6QW6

Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 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

Mechanism of 5' splice site transfer for human spliceosome activation.

Charenton, C.Wilkinson, M.E.Nagai, K.

(2019) Science 364: 362-367

  • DOI: https://doi.org/10.1126/science.aax3289
  • Primary Citation of Related Structures:  
    6QW6, 6QX9

  • PubMed Abstract: 

    The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. ccharent@mrc-lmb.cam.ac.uk mwilkin@mrc-lmb.cam.ac.uk kn@mrc-lmb.cam.ac.uk.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa proteinA [auth X]155Homo sapiensMutation(s): 0 
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PHAROS:  Q8WVK2
GTEx:  ENSG00000124380 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1C [auth 41],
O [auth 51]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2D [auth 42],
P [auth 52]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3E [auth 43],
Q [auth 53]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp3F [auth 4A]683Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117360 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp4G [auth 4B]522Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136875 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31H [auth 4C]499Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105618 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NHP2-like protein 1I [auth 4D]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100138 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'J [auth 4b],
Y [auth 5b]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EK [auth 4e],
Z [auth 5e]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FAA [auth 5f],
L [auth 4f]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GBA [auth 5g],
M [auth 4g]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8R [auth 5A]2,311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseS [auth 5B]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentT [auth 5C]853Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein 4AU [auth 5D]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141759 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 6V [auth 5J]941Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101161 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinW [auth 5O]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX23X [auth 5X]820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
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Find proteins for Q9BUQ8 (Homo sapiens)
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GTEx:  ENSG00000174243 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2DA [auth 62]95Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204392 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3EA [auth 63]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170860 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4FA [auth 64]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130520 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5GA [auth 65]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106355 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6HA [auth 66]80Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164167 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7IA [auth 67]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130332 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8JA [auth 68]96Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128534 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 42KA [auth R]480Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000126254 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 1LA [auth S]800Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175467 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 2MA [auth U]555Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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GTEx:  ENSG00000168883 
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Entity ID: 2
MoleculeChains LengthOrganismImage
U4 snRNAB [auth 4]146Homo sapiens
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Entity ID: 14
MoleculeChains LengthOrganismImage
U5 snRNAN [auth 5]117Homo sapiens
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Entity ID: 22
MoleculeChains LengthOrganismImage
U6 snRNACA [auth 6]88Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomAdG-693087-SPLICE3D
Medical Research Council (United Kingdom)United KingdomMC_U105184330

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.3: 2020-10-07
    Changes: Derived calculations, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Structure summary