1A9N | pdb_00001a9n

CRYSTAL STRUCTURE OF THE SPLICEOSOMAL U2B''-U2A' PROTEIN COMPLEX BOUND TO A FRAGMENT OF U2 SMALL NUCLEAR RNA

• PDB DOI: https://doi.org/10.2210/pdb1A9N/pdb
• NAKB: 1A9N

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


• Deposited: 1998-04-08 Released: 1998-09-23 
• Deposition Author(s): Price, S.R., Evans, P.R., Nagai, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.328 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.282 (Depositor), 0.254 (DCC) 

Literature

Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA.

Price, S.R., Evans, P.R., Nagai, K.

(1998) Nature 394: 645-650

• PubMed: 9716128 
• DOI: https://doi.org/10.1038/29234
• Primary Citation Related Structures: 
  1A9N


• PubMed Abstract: 
  

  We have determined the crystal structure at 2.4 A resolution of a ternary complex between the spliceosomal U2B"/U2A' protein complex and hairpin-loop IV of U2 small nuclear RNA. Unlike its close homologue the U1A protein, U2B" binds to its cognate RNA only in the presence of U2A', which contains leucine-rich repeats in its sequence. The concave surface of a parallel beta-sheet within the leucine-rich-repeat region of U2A' interacts with the ribonucleoprotein domain of U2B" on the surface opposite its RNA-binding surface. The basic carboxy-terminal region of U2A' interacts with the RNA stem. The crystal structure reveals how protein-protein interaction regulates RNA-binding specificity, and how replacing only a few key residues allows the U2B" and U1A proteins to discriminate between their cognate RNA hairpins by forming alternative networks of interactions.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78 kDa 
• Atom Count: 5,188 
• Modeled Residue Count: 571 
• Deposited Residue Count: 592 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
U2A'	C [auth A], D [auth C]	176	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P09661 (Homo sapiens) Explore P09661  Go to UniProtKB:  P09661
GTEx:  ENSG00000131876

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SPLICEOSOMAL U2B''	E [auth B], F [auth D]	96	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P08579 (Homo sapiens) Explore P08579  Go to UniProtKB:  P08579
PHAROS:  P08579 GTEx:  ENSG00000125870

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*CP*UP*GP*GP*UP*AP*UP*UP*GP*CP*AP*GP*UP*AP*CP*CP*UP*CP*CP*AP*GP* GP*U)-3')	A [auth Q], B [auth R]	24	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.328 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.282 (Depositor), 0.254 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.37	α = 90
b = 128.24	β = 90
c = 66.65	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-09-23 
Deposition Author(s): Price, S.R., Evans, P.R., Nagai, K.

Revision History  

• Version 1.0: 1998-09-23
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary