[English] 日本語
Yorodumi
- EMDB-40260: CryoEM map of a de novo designed T=4 icosahedral nanocage hierarc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40260
TitleCryoEM map of a de novo designed T=4 icosahedral nanocage hierarchically built from pseudosymmetric trimers; design Ico(T=4)-4
Map datasharpened map from Local Refinement
Sample
  • Complex: Icos(T=4)-4
    • Protein or peptide: Icos(T=4)-4 chain A
    • Protein or peptide: Icos(T=4)-4 chain B
    • Protein or peptide: Icos(T=4)-4 chain C
    • Protein or peptide: Icos(T=4)-4 chain ho
Keywordsicosahedral nanocage / T=4 / T=4 icosahedra / nanomaterial / computational design / de novo / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.78 Å
AuthorsBorst AJ / Kibler RD / Lee S
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: Four-component protein nanocages designed by programmed symmetry breaking.
Authors: Sangmin Lee / Ryan D Kibler / Green Ahn / Yang Hsia / Andrew J Borst / Annika Philomin / Madison A Kennedy / Buwei Huang / Barry Stoddard / David Baker /
Abstract: Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures. Viruses access more ...Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures. Viruses access more complex higher triangulation number icosahedral architectures by breaking perfect point group symmetry, but nature appears not to have explored similar symmetry breaking for tetrahedral or octahedral symmetries. Here we describe a general design strategy for building higher triangulation number architectures starting from regular polyhedra through pseudosymmetrization of trimeric building blocks. Electron microscopy confirms the structures of T = 4 cages with 48 (tetrahedral), 96 (octahedral) and 240 (icosahedral) subunits, each with 4 distinct chains and 6 different protein-protein interfaces, and diameters of 33 nm, 43 nm and 75 nm, respectively. Higher triangulation number viruses possess very sophisticated functionalities; our general route to higher triangulation number nanocages should similarly enable a next generation of multiple antigen-displaying vaccine candidates and targeted delivery vehicles.
History
DepositionMar 31, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40260.png

Downloads & links

-
Map

FileDownload / File: emd_40260.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from Local Refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.33 Å/pix.
x 360 pix.
= 1199.52 Å		3.33 Å/pix.
x 360 pix.
= 1199.52 Å		3.33 Å/pix.
x 360 pix.
= 1199.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.268
Minimum - Maximum-0.1036961 - 0.71868557
Average (Standard dev.)-0.0025771467 (±0.05261018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1199.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: unsharpened map from Local Refinement

Fileemd_40260_additional_1.map
Annotationunsharpened map from Local Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_40260_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_40260_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Icos(T=4)-4

EntireName: Icos(T=4)-4
Components
  • Complex: Icos(T=4)-4
    • Protein or peptide: Icos(T=4)-4 chain A
    • Protein or peptide: Icos(T=4)-4 chain B
    • Protein or peptide: Icos(T=4)-4 chain C
    • Protein or peptide: Icos(T=4)-4 chain ho

-
Supramolecule #1: Icos(T=4)-4

SupramoleculeName: Icos(T=4)-4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: A hierarchically designed T=4 icosahedral nanocage
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: Icos(T=4)-4 chain A

MacromoleculeName: Icos(T=4)-4 chain A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSLELALKA LQILVNAAYV LAEIARDRGN EELLEKAARL AEEAARQAER IARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE ...String:
MGSLELALKA LQILVNAAYV LAEIARDRGN EELLEKAARL AEEAARQAER IARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVE VAVKAARVAV EAAKQAGDND VLRKVADQAL EIAKAALEQG DIDVAQKAMD VAVEALTQAG GSGGSHHHHH H

-
Macromolecule #2: Icos(T=4)-4 chain B

MacromoleculeName: Icos(T=4)-4 chain B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSPRLVLRA LENMVRAAHT LAEIARDNGN EEWLERAARL AEEVARRAER LAREARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEE LEYAARLAEE AARQAIEIAA QAMEEGNLEL ALKALQIIVN AAYVLAEIAR DRGNEELLEK AASLAEAAAA LAEAIAAILE ...String:
MGSPRLVLRA LENMVRAAHT LAEIARDNGN EEWLERAARL AEEVARRAER LAREARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEE LEYAARLAEE AARQAIEIAA QAMEEGNLEL ALKALQIIVN AAYVLAEIAR DRGNEELLEK AASLAEAAAA LAEAIAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVE VAVKAARVAV EAAKQAGDND VLRKVAEQAL EIAKKAAEQG DVGVMQKAMD VALRAAGQAG GSGGSHHHHH H

-
Macromolecule #3: Icos(T=4)-4 chain C

MacromoleculeName: Icos(T=4)-4 chain C / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIAA QAMEEGNFEL ALEALEIINE AARVLARIAH HRGNQELLEK AASLTHASAA LSRAIAAILE ...String:
MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIAA QAMEEGNFEL ALEALEIINE AARVLARIAH HRGNQELLEK AASLTHASAA LSRAIAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVE VAVKAARVAV EAAKQAGDND VLRKVAEQAL RIAKEAEKQG NVIVAVRAAL VAAQAATEAG DQDVLRKVDE QLERILKEAR KQGGSGGSHH HHHH

-
Macromolecule #4: Icos(T=4)-4 chain ho

MacromoleculeName: Icos(T=4)-4 chain ho / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE ...String:
MGSPELFLQD LRSLVEAARI LARLARQRGD EHALERAARW AEQAARQAER LARQARKEGN LELALKALQI LVNAAYVLAE IARDRGNEEL LEYAARLAEE AARQAIEIWA QAMEEGNQQL RTKAAHIILR AAEVLLEIAR DRGNQELLEK AASLVDAVAA LQQAAAAILE GDVEKAVRAA QEAVKAAKEA GDNDMLRAVA IAALRIAKEA EKQGNVEVAV KAARVAVEAA KQAGDNDVLR KVAEQALRIA KEAEKQGNVE VAVKAARVAV EAAKQAGDND VLRKVAEQAL RIAKEAEKQG NVVVATQAAI VAIQAARLAG DQDVGRKVIE QEERIAKEAR KQGGSGGSHH HHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8 / Details: 25mM Tris, 300mM NaCl
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6678 / Average electron dose: 61.463 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6896
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more