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- EMDB-29856: C3HR3_9r_shift4: Extendable repeat protein fiber -

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Basic information

Entry
Database: EMDB / ID: EMD-29856
TitleC3HR3_9r_shift4: Extendable repeat protein fiber
Map dataSharpened map
Sample
  • Complex: C3HR3_8r
    • Protein or peptide: C3HR3_9r_shift4
KeywordsOligomer / repeat protein / DE NOVO PROTEIN
Biological speciesunidentified (others) / synthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsBethel NP / Borst AJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)GT11817 United States
CitationJournal: Nat Chem / Year: 2023
Title: Precisely patterned nanofibres made from extendable protein multiplexes.
Authors: Neville P Bethel / Andrew J Borst / Fabio Parmeggiani / Matthew J Bick / T J Brunette / Hannah Nguyen / Alex Kang / Asim K Bera / Lauren Carter / Marcos C Miranda / Ryan D Kibler / Mila Lamb ...Authors: Neville P Bethel / Andrew J Borst / Fabio Parmeggiani / Matthew J Bick / T J Brunette / Hannah Nguyen / Alex Kang / Asim K Bera / Lauren Carter / Marcos C Miranda / Ryan D Kibler / Mila Lamb / Xinting Li / Banumathi Sankaran / David Baker /
Abstract: Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the ...Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C to C and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.
History
DepositionFeb 17, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29856.png

Downloads & links

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Map

FileDownload / File: emd_29856.map.gz / Format: CCP4 / Size: 169.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 0.885 Å
Density
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.76130366 - 0.8842334
Average (Standard dev.)0.00029345628 (±0.03083164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions354354354
Spacing354354354
CellA=B=C: 313.29 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_29856_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_29856_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_29856_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C3HR3_8r

EntireName: C3HR3_8r
Components
  • Complex: C3HR3_8r
    • Protein or peptide: C3HR3_9r_shift4

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Supramolecule #1: C3HR3_8r

SupramoleculeName: C3HR3_8r / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 141 KDa

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Macromolecule #1: C3HR3_9r_shift4

MacromoleculeName: C3HR3_9r_shift4 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 55.922121 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVYERLKELI EENPEIQEIL ELWKFIGRED VVEKLFEVIK WAVEEGGNNM VFISLLKEIL SNPEIFEILL KWVDIGREDV VKKLFSVIK QAVEDGGNNM VFLSLLKELL SNPEIFEILL LWVEINREDV VKKFFDVIKW AVERGGNNPK FLSLLKLILS N PEIFKILL ...String:
MVYERLKELI EENPEIQEIL ELWKFIGRED VVEKLFEVIK WAVEEGGNNM VFISLLKEIL SNPEIFEILL KWVDIGREDV VKKLFSVIK QAVEDGGNNM VFLSLLKELL SNPEIFEILL LWVEINREDV VKKFFDVIKW AVERGGNNPK FLSLLKLILS N PEIFKILL LWVYENKEEV VKKLFDVLLY AVKEGGDNEK FLELLKEILS NPEIFEILLE WVEENKEDVV KKLFDVIKYA VE RGGDNEK FYELLKLLLS NPEIFKILLE WVEINKEDVV KKFFDVIKWA VEEGGDNPVF YRLLKLILSN PEIFKILLEW VDI NNEDVV KKLFSVIKQA VEDGGNNMVF IDLLELILSN PEIFEILLLW VHINREDVVK KLFDVIKWAV EDGGNNMVFI HLLR KLLSN PEIFEILLLW VDIGREEVVK KFFEKVLEAV KEGGNDMIEI KKLEEILLDP EKFEELLLEV GSLEHHHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Helical parameters - Δz: 33.048 Å
Applied symmetry - Helical parameters - Δ&Phi: 142.838 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76015
FSC plot (resolution estimation)

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