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: 10.1038/nature07851
  • Structures With Same Primary Citation

  • 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: 
    • 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: 10
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein C0, 9, L, l77Homo sapiensMutation(s): 0 
Gene Names: SNRPC
Find proteins for P09234 (Homo sapiens)
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PHAROS  P09234
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3D, S, T, U126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS  P62318
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and BA, H, I, J174Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
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PHAROS  P14678
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1B, M, N, O119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
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PHAROS  P62314
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2C, P, Q, R118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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PHAROS  P62316
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F1, 2, F, Z86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS  P62306
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein EE, W, X, Y92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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PHAROS  P62304
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G3, 4, 5, G76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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PHAROS  P62308
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein 70 kDa6, 7, 8, K216Homo sapiensMutation(s): 0 
Gene Names: SNRP70SNRNP70RNPU1ZRPU1U1AP1
Find proteins for P08621 (Homo sapiens)
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PHAROS  P08621
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  • Reference Sequence

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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

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0, 9, L, l
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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