3BO3

A relaxed active site following exon ligation by a group I intron

• PDB DOI:  https://doi.org/10.2210/pdb3BO3/pdb
• NAKB: 3BO3

• Classification: NUCLEAR PROTEIN/RNA
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-12-17 Released: 2008-04-01 
• Deposition Author(s): Lipchock, S.V., Strobel, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.325 
• R-Value Work: 0.282 
• R-Value Observed: 0.284 

Literature

A relaxed active site after exon ligation by the group I intron

Lipchock, S.V., Strobel, S.A.

(2008) Proc Natl Acad Sci U S A 105: 5699-5704

• PubMed: 18408159 
• DOI: https://doi.org/10.1073/pnas.0712016105
• Primary Citation of Related Structures:  
  3BO2, 3BO3, 3BO4


• PubMed Abstract: 
  

During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing. These structures reveal a relaxed active site, in which direct metal coordination by the exons is lost after ligation, while other tertiary interactions are retained between the exon and the intron. Consistent with these structural observations, kinetic and thermodynamic measurements show that the scissile phosphate makes direct contact with metals in the ground state before exon ligation and in the transition state, but not after exon ligation. Despite no direct exonic interactions and even in the absence of the scissile phosphate, two metal ions remain bound within the active site. Together, these data suggest that release of the ligated exons from the intron is preceded by a change in substrate-metal coordination before tertiary hydrogen bonding contacts to the exons are broken.

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Organizational Affiliation: 

Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.39 kDa 
• Atom Count: 5,623 
• Modelled Residue Count: 317 
• Deposited Residue Count: 317 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	D [auth A]	95	Homo sapiens	Mutation(s): 2  Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens) Explore P09012  Go to UniProtKB:  P09012
PHAROS:  P09012

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Group I intron P9	A [auth B]	197	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*G)-3')	B [auth C]	16	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*AP*UP*AP*CP*GP*GP*CP*C)-3')	C [auth D]	9	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	E [auth B], F [auth B], G [auth B], I [auth B], 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.325 
• R-Value Work: 0.282 
• R-Value Observed: 0.284 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.608	α = 90
b = 109.608	β = 90
c = 242.138	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Lipchock, S.V., Strobel, S.A.

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations