7JNH

Crystal structure of a double-ENE RNA stability element in complex with a 28-mer poly(A) RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction.

Torabi, S.F.Vaidya, A.T.Tycowski, K.T.DeGregorio, S.J.Wang, J.Shu, M.D.Steitz, T.A.Steitz, J.A.

(2021) Science 371

  • DOI: https://doi.org/10.1126/science.abe6523
  • Primary Citation of Related Structures:  
    7JNH

  • PubMed Abstract: 

    Polyadenylate [poly(A)] tail addition to the 3' end of a wide range of RNAs is a highly conserved modification that plays a central role in cellular RNA function. Elements for nuclear expression (ENEs) are cis-acting RNA elements that stabilize poly(A) tails by sequestering them in RNA triplex structures. A crystal structure of a double ENE from a rice hAT transposon messenger RNA complexed with poly(A) 28 at a resolution of 2.89 angstroms reveals multiple modes of interaction with poly(A), including major-groove triple helices, extended minor-groove interactions with RNA double helices, a quintuple-base motif that transitions poly(A) from minor-groove associations to major-groove triple helices, and a poly(A) 3'-end binding pocket. Our findings both expand the repertoire of motifs involved in long-range RNA interactions and provide insights into how polyadenylation can protect an RNA's extreme 3' end.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536, USA.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
28-mer poly(A) RNA28synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
Core double ENE RNA (Xtal construct) from Oryza sativa transposon,Core double ENE RNA (Xtal construct) from Oryza sativa transposon86Oryza sativa
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download Ideal Coordinates CCD File 
F [auth A]
J [auth B]
K [auth B]
L [auth B]
M [auth B]
F [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
SPD
Query on SPD

Download Ideal Coordinates CCD File 
U [auth B]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
SR
Query on SR

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
V [auth B],
W [auth B],
X [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.973α = 90
b = 93.973β = 90
c = 202.171γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01CA16038
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01GM022778
Damon Runyon Cancer Research FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description