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
  • 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) ...

    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 LengthOrganismDetailsImage
hPrp6A [auth G]941Homo sapiensMutation(s): 0 
Gene Names: PRPF6C20orf14
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U5-40KB [auth D]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
hBrr2C2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
hDim1D [auth E]142Homo sapiensMutation(s): 0 
Gene Names: TXNL4ADIM1TXNL4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
hPrp8E [auth A]2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
hPrp28F820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
hSnu114G [auth B]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
SmBH [auth O], Z [auth o]240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 9
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SmD1I [auth P], AA [auth p]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 10
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SmD2J [auth Q], BA [auth q]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 11
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SmD3K [auth R], CA [auth r]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
SmEL [auth S], DA [auth s]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
SmFM [auth T], EA [auth t]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
SmGN [auth U], FA [auth u]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
LSm8O [auth 8]96Homo sapiensMutation(s): 0 
Gene Names: LSM8
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Entity ID: 16
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LSm6P [auth 6]80Homo sapiensMutation(s): 0 
Gene Names: LSM6
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Entity ID: 17
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LSm5Q [auth 5]91Homo sapiensMutation(s): 0 
Gene Names: LSM5
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Entity ID: 18
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LSm4R [auth 4]139Homo sapiensMutation(s): 0 
Gene Names: LSM4
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Entity ID: 19
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LSm3S [auth 3]102Homo sapiensMutation(s): 0 
Gene Names: LSM3MDS017
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Entity ID: 20
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LSm2T [auth 2]95Homo sapiensMutation(s): 0 
Gene Names: LSM2C6orf28G7B
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Entity ID: 21
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LSm7U [auth 7]103Homo sapiensMutation(s): 0 
Gene Names: LSM7
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
hPrp3V [auth K]683Homo sapiensMutation(s): 0 
Gene Names: PRPF3HPRP3PRP3
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
hPrp4W [auth L]521Homo sapiensMutation(s): 0 
Gene Names: PRPF4PRP4
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
hPrp31X [auth J]499Homo sapiensMutation(s): 0 
Gene Names: PRPF31PRP31
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
hSnu13Y [auth I]128Homo sapiensMutation(s): 0 
Gene Names: SNU13NHP2L1
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
hSad1GA [auth V]565Homo sapiensMutation(s): 0 
Gene Names: USP39CGI-21HSPC332PRO2855
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Entity ID: 27
MoleculeChainsLengthOrganismImage
U4 snRNAHA [auth M]145Homo sapiens
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Entity ID: 28
MoleculeChainsLengthOrganismImage
U6 snRNAIA [auth N]106Homo sapiens
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Entity ID: 29
MoleculeChainsLengthOrganismImage
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 

Structure Validation

View Full Validation Report




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