[English] 日本語
Yorodumi
- EMDB-78467: tC19Z RNA polymerase ribozyme, apo state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-78467
TitletC19Z RNA polymerase ribozyme, apo state
Map data
Sample
  • Complex: tC19Z RNA polymerase ribozyme
    • RNA: tC19Z RNA polymerase ribozyme
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordssynthetic / polymerase / ribozyme / apo / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHingey J / Spellmon N / Yu Z / Toor N / Rudolfs B / Mancino A / Haack DB / Das R
Funding support United States, 4 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)2330652 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122579 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM141706 United States
CitationJournal: To Be Published
Title: Predictive improvement of an RNA polymerase ribozyme from its substrate-free cryo-EM structure
Authors: Szokoli D / Hingey J / Zhiheng Y / Wu V / Toor N / Spellmon N / Rudolfs B / Mencino A / Haack DB / Das R
History
DepositionAug 4, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_78467.png

Downloads & links

-
Map

FileDownload / File: emd_78467.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 420 pix.
= 308.112 Å		0.73 Å/pix.
x 420 pix.
= 308.112 Å		0.73 Å/pix.
x 420 pix.
= 308.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.4928882 - 0.9217534
Average (Standard dev.)0.000101135745 (±0.011354967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 308.112 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_78467_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: This map has greater detail in the Mg...

Fileemd_78467_additional_2.map
AnnotationThis map has greater detail in the Mg seam, but is lower resolution at the periphery.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_78467_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_78467_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : tC19Z RNA polymerase ribozyme

EntireName: tC19Z RNA polymerase ribozyme
Components
  • Complex: tC19Z RNA polymerase ribozyme
    • RNA: tC19Z RNA polymerase ribozyme
  • Ligand: MAGNESIUM ION
  • Ligand: water

-
Supramolecule #1: tC19Z RNA polymerase ribozyme

SupramoleculeName: tC19Z RNA polymerase ribozyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

-
Macromolecule #1: tC19Z RNA polymerase ribozyme

MacromoleculeName: tC19Z RNA polymerase ribozyme / type: rna / ID: 1
Details: tC19Z is inserted via L4 into a circularly permuted group II intron scaffold
Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 194.941016 KDa
SequenceString: GUCAUUGAAA AAAAAAGACA AAUCUGCCCU CAGAGCUUGA GAACAUCCAG AAGUCAGCAG AAGUCAUAGU ACCCUUCGGG GGAAGGACG GAACAAGUAU GGCGUUCGCG CCAUGCUUGA ACCACCGUAU ACCGAACGGU ACGUACGGUG GUGAAACAAA C AAAUAAAC ...String:
GUCAUUGAAA AAAAAAGACA AAUCUGCCCU CAGAGCUUGA GAACAUCCAG AAGUCAGCAG AAGUCAUAGU ACCCUUCGGG GGAAGGACG GAACAAGUAU GGCGUUCGCG CCAUGCUUGA ACCACCGUAU ACCGAACGGU ACGUACGGUG GUGAAACAAA C AAAUAAAC UAAAUUAUGU GUGCCCGGCA UGGGUGCAGU CUAUAGGGUG AGAGUCCCGA ACUGUGAAGG CAGAAGUAAC AG UUAGCCU AACGCAAGGG UGUCCGUGGC GACAUGGAAU CUGAAGGAAG CGGACGGCAA ACCUUCGGUC UGAGGAACAC GAA CUUCAU AUGAGGCUAG GUAUCAAUGG AUGAGUUUGC AUAACAAAAC AAAGUCCUUU CUGCCAAAGU UGGUACAGAG UAAA UGAAG CAGAUUGAUG AAGGGAAAGA CUGCAUUCUU ACCCGGGGAG GUCUGGAUGC AGAGGAGGCA GCCUUCGGUG GCGCG AUAG CGCCAACGUU CUCAACAGAC ACCCAAUACU CCCGCUUCGG CGGGUGGGGA UAACACCUGA CGAAAAGGCG AUGUUA GAC ACGCCCAGGU CAUAAUCCCC GGAGCUUCGG CUCCGGAUC

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 25 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k 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: 0.4 µm
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 152136
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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