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- EMDB-23174: Crown C5_Crn_HF-12_26 -

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Basic information

Entry
Database: EMDB / ID: EMD-23174
TitleCrown C5_Crn_HF-12_26
Map data
Sample
  • Complex: C5_Crn_HF-12_26
    • Protein or peptide: C5_Crn_HF-12_26
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsPark YJ / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 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
DepositionDec 21, 2020-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJun 2, 2021-
Current statusJun 2, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.36
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.36
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23174.png

Downloads & links

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Map

FileDownload / File: emd_23174.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36 / Movie #1: 0.36
Minimum - Maximum-1.1650076 - 2.4189448
Average (Standard dev.)0.006523715 (±0.07042909)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.1652.4190.007

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Supplemental data

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Additional map: #1

Fileemd_23174_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_23174_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_23174_half_map_2.map
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Sample components

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Entire : C5_Crn_HF-12_26

EntireName: C5_Crn_HF-12_26
Components
  • Complex: C5_Crn_HF-12_26
    • Protein or peptide: C5_Crn_HF-12_26

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Supramolecule #1: C5_Crn_HF-12_26

SupramoleculeName: C5_Crn_HF-12_26 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: C5_Crn_HF-12_26

MacromoleculeName: C5_Crn_HF-12_26 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
SequenceString: MGTESKVLEA EMSIKKAEWS AREGNPEKAT EDLMRAMLLI RELDVLAQKT GSAEVLVKAA ALAE KLAKV AREVGDPEMA REAEKLARAL AAKLLSMHAK LLATFLENLR RHLDRLDKHI KQLRDILSE HPHDERVKDV IDLSERSVRI VKKVIKIFED SVRELLKMML ...String:
MGTESKVLEA EMSIKKAEWS AREGNPEKAT EDLMRAMLLI RELDVLAQKT GSAEVLVKAA ALAE KLAKV AREVGDPEMA REAEKLARAL AAKLLSMHAK LLATFLENLR RHLDRLDKHI KQLRDILSE HPHDERVKDV IDLSERSVRI VKKVIKIFED SVRELLKMML KRAEELAKSP DPEDLKAAVD VARA VIEAN PGSNLSRKAM EIIERAAREL SKLPDPEAIA TAIEAASQLA TMAAATGNTD QVRRAAKLM MRIAILAGTD LASAAALDAL LRVLETALQI ATKIIDDANK LLEKLRRSHH HDPKVVETYV ELLK RHEEA VRLLLDVAIM HALIVVMQDA IEAAREGDKD RARKALQDAL ELARLAGTTE AVEAALLVV EAVAVAAARA GATDVVREAL EVALEIARES GTTEAVKLAL EVVASVAIEA ARRGNTDAVR EALE VALEI ARESGTEEAV RLALEVVKRV SDEAKKQGNE DAVKEAEEVR KKIEEES

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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 K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER / Details: Cryosparc Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2969
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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