7ABF

Human pre-Bact-1 spliceosome core structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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

    Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. reinhard.luehrmann@mpibpc.mpg.de hstark1@gwdg.de b.kastner@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologA [auth Q]144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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PHAROS:  P41223
GTEx:  ENSG00000106245 
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UniProt GroupP41223
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38AB [auth I]312Homo sapiensMutation(s): 0 
Gene Names: PRPF38A
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Find proteins for Q8NAV1 (Homo sapiens)
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PHAROS:  Q8NAV1
GTEx:  ENSG00000134748 
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UniProt GroupQ8NAV1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8C [auth A]2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Find proteins for Q6P2Q9 (Homo sapiens)
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PHAROS:  Q6P2Q9
GTEx:  ENSG00000174231 
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UniProt GroupQ6P2Q9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentD [auth r]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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GTEx:  ENSG00000108883 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2E [auth N]199Homo sapiensMutation(s): 0 
Gene Names: ZMAT2
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GTEx:  ENSG00000146007 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein 5F [auth q]73Homo sapiensMutation(s): 0 
Gene Names: UBL5
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GTEx:  ENSG00000198258 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologG [auth R]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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GTEx:  ENSG00000150316 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
WW domain-binding protein 11J [auth X]641Homo sapiensMutation(s): 0 
Gene Names: WBP11NPWBPSIPP1SNP70
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GTEx:  ENSG00000084463 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1K [auth v]536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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GTEx:  ENSG00000100603 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1L [auth G]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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GTEx:  ENSG00000171566 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1N [auth K]439Homo sapiensMutation(s): 0 
Gene Names: MFAP1
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GTEx:  ENSG00000140259 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation regulator 1O [auth A4]1077Homo sapiensMutation(s): 0 
Gene Names: TCERG1CA150TAF2S
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GTEx:  ENSG00000113649 
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Entity ID: 8
MoleculeChainsLengthOrganismImage
U5 small nuclear RNAH [auth 5]116Homo sapiens
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Entity ID: 9
MoleculeChainsLengthOrganismImage
U6 small nuclear RNAI [auth 6]106Homo sapiens
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Entity ID: 13
MoleculeChainsLengthOrganismImage
MINX M3 RNAM [auth Z]230synthetic construct
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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P [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP
Query on GTP

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Q [auth r]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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R [auth r]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references