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 1.4 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: https://doi.org/10.1126/science.aad2085
  • Primary Citation of Related Structures:  
    3JCR

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hPrp6A [auth G]941Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101161 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U5-40KB [auth D]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
hBrr22,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
hDim1D [auth E]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141759 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
hPrp8E [auth A]2,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
hPrp28820Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000174243 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
hSnu114G [auth B]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
SmBH [auth O],
Z [auth o]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
SmD1AA [auth p],
I [auth P]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
SmD2BA [auth q],
J [auth Q]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
SmD3CA [auth r],
K [auth R]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
SmEDA [auth s],
L [auth S]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
SmFEA [auth t],
M [auth T]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
SmGFA [auth u],
N [auth U]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
LSm8O [auth 8]96Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128534 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
LSm6P [auth 6]80Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164167 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
LSm5Q [auth 5]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106355 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
LSm4R [auth 4]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130520 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
LSm3S [auth 3]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170860 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
LSm2T [auth 2]95Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204392 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
LSm7U [auth 7]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130332 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
hPrp3V [auth K]683Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117360 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
hPrp4W [auth L]521Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136875 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
hPrp31X [auth J]499Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105618 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
hSnu13Y [auth I]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100138 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
hSad1GA [auth V]565Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168883 
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Entity ID: 27
MoleculeChains LengthOrganismImage
U4 snRNAHA [auth M]145Homo sapiens
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Entity ID: 28
MoleculeChains LengthOrganismImage
U6 snRNAIA [auth N]106Homo sapiens
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Entity ID: 29
MoleculeChains LengthOrganismImage
U5 snRNAJA [auth H]116Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references