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- EMDB-29904: C5HR2_4r: Extendable repeat protein pentamer -

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Basic information

Entry
Database: EMDB / ID: EMD-29904
TitleC5HR2_4r: Extendable repeat protein pentamer
Map dataSharpened map
Sample
  • Complex: C5HR2_4r
    • Protein or peptide: C5HR2_4r
Keywordsoligomer / repeat protein / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 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 23, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29904.png

Downloads & links

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Map

FileDownload / File: emd_29904.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 352 pix.
= 311.52 Å		0.89 Å/pix.
x 352 pix.
= 311.52 Å		0.89 Å/pix.
x 352 pix.
= 311.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.253
Minimum - Maximum-1.0419571 - 1.5856576
Average (Standard dev.)0.000080696744 (±0.021806393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 311.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_29904_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_29904_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_29904_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 : C5HR2_4r

EntireName: C5HR2_4r
Components
  • Complex: C5HR2_4r
    • Protein or peptide: C5HR2_4r

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Supramolecule #1: C5HR2_4r

SupramoleculeName: C5HR2_4r / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 92.4 KDa

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Macromolecule #1: C5HR2_4r

MacromoleculeName: C5HR2_4r / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.505766 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MVEELKRKLR QAKEDGDEEL LERVKNEMLL LAVVDPRVLV EVLNTAKELG DEEMYKKVKG IMLRLAVVDP RVLVLVLELA EALGDEEMK EKVKNIMLLL AVVDPRVLVL VLELAEELGD EEMKKEVEEI LDKLAEVDPR VAVLKEVAKK EGSWLEHHHH H H

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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 K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42938
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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