4PKD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 ...

    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.


    Related Citations: 
    • Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.
      Pomeranz Krummel, D.A., Oubridge, C., Leung, A.K., Li, J., Nagai, K.
      (2009) Nature 458: 475
    • Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin.
      Oubridge, C., Ito, N., Evans, P.R., Teo, C.H., Nagai, K.
      (1994) Nature 372: 432
    • Functional organization of the Sm core in the crystal structure of human U1 snRNP.
      Weber, G., Trowitzsch, S., Kastner, B., Luhrmann, R., Wahl, M.C.
      (2010) EMBO J 29: 4172

    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kDaB279Sus scrofaHomo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: SNRPASNRNP70RNPU1ZRPU1SNRP70U1AP1
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
PHAROS:  P08621
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
U1 snRNA stem-loops 1 and 2 (55-MER)A [auth V]55Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
F [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth V], D [auth V], E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement

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