[English] 日本語
Yorodumi
- EMDB-41308: Tetrahymena Ribozyme scaffolded Zika Virus xrRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41308
TitleTetrahymena Ribozyme scaffolded Zika Virus xrRNA
Map data
Sample
  • Complex: Tetrahymena Ribozyme scaffolded Zika Virus xrRNA
    • RNA: RNA (440-MER)
  • Ligand: MAGNESIUM ION
KeywordsRibozyme / xrRNA / Scaffold / RNA
Biological speciesTetrahymena (eukaryote) / Zika virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLangeberg CJ / Kieft JS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)7R35GM118070-08 United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM.
Authors: Conner J Langeberg / Jeffrey S Kieft /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules (≤50 kDa) remain challenging targets due to their ...Single-particle cryo-electron microscopy (cryo-EM) can reveal the structures of large and often dynamic molecules, but smaller biomolecules (≤50 kDa) remain challenging targets due to their intrinsic low signal to noise ratio. Methods to help resolve small proteins have been applied but development of similar approaches to aid in structural determination of small, structured RNA elements have lagged. Here, we present a scaffold-based approach that we used to recover maps of sub-25 kDa RNA domains to 4.5-5.0 Å. While lacking the detail of true high-resolution maps, these maps are suitable for model building and preliminary structure determination. We demonstrate this method helped faithfully recover the structure of several RNA elements of known structure, and that it promises to be generalized to other RNAs without disturbing their native fold. This approach may streamline the sample preparation process and reduce the optimization required for data collection. This first-generation scaffold approach provides a robust system to aid in RNA structure determination by cryo-EM and lays the groundwork for further scaffold optimization to achieve higher resolution.
History
DepositionJul 24, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41308.png

Downloads & links

-
Map

FileDownload / File: emd_41308.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 512 pix.
= 433.357 Å		0.85 Å/pix.
x 512 pix.
= 433.357 Å		0.85 Å/pix.
x 512 pix.
= 433.357 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.44696683 - 1.472104
Average (Standard dev.)-0.00017724285 (±0.02035404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 433.3568 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_41308_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41308_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tetrahymena Ribozyme scaffolded Zika Virus xrRNA

EntireName: Tetrahymena Ribozyme scaffolded Zika Virus xrRNA
Components
  • Complex: Tetrahymena Ribozyme scaffolded Zika Virus xrRNA
    • RNA: RNA (440-MER)
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Tetrahymena Ribozyme scaffolded Zika Virus xrRNA

SupramoleculeName: Tetrahymena Ribozyme scaffolded Zika Virus xrRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tetrahymena (eukaryote)

-
Macromolecule #1: RNA (440-MER)

MacromoleculeName: RNA (440-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Zika virus
Molecular weightTheoretical: 142.357188 KDa
SequenceString: GGGUCAGGCC GGCUGAUAUG GAUGCAGUUC ACAGACUAAA UGUCGGUCGG GGAAGAUGUA UUCUUCUCAU AAGAUAUAGU CGGACCUCU CCUUAAUGGG AGCUAGCGGA UGAAGUGAUG CAACACUGGA GCCGCUGGGA ACUAAUUUGU AUGCGAAAGU A UAUUGAUU ...String:
GGGUCAGGCC GGCUGAUAUG GAUGCAGUUC ACAGACUAAA UGUCGGUCGG GGAAGAUGUA UUCUUCUCAU AAGAUAUAGU CGGACCUCU CCUUAAUGGG AGCUAGCGGA UGAAGUGAUG CAACACUGGA GCCGCUGGGA ACUAAUUUGU AUGCGAAAGU A UAUUGAUU AGUUUUGGAG GAGGGAAAAG UUAUCAGGCA UGCACCUGGU AGCUAGUCUU UAAACCAAUA GAUUGCAUCG GU UUAAAAG GCAAGACCGU CAAAUUGCGG GAAAGGGGUC AACAGCCGUU CAGUACCAAG UCUCAGGGGA AACUUUGAGA UGG CCUUGC AAAGGGUAUG GUAAUAAGCU GACGGACAUG GUCCUAACCA CGCAGCCAAG UCCUAAGUCA GUCGCCACAG UUUG GGGAA AGCUGUGCAG CCUGUAACCC CCCCACGAAA GUGGG

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
10.0 mMMgCl2Magnesium Chloride
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 6 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ez0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68847
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
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