[English] 日本語
Yorodumi
- EMDB-40266: apo form of adenosylcobalamin riboswitch dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40266
Titleapo form of adenosylcobalamin riboswitch dimer
Map dataunsharpened map
Sample
  • Organelle or cellular component: apodimer
    • RNA: apo form of adenosylcobalamin riboswitch dimer
KeywordsRNA cobalamin riboswitch / RNA
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsDing J / Deme JC / Stagno JR / Yu P / Lea SM / Wang YX
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Wang Group United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM.
Authors: Jienyu Ding / Justin C Deme / Jason R Stagno / Ping Yu / Susan M Lea / Yun-Xing Wang /
Abstract: RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin ...RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin riboswitch exhibits heterogeneous conformations under 1 mM Mg2+ concentration and ligand binding reduces conformational flexibility. Among all conformers, we determined one apo (5.3 Å) and four holo cryo-electron microscopy structures (overall 3.0-3.5 Å, binding pocket 2.9-3.2 Å). The holo dimers exhibit global motions of helical twisting and bending around the dimer interface. A backbone comparison of the apo and holo states reveals a large structural difference in the P6 extension position. The central strand of the binding pocket, junction 6/3, changes from an 'S'- to a 'U'-shaped conformation to accommodate ligand. Furthermore, the binding pocket can partially form under 1 mM Mg2+ and fully form under 10 mM Mg2+ within the bound-like structure in the absence of ligand. Our results not only demonstrate the stabilizing ligand-induced conformational changes in and around the binding pocket but may also provide further insight into the role of the P6 extension in ligand binding and selectivity.
History
DepositionMar 31, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40266.png

Downloads & links

-
Map

FileDownload / File: emd_40266.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 640 pix.
= 443.52 Å		0.69 Å/pix.
x 640 pix.
= 443.52 Å		0.69 Å/pix.
x 640 pix.
= 443.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.169
Minimum - Maximum-0.19362833 - 0.7029251
Average (Standard dev.)0.00005282243 (±0.011670513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 443.52002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_40266_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: local refinement of binding pocket, B-factor sharpened

Fileemd_40266_additional_1.map
Annotationlocal refinement of binding pocket, B-factor sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: B-factor sharpened map

Fileemd_40266_additional_2.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: local refinement of binding pocket, unsharpened

Fileemd_40266_additional_3.map
Annotationlocal refinement of binding pocket, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_40266_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_40266_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : apodimer

EntireName: apodimer
Components
  • Organelle or cellular component: apodimer
    • RNA: apo form of adenosylcobalamin riboswitch dimer

-
Supramolecule #1: apodimer

SupramoleculeName: apodimer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)

-
Macromolecule #1: apo form of adenosylcobalamin riboswitch dimer

MacromoleculeName: apo form of adenosylcobalamin riboswitch dimer / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Molecular weightTheoretical: 68.273664 KDa
SequenceString: GGUUAAAGCC UUAUGGUCGC UACCAUUGCA CUCCGGUAGC GUUAAAAGGG AAGACGGGUG AGAAUCCCGC GCAGCCCCCG CUACUGUGA GGGAGGACGA AGCCCUAGUA AGCCACUGCC GAAAGGUGGG AAGGCAGGGU GGAGGAUGAG UCCCGAGCCA G GAGACCUG ...String:
GGUUAAAGCC UUAUGGUCGC UACCAUUGCA CUCCGGUAGC GUUAAAAGGG AAGACGGGUG AGAAUCCCGC GCAGCCCCCG CUACUGUGA GGGAGGACGA AGCCCUAGUA AGCCACUGCC GAAAGGUGGG AAGGCAGGGU GGAGGAUGAG UCCCGAGCCA G GAGACCUG CCAUAAGGUU UUAGAAGUUC GCCUUCGGGG GGAAGGUGAA CA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.1 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 306518
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