3JCR

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 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
  • Structures With Same Primary Citation

  • 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 3D Electron Cryomicroscopy, Georg-August Universität Göttingen, D-37077 Göttingen, Germany. Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany. reinhard.luehrmann@mpi-bpc.mpg.de hstark1@gwdg.de henning.urlaub@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hPrp6
G
941Homo sapiensMutation(s): 0 
Gene Names: PRPF6C20orf14
Find proteins for O94906 (Homo sapiens)
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PHAROS  O94906

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U5-40K
D
357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
Find proteins for Q96DI7 (Homo sapiens)
Go to UniProtKB:  Q96DI7
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PHAROS  Q96DI7

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
hBrr2
C
2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
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PHAROS  O75643

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
hDim1
E
142Homo sapiensMutation(s): 0 
Gene Names: TXNL4ADIM1TXNL4
Find proteins for P83876 (Homo sapiens)
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PHAROS  P83876

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
hPrp8
A
2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
Go to UniProtKB:  Q6P2Q9
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PHAROS  Q6P2Q9

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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 UniProtKB:  Q9BUQ8
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PHAROS  Q9BUQ8

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
hSnu114
B
972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
Find proteins for Q15029 (Homo sapiens)
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PHAROS  Q15029

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
SmD1
P, p
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to UniProtKB:  P62314
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PHAROS  P62314

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
SmD2
Q, q
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
Find proteins for P62316 (Homo sapiens)
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PHAROS  P62316

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
SmF
T, t
86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
Find proteins for P62306 (Homo sapiens)
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PHAROS  P62306

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
SmG
U, u
76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
Find proteins for P62308 (Homo sapiens)
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PHAROS  P62308

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
LSm8
8
96Homo sapiensMutation(s): 0 
Gene Names: LSM8
Find proteins for O95777 (Homo sapiens)
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PHAROS  O95777

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
LSm6
6
80Homo sapiensMutation(s): 0 
Gene Names: LSM6
Find proteins for P62312 (Homo sapiens)
Go to UniProtKB:  P62312
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PHAROS  P62312

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
LSm5
5
91Homo sapiensMutation(s): 0 
Gene Names: LSM5
Find proteins for Q9Y4Y9 (Homo sapiens)
Go to UniProtKB:  Q9Y4Y9
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PHAROS  Q9Y4Y9

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
LSm4
4
139Homo sapiensMutation(s): 0 
Gene Names: LSM4
Find proteins for Q9Y4Z0 (Homo sapiens)
Go to UniProtKB:  Q9Y4Z0
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PHAROS  Q9Y4Z0

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
LSm3
3
102Homo sapiensMutation(s): 0 
Gene Names: LSM3MDS017
Find proteins for P62310 (Homo sapiens)
Go to UniProtKB:  P62310
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PHAROS  P62310

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
LSm2
2
95Homo sapiensMutation(s): 0 
Gene Names: LSM2C6orf28G7B
Find proteins for Q9Y333 (Homo sapiens)
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PHAROS  Q9Y333

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
hPrp31
J
499Homo sapiensMutation(s): 0 
Gene Names: PRPF31PRP31
Find proteins for Q8WWY3 (Homo sapiens)
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PHAROS  Q8WWY3

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
hSnu13
I
128Homo sapiensMutation(s): 0 
Gene Names: SNU13NHP2L1
Find proteins for P55769 (Homo sapiens)
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PHAROS  P55769

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
hSad1
V
565Homo sapiensMutation(s): 0 
Gene Names: USP39CGI-21HSPC332PRO2855
Find proteins for Q53GS9 (Homo sapiens)
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PHAROS  Q53GS9

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
SmD3
R, r
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
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PHAROS  P62318

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
SmE
S, s
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
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PHAROS  P62304

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
LSm7
7
103Homo sapiensMutation(s): 0 
Gene Names: LSM7
Find proteins for Q9UK45 (Homo sapiens)
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PHAROS  Q9UK45

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
hPrp3
K
683Homo sapiensMutation(s): 0 
Gene Names: PRPF3HPRP3PRP3
Find proteins for O43395 (Homo sapiens)
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PHAROS  O43395

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
hPrp4
L
521Homo sapiensMutation(s): 0 
Gene Names: PRPF4hCG_29193
Find proteins for Q5T1M7 (Homo sapiens)
Go to UniProtKB:  Q5T1M7

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
SmB
O, o
240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
Find proteins for P14678 (Homo sapiens)
Go to UniProtKB:  P14678
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PHAROS  P14678

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Entity ID: 27
MoleculeChainsLengthOrganism
U4 snRNAM145Homo sapiens

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Entity ID: 29
MoleculeChainsLengthOrganism
U5 snRNAH116Homo sapiens

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Entity ID: 28
MoleculeChainsLengthOrganism
U6 snRNAN106Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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