3JCR

3D structure determination of the human*U4/U6.U5* tri-snRNP complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular architecture of the human U4/U6.U5 tri-snRNP.

Agafonov, D.E.Kastner, B.Dybkov, O.Hofele, R.V.Liu, W.T.Urlaub, H.Luhrmann, R.Stark, H.

(2016) Science 351: 1416-1420

  • DOI: 10.1126/science.aad2085

  • PubMed Abstract: 
  • The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution of 7 angstroms using single-particle cryo-electron ...

    The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution of 7 angstroms using single-particle cryo-electron microscopy (cryo-EM). We fit all known high-resolution structures of tri-snRNP components into the EM density map and validated them by protein cross-linking. Our model reveals how the spatial organization of Brr2 RNA helicase prevents premature U4/U6 RNA unwinding in isolated human tri-snRNPs and how the ubiquitin C-terminal hydrolase-like protein Sad1 likely tethers the helicase Brr2 to its preactivation position. Comparison of our model with cryo-EM three-dimensional structures of the Saccharomyces cerevisiae tri-snRNP and Schizosaccharomyces pombe spliceosome indicates that Brr2 undergoes a marked conformational change during spliceosome activation, and that the scaffolding protein Prp8 is also rearranged to accommodate the spliceosome's catalytic RNA network.


    Organizational Affiliation

    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hPrp6
G
941Homo sapiensMutation(s): 0 
Gene Names: PRPF6 (C20orf14)
Find proteins for O94906 (Homo sapiens)
Go to Gene View: PRPF6
Go to UniProtKB:  O94906
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U5-40K
D
357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40 (PRP8BP, SFP38, WDR57)
Find proteins for Q96DI7 (Homo sapiens)
Go to Gene View: SNRNP40
Go to UniProtKB:  Q96DI7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
hBrr2
C
2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200 (ASCC3L1, HELIC2, KIAA0788)
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
Go to Gene View: SNRNP200
Go to UniProtKB:  O75643
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
hDim1
E
142Homo sapiensMutation(s): 0 
Gene Names: TXNL4A (DIM1, TXNL4)
Find proteins for P83876 (Homo sapiens)
Go to Gene View: TXNL4A
Go to UniProtKB:  P83876
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
hPrp8
A
2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8 (PRPC8)
Find proteins for Q6P2Q9 (Homo sapiens)
Go to Gene View: PRPF8
Go to UniProtKB:  Q6P2Q9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
hPrp28
F
820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
Find proteins for Q9BUQ8 (Homo sapiens)
Go to Gene View: DDX23
Go to UniProtKB:  Q9BUQ8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
hSnu114
B
972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2 (KIAA0031, SNRP116)
Find proteins for Q15029 (Homo sapiens)
Go to Gene View: EFTUD2
Go to UniProtKB:  Q15029
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
SmB
O, o
240Homo 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: 9
MoleculeChainsSequence LengthOrganismDetails
SmD1
P, p
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
SmD2
Q, q
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: 11
MoleculeChainsSequence LengthOrganismDetails
SmD3
R, r
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
SmE
S, s
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
SmF
T, t
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: 14
MoleculeChainsSequence LengthOrganismDetails
SmG
U, u
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: 15
MoleculeChainsSequence LengthOrganismDetails
LSm8
8
96Homo sapiensMutation(s): 0 
Gene Names: LSM8
Find proteins for O95777 (Homo sapiens)
Go to Gene View: LSM8
Go to UniProtKB:  O95777
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
LSm6
6
80Homo sapiensMutation(s): 0 
Gene Names: LSM6
Find proteins for P62312 (Homo sapiens)
Go to Gene View: LSM6
Go to UniProtKB:  P62312
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
LSm5
5
91Homo sapiensMutation(s): 0 
Gene Names: LSM5
Find proteins for Q9Y4Y9 (Homo sapiens)
Go to Gene View: LSM5
Go to UniProtKB:  Q9Y4Y9
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
LSm4
4
139Homo sapiensMutation(s): 0 
Gene Names: LSM4
Find proteins for Q9Y4Z0 (Homo sapiens)
Go to Gene View: LSM4
Go to UniProtKB:  Q9Y4Z0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
LSm3
3
102Homo sapiensMutation(s): 0 
Gene Names: LSM3
Find proteins for P62310 (Homo sapiens)
Go to Gene View: LSM3
Go to UniProtKB:  P62310
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
LSm2
2
95Homo sapiensMutation(s): 0 
Gene Names: LSM2 (C6orf28, G7B)
Find proteins for Q9Y333 (Homo sapiens)
Go to Gene View: LSM2
Go to UniProtKB:  Q9Y333
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
LSm7
7
103Homo sapiensMutation(s): 0 
Gene Names: LSM7
Find proteins for Q9UK45 (Homo sapiens)
Go to Gene View: LSM7
Go to UniProtKB:  Q9UK45
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
hPrp3
K
683Homo sapiensMutation(s): 0 
Gene Names: PRPF3 (HPRP3, PRP3)
Find proteins for O43395 (Homo sapiens)
Go to Gene View: PRPF3
Go to UniProtKB:  O43395
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
hPrp4
L
521Homo sapiensMutation(s): 0 
Gene Names: PRPF4 (PRP4)
Find proteins for O43172 (Homo sapiens)
Go to Gene View: PRPF4
Go to UniProtKB:  O43172
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
hPrp31
J
499Homo sapiensMutation(s): 0 
Gene Names: PRPF31 (PRP31)
Find proteins for Q8WWY3 (Homo sapiens)
Go to Gene View: PRPF31
Go to UniProtKB:  Q8WWY3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
hSnu13
I
128Homo sapiensMutation(s): 0 
Gene Names: SNU13 (NHP2L1)
Find proteins for P55769 (Homo sapiens)
Go to Gene View: SNU13
Go to UniProtKB:  P55769
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
hSad1
V
565Homo sapiensMutation(s): 0 
Gene Names: USP39
Find proteins for Q53GS9 (Homo sapiens)
Go to Gene View: USP39
Go to UniProtKB:  Q53GS9
Entity ID: 27
MoleculeChainsLengthOrganism
U4 snRNAM145Homo sapiens
Entity ID: 28
MoleculeChainsLengthOrganism
U6 snRNAN106Homo sapiens
Entity ID: 29
MoleculeChainsLengthOrganism
U5 snRNAH116Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Structure summary
  • Version 1.2: 2016-04-06
    Type: Database references
  • Version 1.3: 2018-07-18
    Type: Data collection