3CW1

Crystal Structure of Human Spliceosomal U1 snRNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.49 Å

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This is version 1.4 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. 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence 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
GTEx:  ENSG00000100028 
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UniProt GroupP62318
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'F [auth A],
GA [auth J],
O [auth H],
X [auth I]
174Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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PHAROS:  P14678
GTEx:  ENSG00000125835 
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UniProt GroupP14678
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Entity ID: 4
MoleculeChains Sequence 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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PHAROS:  P62314
GTEx:  ENSG00000167088 
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UniProt GroupP62314
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2H [auth C],
IA [auth R],
Q [auth P],
Z [auth Q]
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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GTEx:  ENSG00000125743 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FAA [auth 1],
I [auth F],
JA [auth 2],
R [auth Z]
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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GTEx:  ENSG00000139343 
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UniProt GroupP62306
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Entity ID: 7
MoleculeChains Sequence 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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GTEx:  ENSG00000182004 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GCA [auth 4],
K [auth G],
LA [auth 5],
T [auth 3]
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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GTEx:  ENSG00000143977 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDaDA [auth 7],
L [auth K],
MA [auth 8],
U [auth 6]
216Homo sapiensMutation(s): 0 
Gene Names: SNRNP70RNPU1ZRPU1SNRP70U1AP1
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GTEx:  ENSG00000104852 
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UniProt GroupP08621
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Entity ID: 10
MoleculeChains Sequence 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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GTEx:  ENSG00000124562 
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Entity ID: 1
MoleculeChains LengthOrganismImage
U1 snRNAA [auth V],
B [auth v],
C [auth w],
D [auth x]
138Homo sapiens
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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
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Source and taxonomy, Structure summary