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- EMDB-29847: C3HR3_8r: Extendable repeat protein trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-29847
TitleC3HR3_8r: Extendable repeat protein trimer
Map dataSharpened map
Sample
  • Complex: C3HR3_8r
    • Protein or peptide: C3HR3_8r
KeywordsOligomer / repeat protein / DE NOVO PROTEIN
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.58 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_29847.png

Downloads & links

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Map

FileDownload / File: emd_29847.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: 0.229
Minimum - Maximum-0.6061066 - 1.0379051
Average (Standard dev.)-0.00005761592 (±0.031220792)
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_29847_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_29847_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_29847_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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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_8r

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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_8r

MacromoleculeName: C3HR3_8r / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKFQKLMDLI KANPEIQEII ELYKFVGRED VVKKLEEVIK WAVEEAGDNE KFLKLLELIL SNPEIFEILL EYIYINREDV VKKLFSVIKW AVEEAGDNLV FLRLLENILS NPEIFEILLE YIYIGKEDVV KKLFSVIKWA VEEAGNNLVF LRLLENILSN PEIFEILLEY ...String:
MKFQKLMDLI KANPEIQEII ELYKFVGRED VVKKLEEVIK WAVEEAGDNE KFLKLLELIL SNPEIFEILL EYIYINREDV VKKLFSVIKW AVEEAGDNLV FLRLLENILS NPEIFEILLE YIYIGKEDVV KKLFSVIKWA VEEAGNNLVF LRLLENILSN PEIFEILLEY IYIGKEDVVK KLFSVIKWAV EEAGNNLVFL RLLENILSNP EIFEILLEYI YIGKEDVVKK LFSVIKWAVE EAGNNLVFLR LLENILSNPE IFEILLEYIY IGKEDVVKKL FSVIKWAVEE AGNNPIFLKL LKSLLENPEI FKILLEYCEK NKEDVVKKLF KVIKWAVEEA GNNPIVLDKL KEILEDPEKF KELLEKIEVG KEEEVKAEFK KLIEEVKEEG SWLEHHHHHH

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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

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36408
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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