLALLKL KASTARLKVA TALLRMITEE LKKNPSEDAL VEHNRAIVNH NAIIVENNRI IAAVLELIVR ALNLTDEEVR K ALEELKAS TAELKRATAS LRAITEELKK NPSEDALVEH NRAIVEHNAI IVENNRIIAL VLLLIVLAIG GSGGSGGSGG SG GSGGSGG SGSSKGEELF TGVVPILVEL DGDVNGHKFS VRGEGEGDAT NGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCF ARYPDH MKQHDFFKSA MPEGYVQERT ISFKDDGTYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNFNS HNVY ITADK QKNGIKANFK IRHNVEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSV LSKDPNEKRD HMVLLEFVTA AGITH GMDE LYKGSLEHHH HHH

UniProtKB: Green fluorescent protein

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -148.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 406281
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
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ubg:
DpHF19 filament

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