3PGW

Crystal structure of human U1 snRNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.4 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
  • Also Cited By: 4V5U, 4PKD, 2Y9D, 2Y9C, 2Y9B, 2Y9A

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U1-A
A, P
282Homo sapiensMutation(s): 0 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U1-70K
S, L
437Homo sapiensMutation(s): 0 
Gene Names: SNRNP70 (RNPU1Z, RPU1, SNRP70, U1AP1)
Find proteins for P08621 (Homo sapiens)
Go to Gene View: SNRNP70
Go to UniProtKB:  P08621
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Sm-D3
Z, W
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Sm B
B, Q
231Homo sapiensMutation(s): 0 
Gene Names: SNRPB (COD, SNRPB1)
Find proteins for P14678 (Homo sapiens)
Go to Gene View: SNRPB
Go to UniProtKB:  P14678
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Sm-D1
X, U
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Sm-D2
Y, V
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2 (SNRPD1)
Find proteins for P62316 (Homo sapiens)
Go to Gene View: SNRPD2
Go to UniProtKB:  P62316
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Sm-F
F, I
86Homo sapiensMutation(s): 0 
Gene Names: SNRPF (PBSCF)
Find proteins for P62306 (Homo sapiens)
Go to Gene View: SNRPF
Go to UniProtKB:  P62306
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Sm-E
E, H
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Sm G
G, J
76Homo sapiensMutation(s): 0 
Gene Names: SNRPG (PBSCG)
Find proteins for P62308 (Homo sapiens)
Go to Gene View: SNRPG
Go to UniProtKB:  P62308
Entity ID: 10
MoleculeChainsLengthOrganism
U1 snRNAR,N164Homo sapiens
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: 4.4 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.299 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 358.420α = 90.00
b = 88.220β = 111.88
c = 150.900γ = 90.00
Software Package:
Software NamePurpose
gclientdata collection
MAR345data collection
CNSrefinement
XDSdata reduction
SHARPphasing
PHASERphasing
XDSdata scaling
PHENIXrefinement
RemDAqdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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