4E8N

Structure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Visualizing Group II Intron Catalysis through the Stages of Splicing.

Marcia, M.Pyle, A.M.

(2012) Cell 151: 497-507

  • DOI: https://doi.org/10.1016/j.cell.2012.09.033
  • Primary Citation of Related Structures:  
    4E8K, 4E8M, 4E8N, 4E8P, 4E8Q, 4E8R, 4E8T, 4E8V, 4FAQ, 4FAR, 4FAU, 4FAW, 4FAX, 4FB0

  • PubMed Abstract: 

    Group II introns are self-splicing ribozymes that share a reaction mechanism and a common ancestor with the eukaryotic spliceosome, thereby providing a model system for understanding the chemistry of pre-mRNA splicing. Here we report 14 crystal structures of a group II intron at different stages of catalysis. We provide a detailed mechanism for the first step of splicing, we describe a reversible conformational change between the first and the second steps of splicing, and we present the ligand-free intron structure after splicing in an active state that corresponds to the retrotransposable form of the intron. During each reaction, the reactants are aligned and activated by a heteronuclear four-metal-ion center that contains a metal cluster and obligate monovalent cations, and they adopt a structural arrangement similar to that of protein endonucleases. Based on our data, we propose a model for the splicing cycle and show that it is applicable to the eukaryotic spliceosome.


  • Organizational Affiliation

    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Group IIC intron393Oceanobacillus iheyensis
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
VA [auth A],
WA [auth A],
XA [auth A],
YA [auth A]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SPM
Query on SPM

Download Ideal Coordinates CCD File 
UA [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
B [auth A]
BA [auth A]
C [auth A]
CA [auth A]
AA [auth A],
B [auth A],
BA [auth A],
C [auth A],
CA [auth A],
D [auth A],
DA [auth A],
E [auth A],
EA [auth A],
F [auth A],
FA [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NH4
Query on NH4

Download Ideal Coordinates CCD File 
GA [auth A]
HA [auth A]
IA [auth A]
JA [auth A]
KA [auth A]
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth A]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.889α = 90
b = 95.43β = 90
c = 224.554γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
ADSCdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description