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- EMDB-22305: CryoEM structure of designed helical fusion protein C4_nat_HFuse-7900 -

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Basic information

Entry
Database: EMDB / ID: EMD-22305
TitleCryoEM structure of designed helical fusion protein C4_nat_HFuse-7900
Map data
Sample
  • Complex: Designed fusion of helical bundle and helical repeat proteins
    • Protein or peptide: C4_nat_HFuse-7900
Keywordshelical bundle / helical repeat / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRedler RL / Edman NI
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1629214 United States
CitationJournal: Nat Commun / Year: 2021
Title: Design of multi-scale protein complexes by hierarchical building block fusion.
Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una ...Authors: Yang Hsia / Rubul Mout / William Sheffler / Natasha I Edman / Ivan Vulovic / Young-Jun Park / Rachel L Redler / Matthew J Bick / Asim K Bera / Alexis Courbet / Alex Kang / T J Brunette / Una Nattermann / Evelyn Tsai / Ayesha Saleem / Cameron M Chow / Damian Ekiert / Gira Bhabha / David Veesler / David Baker /
Abstract: A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two ...A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.
History
DepositionJul 16, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0158
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0158
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xss
  • Surface level: 0.0158
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22305.png

Downloads & links

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Map

FileDownload / File: emd_22305.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 250 pix.
= 214.75 Å		0.86 Å/pix.
x 250 pix.
= 214.75 Å		0.86 Å/pix.
x 250 pix.
= 214.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.859 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0158 / Movie #1: 0.0158
Minimum - Maximum-0.056515362 - 0.07906761
Average (Standard dev.)-0.0007243884 (±0.0029319269)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 214.75 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8590.8590.859
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z214.750214.750214.750
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0570.079-0.001

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Supplemental data

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Sample components

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Entire : Designed fusion of helical bundle and helical repeat proteins

EntireName: Designed fusion of helical bundle and helical repeat proteins
Components
  • Complex: Designed fusion of helical bundle and helical repeat proteins
    • Protein or peptide: C4_nat_HFuse-7900

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Supramolecule #1: Designed fusion of helical bundle and helical repeat proteins

SupramoleculeName: Designed fusion of helical bundle and helical repeat proteins
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: C4_nat_HFuse-7900

MacromoleculeName: C4_nat_HFuse-7900 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 28.706484 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ASSWVMLGLL LSLLNRLSLA AEAYKKAIEL DPNDALAWLL LGSVLLLLGR EEEAEEAARK AIELKPEMDS ARRLEGIIEL IRRAREAAE RAQEAAERTG DPRVRELARE LKRLAQEAAE EVRRDPDSKD VNEALKLIVE AIEAAVRALE AAERTGDPEV R ELARELVR ...String:
ASSWVMLGLL LSLLNRLSLA AEAYKKAIEL DPNDALAWLL LGSVLLLLGR EEEAEEAARK AIELKPEMDS ARRLEGIIEL IRRAREAAE RAQEAAERTG DPRVRELARE LKRLAQEAAE EVRRDPDSKD VNEALKLIVE AIEAAVRALE AAERTGDPEV R ELARELVR LAVEAAEEVQ RNPSSSDVNE ALKLIVEAID AAVRALEAAE KTGDPEVREL ARELVRLAVE AAEEVQRNPS SE EVNEALK DIVKAIQEAV ESL

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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

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.05 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 144329
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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