[English] 日本語
Yorodumi
- EMDB-52510: MEDUSA-Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52510
TitleMEDUSA-Complex
Map data
Sample
  • Complex: MEDUSA complex
KeywordsMultivalency / supramolecular assemblies / FNAP / directed evolution / antivirals / SELEX / aptamers / DNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsDuhoo Y / Kononenko A
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationPCEGP2_181137 Switzerland
CitationJournal: Nat Nanotechnol / Year: 2025
Title: Evolution of multivalent supramolecular assemblies of aptamers with target-defined spatial organization.
Authors: Artem Kononenko / Vincenzo Caroprese / Yoan Duhoo / Cem Tekin / Maartje M C Bastings /
Abstract: Rapid identification of neutralizing molecules against new and mutating viruses is key to efficiently combating biorisk. Current binder identification techniques use a monovalent library of potential ...Rapid identification of neutralizing molecules against new and mutating viruses is key to efficiently combating biorisk. Current binder identification techniques use a monovalent library of potential binders. Interestingly, proteins on pathogens are often homo-oligomeric-for example, the SARS-CoV-2 spike protein is a homotrimer. Here we describe a simple strategy, MEDUSA (multivalent evolved DNA-based supramolecular assembly), to evolve multivalent assemblies of aptamers with precise interligand spacing and three-fold symmetry, mirroring the geometric structure of many viral capsid proteins. MEDUSA allowed the selection of potent SARS-CoV-2 spike binders structurally distinct from any known aptamers. Decoupling the geometric and structural rigidity contributions toward selectivity made it possible to connect form to function, as demonstrated by the design of tunable fluorescent sensors. This approach offers a blueprint for targeting geometrically defined pathogen structures and developing rapid-response tools for emerging pathogens.
History
DepositionJan 10, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52510.png

Downloads & links

-
Map

FileDownload / File: emd_52510.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.72 Å/pix.
x 128 pix.
= 476.16 Å		3.72 Å/pix.
x 128 pix.
= 476.16 Å		3.72 Å/pix.
x 128 pix.
= 476.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.176
Minimum - Maximum-0.24061507 - 3.2080772
Average (Standard dev.)-0.0002379349 (±0.0351977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 476.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_52510_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52510_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MEDUSA complex

EntireName: MEDUSA complex
Components
  • Complex: MEDUSA complex

-
Supramolecule #1: MEDUSA complex

SupramoleculeName: MEDUSA complex / type: complex / ID: 1 / Parent: 0
Details: Nano assembly of functionalized nucleic acid polymer on the DNA scaffold.
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 69 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.35 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
1.0 unitPBSphosphate Saline Buffer
1.0 mMMgCl2Magnesium Choride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Details: 15mA on GloQube Plus
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 1196 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Calibrated magnification: 150000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 542921
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5620
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 1 / Avg.num./class: 5620 / Software - Name: cryoSPARC (ver. 4)
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://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