3CW1

Crystal Structure of Human Spliceosomal U1 snRNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.49 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: https://doi.org/10.1038/nature07851
  • Primary Citation of Related Structures:  
    3CW1

  • 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 excision ...

    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: 
    • 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
    • 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
    • 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 U S A 97: 9396
    • 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
    • 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
    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3E [auth D],
FA [auth U],
N [auth S],
W [auth T]		126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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PHAROS:  P62318
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UniProt GroupP62318
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and BF [auth A],
GA [auth J],
O [auth H],
X [auth I]		174Homo sapiensMutation(s): 0 
Gene Names: SNRPB, COD, SNRPB1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1G [auth B],
HA [auth O],
P [auth M],
Y [auth N]		119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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UniProt GroupP62314
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2H [auth C],
IA [auth R],
Q [auth P],
Z [auth Q]		118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2, SNRPD1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FAA [auth 1],
I [auth F],
JA [auth 2],
R [auth Z]		86Homo sapiensMutation(s): 0 
Gene Names: SNRPF, PBSCF
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EBA [auth X],
J [auth E],
KA [auth Y],
S [auth W]		92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GCA [auth 4],
K [auth G],
LA [auth 5],
T [auth 3]		76Homo sapiensMutation(s): 0 
Gene Names: SNRPG, PBSCG
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDaDA [auth 7],
L [auth K],
MA [auth 8],
U [auth 6]		216Homo sapiensMutation(s): 0 
Gene Names: SNRP70, SNRNP70, RNPU1Z, RPU1, U1AP1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein CEA [auth 0],
M [auth L],
NA [auth l],
V [auth 9]		77Homo sapiensMutation(s): 0 
Gene Names: SNRPC
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U1 snRNAA [auth V],
B [auth v],
C [auth w],
D [auth x]		138Homo sapiens
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.49 Å
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.471α = 95.42
b = 127.075β = 105.92
c = 152.024γ = 101.8
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHARPphasing
Omodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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