7EZ2

Holo L-16 ScaI Tetrahymena ribozyme

  • Classification: RNA
  • Organism(s): Tetrahymena thermophila
  • Expression System: synthetic construct
  • Mutation(s): No 

  • Deposited: 2021-06-01 Released: 2021-08-25 
  • Deposition Author(s): Su, Z., Zhang, K., Kappel, K., Luo, B., Das, R., Chiu, W.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), National Science Foundation (NSF, China), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 angstrom resolution.

Su, Z.Zhang, K.Kappel, K.Li, S.Palo, M.Z.Pintilie, G.D.Rangan, R.Luo, B.Wei, Y.Das, R.Chiu, W.

(2021) Nature 596: 603-607

  • DOI: https://doi.org/10.1038/s41586-021-03803-w
  • Primary Citation of Related Structures:  
    7EZ0, 7EZ2

  • PubMed Abstract: 

    Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution 1-3 . However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure-function relationships 4 , but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure-function relationships in ribozymes.


  • Organizational Affiliation

    The State Key Laboratory of Biotherapy and Cancer Center, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China. zsu@scu.edu.cn.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
Holo L-16 ScaI Tetrahymena ribozyme S18Tetrahymena thermophila
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
Holo L-16 ScaI Tetrahymena ribozyme S26Tetrahymena thermophila
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
Holo L-16 ScaI Tetrahymena ribozymeC [auth N]392Tetrahymena thermophila
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth N]
BA [auth N]
CA [auth N]
D [auth N]
DA [auth N]
AA [auth N],
BA [auth N],
CA [auth N],
D [auth N],
DA [auth N],
E [auth N],
EA [auth N],
F [auth N],
FA [auth N],
G [auth N],
GA [auth N],
H [auth N],
HA [auth N],
I [auth N],
J [auth N],
K [auth N],
L [auth N],
M [auth N],
N,
O [auth N],
P [auth N],
Q [auth N],
R [auth N],
S [auth N],
T [auth N],
U [auth N],
V [auth N],
W [auth N],
X [auth N],
Y [auth N],
Z [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX1.15.2-3472
MODEL REFINEMENTCoot0.8.7

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32070049
National Science Foundation (NSF, China)China82041016
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI120943
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD021600

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Data collection