3PGW

Crystal structure of human U1 snRNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.40 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.299 

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This is version 1.2 of the entry. See complete history. 


Literature

Functional organization of the Sm core in the crystal structure of human U1 snRNP.

Weber, G., Trowitzsch, S., Kastner, B., Luhrmann, R., Wahl, M.C.

(2010) EMBO J 29: 4172-4184

  • DOI: https://doi.org/10.1038/emboj.2010.295
  • Primary Citation of Related Structures:  
    3PGW

  • PubMed Abstract: 

    • U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5'-splice site early during spliceosome assembly. It represents a prototype spliceosomal subunit containing a paradigmatic Sm core RNP. The crystal structure of human U1 snRNP obtained from natively purified material by in situ limited proteolysis at 4 ...

    U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5'-splice site early during spliceosome assembly. It represents a prototype spliceosomal subunit containing a paradigmatic Sm core RNP. The crystal structure of human U1 snRNP obtained from natively purified material by in situ limited proteolysis at 4.4 Å resolution reveals how the seven Sm proteins, each recognize one nucleotide of the Sm site RNA using their Sm1 and Sm2 motifs. Proteins D1 and D2 guide the snRNA into and out of the Sm ring, and proteins F and E mediate a direct interaction between the Sm site termini. Terminal extensions of proteins D1, D2 and B/B', and extended internal loops in D2 and B/B' support a four-way RNA junction and a 3'-terminal stem-loop on opposite sides of the Sm core RNP, respectively. On a higher organizational level, the core RNP presents multiple attachment sites for the U1-specific 70K protein. The intricate, multi-layered interplay of proteins and RNA rationalizes the hierarchical assembly of U snRNPs in vitro and in vivo.

    Organizational Affiliation: 

    Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1-AA,
J [auth P]		282Homo sapiensMutation(s): 0 
Gene Names: SNRPA
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U1-70KB [auth S],
K [auth L]		437Homo sapiensMutation(s): 0 
Gene Names: SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sm-D3C [auth Z],
L [auth W]		126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Sm BD [auth B],
M [auth Q]		231Homo sapiensMutation(s): 0 
Gene Names: SNRPB, COD, SNRPB1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Sm-D1E [auth X],
N [auth U]		119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Sm-D2F [auth Y],
O [auth V]		118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2, SNRPD1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Sm-FG [auth F],
P [auth I]		86Homo sapiensMutation(s): 0 
Gene Names: SNRPF, PBSCF
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Sm-EH [auth E],
Q [auth H]		92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Sm GI [auth G],
R [auth J]		76Homo sapiensMutation(s): 0 
Gene Names: SNRPG, PBSCG
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Entity ID: 10
MoleculeChainsLengthOrganismImage
U1 snRNAS [auth R],
T [auth N]		164Homo sapiens
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Entity ID: 11
MoleculeChainsLengthOrganismImage
DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3'U [auth D],
V [auth M]		9N/A
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.40 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.299 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 358.42α = 90
b = 88.22β = 111.88
c = 150.9γ = 90
Software Package:
Software NamePurpose
gclientdata collection
MAR345data collection
RemDAqdata collection
PHASERphasing
SHARPphasing
PHENIXrefinement
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description