7ABI

Human pre-Bact-2 spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.

Townsend, C.Leelaram, M.N.Agafonov, D.E.Dybkov, O.Will, C.L.Bertram, K.Urlaub, H.Kastner, B.Stark, H.Luhrmann, R.

(2020) Science 370

  • DOI: https://doi.org/10.1126/science.abc3753
  • Primary Citation of Related Structures:  
    7AAV, 7ABF, 7ABG, 7ABH, 7ABI

  • PubMed Abstract: 

    Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B act complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B act complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA.


  • Organizational Affiliation

    Department of Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinA [auth D]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3B [auth E]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FC [auth b],
HA [auth i]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'D [auth W]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4E [auth w]424Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143368 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GF [auth d],
NA [auth k]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusG [auth U]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5H [auth x]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169976 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''J [auth B]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6K [auth z]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115128 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein 5L [auth q]73Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198258 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseM [auth s]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1N [auth v]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
BUD13 homologO [auth 3]619Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137656 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1P [auth 0]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163877 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homolog144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2R [auth 1]322Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134597 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinS [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2T [auth N]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000146007 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-catenin-like protein 1U [auth S]563Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132792 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentV [auth r]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologW [auth R]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 1X [auth Y]904Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000133226 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
DNA/RNA-binding protein KIN17Y [auth 7]393Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000151657 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1Z [auth M]855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1AA [auth K]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140259 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1BA [auth O]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5ACA [auth y]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1EA [auth G]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2FA [auth h],
ZA [auth a]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EGA [auth o]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000084072 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RING-type E3 ubiquitin-protein ligase PPIL2IA [auth t]520Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000100023 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'JA [auth m],
VA [auth f]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3BB [auth e],
LA [auth l]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8MA [auth A]2,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17OA [auth 8]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EDB [auth c],
PA [auth j]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38AQA [auth I]312Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134748 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1RA [auth n],
XA [auth g]
119Homo sapiensMutation(s): 0 
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Find proteins for P62314 (Homo sapiens)
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GTEx:  ENSG00000167088 
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UniProt GroupP62314
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22SA [auth P]420Homo sapiensMutation(s): 0 
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Find proteins for Q9NW64 (Homo sapiens)
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PHAROS:  Q9NW64
GTEx:  ENSG00000086589 
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UniProt GroupQ9NW64
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1UA [auth p]793Homo sapiensMutation(s): 0 
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Find proteins for Q15459 (Homo sapiens)
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GTEx:  ENSG00000099995 
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UniProt GroupQ15459
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2WA [auth F]464Homo sapiensMutation(s): 0 
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Find proteins for Q15428 (Homo sapiens)
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GTEx:  ENSG00000104897 
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UniProt GroupQ15428
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3YA [auth 4]501Homo sapiensMutation(s): 0 
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Find proteins for Q12874 (Homo sapiens)
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GTEx:  ENSG00000183431 
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UniProt GroupQ12874
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1AB [auth u]1,304Homo sapiensMutation(s): 0 
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Find proteins for O75533 (Homo sapiens)
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GTEx:  ENSG00000115524 
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UniProt GroupO75533
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2CB [auth T]895Homo sapiensMutation(s): 0 
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Find proteins for Q13435 (Homo sapiens)
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GTEx:  ENSG00000087365 
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UniProt GroupQ13435
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Entity ID: 9
MoleculeChains LengthOrganismImage
U6 snRNAI [auth 6]106Homo sapiens
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Entity ID: 30
MoleculeChains LengthOrganismImage
U2 snRNADA [auth 2]188Homo sapiens
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Entity ID: 36
MoleculeChains LengthOrganismImage
MINX M3 pre-mRNAKA [auth Z]324synthetic construct
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Entity ID: 44
MoleculeChains LengthOrganismImage
U5 snRNATA [auth 5]116Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany860

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release