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- EMDB-23169: Dihedral ring D2_Wm-02 -

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Basic information

Entry
Database: EMDB / ID: EMD-23169
TitleDihedral ring D2_Wm-02
Map data
Sample
  • Complex: D2_Wm-02
    • Protein or peptide: D2_Wm-02A
    • Protein or peptide: D2_Wm-02B
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / negative staining / Resolution: 19.0 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: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23169.png

Downloads & links

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Map

FileDownload / File: emd_23169.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.4 Å/pix.
x 80 pix.
= 512. Å		6.4 Å/pix.
x 80 pix.
= 512. Å		6.4 Å/pix.
x 80 pix.
= 512. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-0.9745522 - 8.529947
Average (Standard dev.)-0.01655915 (±0.33637622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 512.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.46.46.4
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000512.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.9758.530-0.017

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Supplemental data

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Additional map: #1

Fileemd_23169_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_23169_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_23169_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : D2_Wm-02

EntireName: D2_Wm-02
Components
  • Complex: D2_Wm-02
    • Protein or peptide: D2_Wm-02A
    • Protein or peptide: D2_Wm-02B

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Supramolecule #1: D2_Wm-02

SupramoleculeName: D2_Wm-02 / 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: D2_Wm-02A

MacromoleculeName: D2_Wm-02A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
SequenceString: MGTREEIIRE LARSLAEQAE LTARLERSLR EQERLQREGS SDEDVRELIR EQKELVREIL KLIA EQILL IAELLLASTR SEAAELALRA IRNAIEACKN ADNEEMCRQL MRMAQNALEL ATQAPDAEA AKAALRAIDL AVELASRHPG SQAADDALKL AQQAAEAVKL ...String:
MGTREEIIRE LARSLAEQAE LTARLERSLR EQERLQREGS SDEDVRELIR EQKELVREIL KLIA EQILL IAELLLASTR SEAAELALRA IRNAIEACKN ADNEEMCRQL MRMAQNALEL ATQAPDAEA AKAALRAIDL AVELASRHPG SQAADDALKL AQQAAEAVKL ALDLYREHPN ADIADLCRKA AKEA AEAAS KAAELAQRHP DSQAARDAIK LASQAAEAVK LACELAQEHP NAEIAKMCIL AASAAALMA SIAAILAQRH PDSQIARDLI RLASELAEMV KRMCERGGSW GLEHHHHHH

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Macromolecule #2: D2_Wm-02B

MacromoleculeName: D2_Wm-02B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
SequenceString: MGTREELAKE LLRSLREQAE SLARQLRLLK ELERLQREGS SDEDVRELLR EIKELAAEQI KLIM EQLLL IAELMLGRSE AAELALEAIR LALELCRQST DQEQCTDLLR QATEALETAT RYPDDTNAK AKLMAITARL LAQQLRTQHP DSQAARDAEK LADQAEKAVR ...String:
MGTREELAKE LLRSLREQAE SLARQLRLLK ELERLQREGS SDEDVRELLR EIKELAAEQI KLIM EQLLL IAELMLGRSE AAELALEAIR LALELCRQST DQEQCTDLLR QATEALETAT RYPDDTNAK AKLMAITARL LAQQLRTQHP DSQAARDAEK LADQAEKAVR LAKRLYEEHP NADKSELCSQ LAYA AALLA SIAAMLAQRH PDSQEARDMI RIASELAELV KEICER

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: UF

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21778
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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