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: 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
U5 small nuclear ribonucleoprotein 40 kDa proteinA [auth D]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3B [auth E]1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FC [auth b], HA [auth i]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'D [auth W]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4E [auth w]424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GF [auth d], NA [auth k]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Intron-binding protein aquariusG [auth U]1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5H [auth x]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''J [auth B]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6K [auth z]125Homo sapiensMutation(s): 0 
Gene Names: SF3B6SAP14SF3B14SF3B14ACGI-110HSPC175HT006
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein 5L [auth q]73Homo sapiensMutation(s): 0 
Gene Names: UBL5
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseM [auth s]2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1N [auth v]536Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
BUD13 homologO [auth 3]619Homo sapiensMutation(s): 0 
Gene Names: BUD13
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Smad nuclear-interacting protein 1P [auth 0]396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologQ144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 2R [auth 1]322Homo sapiensMutation(s): 0 
Gene Names: RBMX2CGI-79
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinS [auth L]802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger matrin-type protein 2T [auth N]199Homo sapiensMutation(s): 0 
Gene Names: ZMAT2
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-catenin-like protein 1U [auth S]563Homo sapiensMutation(s): 0 
Gene Names: CTNNBL1C20orf33PP8304
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentV [auth r]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologW [auth R]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 1X [auth Y]904Homo sapiensMutation(s): 0 
Gene Names: SRRM1SRM160
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
DNA/RNA-binding protein KIN17Y [auth 7]393Homo sapiensMutation(s): 0 
Gene Names: KINBTCDKIN17
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1Z [auth M]855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Microfibrillar-associated protein 1AA [auth K]439Homo sapiensMutation(s): 0 
Gene Names: MFAP1
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1BA [auth O]848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5ACA [auth y]110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1EA [auth G]514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2ZA [auth a], FA [auth h]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EGA [auth o]301Homo sapiensMutation(s): 0 
Gene Names: PPIECYP33
EC: 5.2.1.8
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
RING-type E3 ubiquitin-protein ligase PPIL2IA [auth t]520Homo sapiensMutation(s): 0 
Gene Names: PPIL2
EC: 2.3.2.27
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'VA [auth f], JA [auth m]240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3BB [auth e], LA [auth l]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8MA [auth A]2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17OA [auth 8]579Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EDB [auth c], PA [auth j]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 38AQA [auth I]312Homo sapiensMutation(s): 0 
Gene Names: PRPF38A
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1XA [auth g], RA [auth n]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22SA [auth P]420Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1UA [auth p]793Homo sapiensMutation(s): 0 
Gene Names: SF3A1SAP114
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2WA [auth F]464Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3YA [auth 4]501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1AB [auth u]1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2CB [auth T]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
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Entity ID: 9
MoleculeChainsLengthOrganismImage
U6 snRNAI [auth 6]106Homo sapiens
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Entity ID: 30
MoleculeChainsLengthOrganismImage
U2 snRNADA [auth 2]188Homo sapiens
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Entity ID: 36
MoleculeChainsLengthOrganismImage
MINX M3 pre-mRNAKA [auth Z]324synthetic construct
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Entity ID: 44
MoleculeChainsLengthOrganismImage
U5 snRNATA [auth 5]116Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
GB [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
EB [auth r]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
FB [auth r]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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: 2021-02-10
    Type: Initial release