7AAV

Human pre-Bact-2 spliceosome core structure

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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: 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 ...

    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
116 kDa U5 small nuclear ribonucleoprotein componentA [auth r]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2, KIAA0031, SNRP116
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologB [auth Q]144Homo sapiensMutation(s): 0 
Gene Names: BUD31, EDG2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinC [auth L]802Homo sapiensMutation(s): 0 
Gene Names: CDC5L, KIAA0432, PCDC5RP
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologD [auth R]229Homo sapiensMutation(s): 0 
Gene Names: CWC15, C11orf5, AD-002, HSPC148
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1E [auth K]439Homo sapiensMutation(s): 0 
Gene Names: MFAP1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1F [auth G]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17H [auth 8]579Homo sapiensMutation(s): 0 
Gene Names: CDC40, EHB3, PRP17, PRPF17
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38A312Homo sapiensMutation(s): 0 
Gene Names: PRPF38A
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8J [auth A]2,335Homo sapiensMutation(s): 0 
Gene Names: PRPF8, PRPC8
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22K [auth P]420Homo sapiensMutation(s): 0 
Gene Names: RBM22, ZC3H16, 199G4
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1L [auth v]536Homo sapiensMutation(s): 0 
Gene Names: SNW1, SKIIP, SKIP
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2M [auth N]199Homo sapiensMutation(s): 0 
Gene Names: ZMAT2
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein 5Q [auth q]73Homo sapiensMutation(s): 0 
Gene Names: UBL5
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Entity ID: 7
MoleculeChainsLengthOrganismImage
MINX M3 pre-mRNAG [auth Z]230synthetic construct
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Entity ID: 14
MoleculeChainsLengthOrganismImage
U2 snRNAN [auth 2]188Homo sapiens
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Entity ID: 15
MoleculeChainsLengthOrganismImage
U5 snRNAO [auth 5]116Homo sapiens
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Entity ID: 16
MoleculeChainsLengthOrganismImage
U6 snRNAP [auth 6]106Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KGN
Query on KGN
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T [auth A]D-chiro inositol hexakisphosphate
C6 H18 O24 P6
IMQLKJBTEOYOSI-LKPKBOIGSA-N		 Ligand Interaction
GTP
Query on GTP
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R [auth r]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
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S [auth r]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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
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