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: 2.5 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 

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:  
  • Also Cited By: 4WZJ

  • 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 co ...

    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: 
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kDa
B
279Homo sapiensSus scrofa
This entity is chimeric
Mutation(s): 1 
Gene Names: SNRNP70 (RNPU1Z, RPU1, SNRP70, U1AP1), SNRPA
Find proteins for P08621 (Homo sapiens)
Go to Gene View: SNRNP70
Go to UniProtKB:  P08621
Find proteins for Q06AA4 (Sus scrofa)
Go to Gene View: SNRPA
Go to UniProtKB:  Q06AA4
Entity ID: 1
MoleculeChainsLengthOrganism
U1 snRNA stem-loops 1 and 2 (55-MER)V55Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
V
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.220α = 90.00
b = 66.600β = 110.95
c = 93.730γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Nakajima FoundationJapan--

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references