|Entry||Database: EMDB / ID: EMD-23401|
|Title||Cryo-EM structure of the B dENE construct complexed with a 28-mer poly(A)|
|Sample||dENE construct complexed with a 28-mer poly(A):|
(nucleic-acidNucleic acid) x 2
|Biological species||Oryza sativa (rice) / synthetic construct (others)|
|Method||single particle reconstruction / cryo EM / Resolution: 5.6 Å|
|Authors||Torabi S / Chen Y / Zhang K / Wang J / DeGregorio S / Vaidya A / Su Z / Pabit S / Chiu W / Pollack L / Steitz J|
|Funding support|| United States, 3 items |
|Citation||Journal: Proc Natl Acad Sci U S A / Year: 2021|
Title: Structural analyses of an RNA stability element interacting with poly(A).
Authors: Seyed-Fakhreddin Torabi / Yen-Lin Chen / Kaiming Zhang / Jimin Wang / Suzanne J DeGregorio / Anand T Vaidya / Zhaoming Su / Suzette A Pabit / Wah Chiu / Lois Pollack / Joan A Steitz /
Abstract: Cis-acting RNA elements are crucial for the regulation of polyadenylated RNA stability. The element for nuclear expression (ENE) contains a U-rich internal loop flanked by short helices. An ENE ...Cis-acting RNA elements are crucial for the regulation of polyadenylated RNA stability. The element for nuclear expression (ENE) contains a U-rich internal loop flanked by short helices. An ENE stabilizes RNA by sequestering the poly(A) tail via formation of a triplex structure that inhibits a rapid deadenylation-dependent decay pathway. Structure-based bioinformatic studies identified numerous ENE-like elements in evolutionarily diverse genomes, including a subclass containing two ENE motifs separated by a short double-helical region (double ENEs [dENEs]). Here, the structure of a dENE derived from a rice transposable element (TWIFB1) before and after poly(A) binding (∼24 kDa and ∼33 kDa, respectively) is investigated. We combine biochemical structure probing, small angle X-ray scattering (SAXS), and cryo-electron microscopy (cryo-EM) to investigate the dENE structure and its local and global structural changes upon poly(A) binding. Our data reveal 1) the directionality of poly(A) binding to the dENE, and 2) that the dENE-poly(A) interaction involves a motif that protects the 3'-most seven adenylates of the poly(A). Furthermore, we demonstrate that the dENE does not undergo a dramatic global conformational change upon poly(A) binding. These findings are consistent with the recently solved crystal structure of a dENE+poly(A) complex [S.-F. Torabi , 371, eabe6523 (2021)]. Identification of additional modes of poly(A)-RNA interaction opens new venues for better understanding of poly(A) tail biology.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_23401.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 0.82 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire dENE construct complexed with a 28-mer poly(A)
|Entire||Name: dENE construct complexed with a 28-mer poly(A) / Number of components: 3|
-Component #1: protein, dENE construct complexed with a 28-mer poly(A)
|Protein||Name: dENE construct complexed with a 28-mer poly(A) / Recombinant expression: No|
|Mass||Experimental: 33 kDa|
|Source||Species: Oryza sativa (rice)|
-Component #2: nucleic-acid, B dENE construct
|nucleic acid||Name: B dENE construct / Class: RNA / Structure: OTHER / Synthetic: No|
GGGUACUCUU UUCUUUGUCA UGGUUUUCUC AGGCGAAAGU CUGAGUUUUU ACAUGACAAA GUUUUUAACG AGGCCC
|Mass||Theoretical: 24.242186 kDa|
|Source||Species: Oryza sativa (rice)|
-Component #3: nucleic-acid, poly(A)
|nucleic acid||Name: poly(A)Polyadenylation / Class: RNA / Structure: OTHER / Synthetic: No|
AAAAAAAAAA AAAAAAAAAA AAAAAAAA
|Mass||Theoretical: 9.172806 kDa|
|Source||Species: synthetic construct (others)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7|
|Vitrification||Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 283486|
|3D reconstruction||Software: cryoSPARC / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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. See below links for details.
- 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.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
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.
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