3CW1

Crystal Structure of Human Spliceosomal U1 snRNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.493 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 475-480

  • DOI: 10.1038/nature07851
  • Also Cited By: 4V5U, 4PKD, 2Y9D, 2Y9C, 2Y9B, 2Y9A

  • PubMed Abstract: 
  • Human spliceosomal U1 small nuclear ribonucleoprotein particles (snRNPs), which consist of U1 small nuclear RNA and ten proteins, recognize the 5' splice site within precursor messenger RNAs and initiate the assembly of the spliceosome for intron exc ...

    Human spliceosomal U1 small nuclear ribonucleoprotein particles (snRNPs), which consist of U1 small nuclear RNA and ten proteins, recognize the 5' splice site within precursor messenger RNAs and initiate the assembly of the spliceosome for intron excision. An electron density map of the functional core of U1 snRNP at 5.5 A resolution has enabled us to build the RNA and, in conjunction with site-specific labelling of individual proteins, to place the seven Sm proteins, U1-C and U1-70K into the map. Here we present the detailed structure of a spliceosomal snRNP, revealing a hierarchical network of intricate interactions between subunits. A striking feature is the amino (N)-terminal polypeptide of U1-70K, which extends over a distance of 180 A from its RNA binding domain, wraps around the core domain consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition. The structure of U1 snRNP provides insights into U1 snRNP assembly and suggests a possible mechanism of 5'-splice-site recognition.


    Related Citations: 
    • Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis
      Leung, A.K.W.,Nagai, K.,Li, J.
      (2011) Nature 473: 536
    • Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model.
      Krol, A.,Westhof, E.,Bach, M.,Luhrmann, R.,Ebel, J.P.,Carbon, P.
      (1990) Nucleic Acids Res. 18: 3803
    • 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
    • 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
    • The structure and biochemical properties of the human spliceosomal protein U1C.
      Muto, Y.,Pomeranz Krummel, D.,Oubridge, C.,Hernandez, H.,Robinson, C.V.,Neuhaus, D.,Nagai, K.
      (2004) J.Mol.Biol. 341: 185
    • A retroviral RNA kissing complex containing only two G.C base pairs.
      Kim, C.H.,Tinoco, I.
      (2000) Proc.Natl.Acad.Sci.USA 97: 9396


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
D, S, T, U
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B
A, H, I, J
174Homo 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: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
B, M, N, O
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
C, P, Q, R
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: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
F, Z, 1, 2
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: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
E, W, X, Y
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
G, 3, 4, 5
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: 9
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa
K, 6, 7, 8
216Homo sapiensMutation(s): 0 
Gene Names: SNRNP70 (RNPU1Z, RPU1, SNRP70, U1AP1)
Find proteins for P08621 (Homo sapiens)
Go to Gene View: SNRNP70
Go to UniProtKB:  P08621
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C
L, 9, 0, l
77Homo sapiensMutation(s): 0 
Gene Names: SNRPC
Find proteins for P09234 (Homo sapiens)
Go to Gene View: SNRPC
Go to UniProtKB:  P09234
Entity ID: 1
MoleculeChainsLengthOrganism
U1 snRNAV,v,w,x138Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
0, 9, l, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.493 Å
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 126.471α = 95.42
b = 127.075β = 105.92
c = 152.024γ = 101.80
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHARPphasing
Omodel building
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-31
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Refinement description