U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.

Kondo, Y.Oubridge, C.van Roon, A.M.Nagai, K.

(2015) Elife 4

  • DOI: https://doi.org/10.7554/eLife.04986
  • Primary Citation of Related Structures:  
    4PJO, 4PKD

  • PubMed Abstract: 

    U1 snRNP binds to the 5' exon-intron junction of pre-mRNA and thus plays a crucial role at an early stage of pre-mRNA splicing. We present two crystal structures of engineered U1 sub-structures, which together reveal at atomic resolution an almost complete network of protein-protein and RNA-protein interactions within U1 snRNP, and show how the 5' splice site of pre-mRNA is recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between pre-mRNA and the 5'-end of U1 snRNA. The binding of the RNA duplex is stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA backbone around the splice junction but U1-C makes no base-specific contacts with pre-mRNA. The structure, together with RNA binding assays, shows that the selection of 5'-splice site nucleotides by U1 snRNP is achieved predominantly through basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched 5'-splice sites.

  • Organizational Affiliation

    Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kDa279Sus scrofaHomo sapiens
This entity is chimeric
Mutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q06AA4 (Sus scrofa)
Explore Q06AA4 
Go to UniProtKB:  Q06AA4
Find proteins for P08621 (Homo sapiens)
Explore P08621 
Go to UniProtKB:  P08621
GTEx:  ENSG00000104852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP08621Q06AA4
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
U1 snRNA stem-loops 1 and 2 (55-MER)A [auth V]55Homo sapiens
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.22α = 90
b = 66.6β = 110.95
c = 93.73γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Nakajima FoundationJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description