7ABG

Human pre-Bact-1 spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
Nuclear cap-binding protein subunit 1A [auth A5]790Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136937 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7B [auth A2]103Homo sapiensMutation(s): 0 
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PHAROS:  Q9UK45
GTEx:  ENSG00000130332 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6C [auth z]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115128 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2D [auth F]464Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104897 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinE [auth D]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'F [auth W]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''G [auth B]225Homo sapiensMutation(s): 0 
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PHAROS:  P08579
GTEx:  ENSG00000125870 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseH [auth s]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologI [auth Q]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear cap-binding protein subunit 2J [auth A1]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114503 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like protein802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologM [auth R]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2N [auth V]95Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204392 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3O [auth 9]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170860 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4P [auth C]139Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130520 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5Q [auth H]91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106355 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6R [auth J]80Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164167 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8T [auth A3]96Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128534 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1U [auth K]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140259 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AV [auth y]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100410 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1W [auth G]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8Y [auth A]2,335Homo sapiensMutation(s): 0 
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Find proteins for Q6P2Q9 (Homo sapiens)
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PHAROS:  Q6P2Q9
GTEx:  ENSG00000174231 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38AZ [auth I]312Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134748 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22AA [auth P]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1BA [auth p]793Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099995 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3CA [auth 4]501Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183431 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation regulator 1DA [auth A4]1,098Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113649 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1EA [auth u]1,304Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115524 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2FA [auth T]895Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087365 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3GA [auth E]1,217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000189091 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4HA [auth w]424Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143368 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5IA [auth x]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169976 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1JA [auth v]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1KA [auth 0]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163877 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2LA [auth N]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000146007 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentMA [auth r]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 1NA [auth Y]904Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000133226 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine-rich splicing factor 1PA [auth A6]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136450 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2QA [auth h],
ZA [auth a]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FCB [auth b],
RA [auth i]
86Homo sapiensMutation(s): 0 
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Find proteins for P62306 (Homo sapiens)
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GTEx:  ENSG00000139343 
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UniProt GroupP62306
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'SA [auth m],
XA [auth f]
240Homo sapiensMutation(s): 0 
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Find proteins for P14678 (Homo sapiens)
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GTEx:  ENSG00000125835 
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UniProt GroupP14678
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3AB [auth e],
TA [auth l]
126Homo sapiensMutation(s): 0 
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Find proteins for P62318 (Homo sapiens)
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PHAROS:  P62318
GTEx:  ENSG00000100028 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GDB [auth d],
UA [auth k]
76Homo sapiensMutation(s): 0 
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Find proteins for P62308 (Homo sapiens)
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PHAROS:  P62308
GTEx:  ENSG00000143977 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EBB [auth c],
VA [auth j]
92Homo sapiensMutation(s): 0 
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Find proteins for P62304 (Homo sapiens)
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PHAROS:  P62304
GTEx:  ENSG00000182004 
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UniProt GroupP62304
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1WA [auth n],
YA [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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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein 5EB [auth q]73Homo sapiensMutation(s): 0 
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Find proteins for Q9BZL1 (Homo sapiens)
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PHAROS:  Q9BZL1
GTEx:  ENSG00000198258 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
WW domain-binding protein 11FB [auth X]641Homo sapiensMutation(s): 0 
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Find proteins for Q9Y2W2 (Homo sapiens)
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PHAROS:  Q9Y2W2
GTEx:  ENSG00000084463 
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Entity ID: 11
MoleculeChains LengthOrganismImage
U5 snRNAK [auth 5]116Homo sapiens
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Entity ID: 19
MoleculeChains LengthOrganismImage
U2 snRNAS [auth 2]188Homo sapiens
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Entity ID: 24
MoleculeChains LengthOrganismImage
MINX M3 pre-mRNAX [auth Z]230synthetic construct
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Entity ID: 41
MoleculeChains LengthOrganismImage
U6 snRNAOA [auth 6]106Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany860

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references