4WZJ

Spliceosomal U4 snRNP core domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 4V5U - determined by Leung, A.K.W., Nagai, K., Li, J.  

Literature

Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis.

Leung, A.K.Nagai, K.Li, J.

(2011) Nature 473: 536-539

  • DOI: 10.1038/nature09956
  • Primary Citation of Related Structures:  
  • Also Cited By: 3CW1

  • PubMed Abstract: 
  • The spliceosome is a dynamic macromolecular machine that assembles on pre-messenger RNA substrates and catalyses the excision of non-coding intervening sequences (introns). Four of the five major components of the spliceosome, U1, U2, U4 and U5 small ...

    The spliceosome is a dynamic macromolecular machine that assembles on pre-messenger RNA substrates and catalyses the excision of non-coding intervening sequences (introns). Four of the five major components of the spliceosome, U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), contain seven Sm proteins (SmB/B', SmD1, SmD2, SmD3, SmE, SmF and SmG) in common. Following export of the U1, U2, U4 and U5 snRNAs to the cytoplasm, the seven Sm proteins, chaperoned by the survival of motor neurons (SMN) complex, assemble around a single-stranded, U-rich sequence called the Sm site in each small nuclear RNA (snRNA), to form the core domain of the respective snRNP particle. Core domain formation is a prerequisite for re-import into the nucleus, where these snRNPs mature via addition of their particle-specific proteins. Here we present a crystal structure of the U4 snRNP core domain at 3.6 Å resolution, detailing how the Sm site heptad (AUUUUUG) binds inside the central hole of the heptameric ring of Sm proteins, interacting one-to-one with SmE-SmG-SmD3-SmB-SmD1-SmD2-SmF. An irregular backbone conformation of the Sm site sequence combined with the asymmetric structure of the heteromeric protein ring allows each base to interact in a distinct manner with four key residues at equivalent positions in the L3 and L5 loops of the Sm fold. A comparison of this structure with the U1 snRNP at 5.5 Å resolution reveals snRNA-dependent structural changes outside the Sm fold, which may facilitate the binding of particle-specific proteins that are crucial to biogenesis of spliceosomal snRNPs.


    Related Citations: 
    • Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.
      Kambach, C.,Walke, S.,Young, R.,Avis, J.M.,de la Fortelle, E.,Raker, V.A.,Luhrmann, R.,Li, J.,Nagai, K.
      (1999) Cell 96: 375
    • RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex.
      Toro, I.,Thore, S.,Mayer, C.,Basquin, J.,Seraphin, B.,Suck, D.
      (2001) Embo J. 20: 2293
    • 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: --
    • Re-refinement of the spliceosomal U4 snRNP core-domain structure
      Li, J.,Leung, A.K.,Kondo, Y.,Oubridge, C.,Nagai, K.
      (2016) Acta Crystallogr.,Sect.D 72: 131


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
A, H, O, AA, HH, OO, AAA, HHH, OOO, AAAA, HHHH, OOOO
125Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
B, I, P, BB, II, PP, BBB, III, PPP, BBBB, IIII, PPPP
95Homo sapiensMutation(s): 0 
Gene Names: SNRPB (COD, SNRPB1)
Find proteins for P14678 (Homo sapiens)
Go to Gene View: SNRPB
Go to UniProtKB:  P14678
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
C, J, Q, CC, JJ, QQ, CCC, JJJ, QQQ, CCCC, JJJJ, QQQQ
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
D, K, R, DD, KK, RR, DDD, KKK, RRR, DDDD, KKKK, RRRR
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2 (SNRPD1)
Find proteins for P62316 (Homo sapiens)
Go to Gene View: SNRPD2
Go to UniProtKB:  P62316
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
F, M, T, FF, MM, TT, FFF, MMM, TTT, FFFF, MMMM, TTTT
86Homo sapiensMutation(s): 0 
Gene Names: SNRPF (PBSCF)
Find proteins for P62306 (Homo sapiens)
Go to Gene View: SNRPF
Go to UniProtKB:  P62306
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
E, L, S, EE, LL, SS, EEE, LLL, SSS, EEEE, LLLL, SSSS
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
G, N, U, GG, NN, UU, GGG, NNN, UUU, GGGG, NNNN, UUUU
76Homo sapiensMutation(s): 0 
Gene Names: SNRPG (PBSCG)
Find proteins for P62308 (Homo sapiens)
Go to Gene View: SNRPG
Go to UniProtKB:  P62308
Entity ID: 8
MoleculeChainsLengthOrganism
U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor.V,X,Y,VV,XX,YY,VVV,XXX,YYY,VVVV,XXXX,YYYY68Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 248.010α = 90.00
b = 248.010β = 90.00
c = 251.940γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Database references, Structure summary
  • Version 1.2: 2016-01-13
    Type: Database references
  • Version 1.3: 2018-04-18
    Type: Data collection, Database references, Source and taxonomy