[English] 日本語
Yorodumi
- EMDB-53787: Paranemic crossover triangle (PXT) with 2'-Fluoro-modified pyrimi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53787
TitleParanemic crossover triangle (PXT) with 2'-Fluoro-modified pyrimidines (FY RNA)
Map datacryo-EM map of 2-prime-fluoro-modified pyrimidine RNA Paranemic crossover triangle (PXT) origami structure.
Sample
  • Complex: Single-stranded PXT made of 2'fluoro modified pyrimidine RNA
    • RNA: DNA/RNA (238-MER)
Keywordsorigami / modified nucleic acids / XNA / RNA / crossover / tetra-loop / 2'fluoro
Biological speciessynthetic construct (others) / synthetic RNA (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.41 Å
AuthorsKristoffersen EL / Andersen ES / Zwergius NH
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0070452 Denmark
CitationJournal: To Be Published
Title: Serum-stable RNA origami nanodevices
Authors: Kristoffersen EL / Zwergius NH / Vallina NS / Gluck N / Stange A / Desdorf L / Civit L / Geary C / Kjems J / Valero J / Andersen ES
History
DepositionMay 15, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53787.png

Downloads & links

-
Map

FileDownload / File: emd_53787.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of 2-prime-fluoro-modified pyrimidine RNA Paranemic crossover triangle (PXT) origami structure.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 258.8 Å		0.65 Å/pix.
x 400 pix.
= 258.8 Å		0.65 Å/pix.
x 400 pix.
= 258.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0655
Minimum - Maximum-0.1005047 - 0.24808745
Average (Standard dev.)-0.00008133533 (±0.006175731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 258.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A of 2-prime-fluoro-modified pyrimidine RNA Paranemic...

Fileemd_53787_half_map_1.map
AnnotationHalf map A of 2-prime-fluoro-modified pyrimidine RNA Paranemic crossover triangle (PXT) origami structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B of 2-prime-fluoro-modified pyrimidine RNA Paranemic...

Fileemd_53787_half_map_2.map
AnnotationHalf map B of 2-prime-fluoro-modified pyrimidine RNA Paranemic crossover triangle (PXT) origami structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Single-stranded PXT made of 2'fluoro modified pyrimidine RNA

EntireName: Single-stranded PXT made of 2'fluoro modified pyrimidine RNA
Components
  • Complex: Single-stranded PXT made of 2'fluoro modified pyrimidine RNA
    • RNA: DNA/RNA (238-MER)

-
Supramolecule #1: Single-stranded PXT made of 2'fluoro modified pyrimidine RNA

SupramoleculeName: Single-stranded PXT made of 2'fluoro modified pyrimidine RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: In vitro transcribed using mutant (Y639F) T7 RNA polymerase
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: DNA/RNA (238-MER)

MacromoleculeName: DNA/RNA (238-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic RNA (others)
Molecular weightTheoretical: 76.642805 KDa
SequenceString: GGAA(UFT)A(UFT)(CFZ)G(UFT) (CFZ)A(UFT)GG(UFT)GA(UFT)(UFT) (CFZ)G(UFT)(CFZ)A(CFZ) (CFZ)A(UFT) GAGG(CFZ)(UFT)AGA(UFT) (CFZ)(UFT)(CFZ)A(UFT)A(UFT)(CFZ)(UFT)A G(CFZ)G (CFZ)(UFT)(UFT)(UFT)(CFZ)G ...String:
GGAA(UFT)A(UFT)(CFZ)G(UFT) (CFZ)A(UFT)GG(UFT)GA(UFT)(UFT) (CFZ)G(UFT)(CFZ)A(CFZ) (CFZ)A(UFT) GAGG(CFZ)(UFT)AGA(UFT) (CFZ)(UFT)(CFZ)A(UFT)A(UFT)(CFZ)(UFT)A G(CFZ)G (CFZ)(UFT)(UFT)(UFT)(CFZ)G AG(CFZ)G(CFZ)(UFT)AGAG (UFT)(CFZ)(CFZ)(UFT)(UFT)A(UFT) (CFZ)(UFT) AG(CFZ)(CFZ)GG(UFT)(UFT)(UFT)A (UFT)A(CFZ)(UFT)(UFT)(UFT)(CFZ)GAG (UFT)G (UFT)GAA(CFZ)(CFZ)(CFZ) GA(UFT)A(UFT)(UFT)(CFZ)(CFZ)G(CFZ) GGA(UFT)(CFZ)A(CFZ) (UFT)A (UFT)GAG(UFT)(CFZ)G(UFT)(UFT)(CFZ) G(CFZ)GG(CFZ)(UFT)(CFZ)A(UFT)A G(UFT) (CFZ)(CFZ)GG(CFZ)(UFT)(CFZ) AAAGGA(CFZ)A(UFT)(CFZ) A(UFT)GG(CFZ)(CFZ)(UFT)G(UFT) (UFT)(CFZ)G(CFZ)AGG(UFT)(UFT)G (UFT)GA(UFT)(UFT)A(UFT)GAG (UFT)GAG(CFZ)(CFZ)GGG (UFT)AAGG(CFZ)A(UFT)A(CFZ) (CFZ)G(UFT)(UFT)(CFZ)G(CFZ)GG(UFT) A(UFT)G(UFT)(CFZ) (UFT)(UFT)A(CFZ) GA(UFT)(CFZ)(CFZ)G(CFZ)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
40.0 mMHEPES
5.0 mMMagnesium ChlorideMgCl2
50.0 mMPotassium ChlorideKCl
GridModel: Au-flat 1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.015 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4449 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 434756
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://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