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 

wwPDB Validation 3D Report Full Report


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: 10.1038/emboj.2010.295
  • Structures With Same Primary Citation

  • 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 na ...

    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 LengthOrganismDetails
U1-AA, P282Homo sapiensMutation(s): 0 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
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PHAROS  P09012
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U1-70KL, S437Homo sapiensMutation(s): 0 
Gene Names: SNRNP70RNPU1ZRPU1SNRP70U1AP1
Find proteins for P08621 (Homo sapiens)
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PHAROS  P08621
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Sm-D3W, Z126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS  P62318
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Sm BB, Q231Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
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PHAROS  P14678
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Sm-D1U, X119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
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PHAROS  P62314
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Sm-D2V, Y118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
Find proteins for P62316 (Homo sapiens)
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PHAROS  P62316
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Sm-FF, I86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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PHAROS  P62306
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Sm-EE, H92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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PHAROS  P62304
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Sm GG, J76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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PHAROS  P62308
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  • Reference Sequence

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Entity ID: 10
MoleculeChainsLengthOrganism
U1 snRNAN, R164Homo sapiens
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 11
MoleculeChainsLengthOrganism
DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3'D, M9N/A
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 

  • 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