6QDV

Human post-catalytic P complex spliceosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation.

Fica, S.M.Oubridge, C.Wilkinson, M.E.Newman, A.J.Nagai, K.

(2019) Science 363: 710-714

  • DOI: 10.1126/science.aaw5569
  • Primary Citation of Related Structures:  
    6QDV

  • PubMed Abstract: 
  • During exon ligation, the Saccharomyces cerevisiae spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8 ...

    During exon ligation, the Saccharomyces cerevisiae spliceosome recognizes the 3'-splice site (3'SS) of precursor messenger RNA (pre-mRNA) through non-Watson-Crick pairing with the 5'SS and the branch adenosine, in a conformation stabilized by Prp18 and Prp8. Here we present the 3.3-angstrom cryo-electron microscopy structure of a human postcatalytic spliceosome just after exon ligation. The 3'SS docks at the active site through conserved RNA interactions in the absence of Prp18. Unexpectedly, the metazoan-specific FAM32A directly bridges the 5'-exon and intron 3'SS of pre-mRNA and promotes exon ligation, as shown by functional assays. CACTIN, SDE2, and NKAP-factors implicated in alternative splicing-further stabilize the catalytic conformation of the spliceosome during exon ligation. Together these four proteins act as exon ligation factors. Our study reveals how the human spliceosome has co-opted additional proteins to modulate a conserved RNA-based mechanism for 3'SS selection and to potentially fine-tune alternative splicing at the exon ligation stage.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. sfica@mrc-lmb.cam.ac.uk kn@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIID [auth 7]390Homo sapiensMutation(s): 0 
Gene Names: EIF4A3DDX48KIAA0111
EC: 3.6.4.13
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein 8AE [auth 8]91Homo sapiensMutation(s): 0 
Gene Names: RBM8ARBM8HSPC114MDS014
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Protein mago nashi homolog 2F [auth 9]144Homo sapiensMutation(s): 0 
Gene Names: MAGOHBMAGOH2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8G [auth A]2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseH [auth B]1722Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentI [auth C]899Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
PRKR-interacting protein 1J [auth D]123Homo sapiensMutation(s): 0 
Gene Names: PRKRIP1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
CactinL [auth F]122Homo sapiensMutation(s): 0 
Gene Names: CACTINC19orf29
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Protein FAM32AM [auth G]60Homo sapiensMutation(s): 0 
Gene Names: FAM32AOTAG12CGI-144
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologN [auth H]908Homo sapiensMutation(s): 0 
Gene Names: CWC22KIAA1604NCM
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1P [auth J]320Homo sapiensMutation(s): 0 
Gene Names: PLRG1
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1Q [auth K]295Homo sapiensMutation(s): 0 
Gene Names: SNW1SKIIPSKIP
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologR [auth L]144Homo sapiensMutation(s): 0 
Gene Names: BUD31EDG2
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22S [auth M]289Homo sapiensMutation(s): 0 
Gene Names: RBM22ZC3H16199G4
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinT [auth N]306Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinU [auth O]802Homo sapiensMutation(s): 0 
Gene Names: CDC5LKIAA0432PCDC5RP
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologV [auth P]229Homo sapiensMutation(s): 0 
Gene Names: CWC15C11orf5AD-002HSPC148
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2W [auth R]26Homo sapiensMutation(s): 0 
Gene Names: SRRM2KIAA0324SRL300SRM300HSPC075
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1X [auth S]848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1CRNCGI-201MSTP021
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1Y [auth T]855Homo sapiensMutation(s): 0 
Gene Names: XAB2HCNPKIAA1177SYF1PP3898
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Intron-binding protein aquariusZ [auth U]1485Homo sapiensMutation(s): 0 
Gene Names: AQRKIAA0560
EC: 3.6.4.13
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX8AA [auth V]1220Homo sapiensMutation(s): 0 
Gene Names: DHX8DDX8
EC: 3.6.4.13
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'BA [auth W]162Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''CA [auth Y]92Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NF-kappa-B-activating proteinDA [auth Z]30Homo sapiensMutation(s): 0 
Gene Names: NKAP
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'EA [auth b], NA [auth k]82Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7FA [auth c]586Homo sapiensMutation(s): 0 
Gene Names: SLU7
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3GA [auth d], QA [auth n]84Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EHA [auth e], SA [auth p]81Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FIA [auth f], TA [auth q]72Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GJA [auth g], UA [auth r]73Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1KA [auth h], OA [auth l]80Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1LA [auth i]164Homo sapiensMutation(s): 0 
Gene Names: PPIL1CYPL1CGI-124UNQ2425/PRO4984
EC: 5.2.1.8
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Find proteins for Q9Y3C6 (Homo sapiens)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2MA [auth j], PA [auth m]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17RA [auth o]513Homo sapiensMutation(s): 0 
Gene Names: CDC40EHB3PRP17PRPF17
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27VA [auth s]225Homo sapiensMutation(s): 0 
Gene Names: BCAS2DAM1
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19WA [auth t], XA [auth u], YA [auth v], ZA [auth w]504Homo sapiensMutation(s): 0 
Gene Names: PRPF19NMP200PRP19SNEV
EC: 2.3.2.27
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2AB [auth y]144Homo sapiensMutation(s): 0 
Gene Names: SYF2CBPINGCIPIP
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Replication stress response regulator SDE2BB [auth z]34Homo sapiensMutation(s): 0 
Gene Names: SDE2C1orf55
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U2 snRNAA [auth 2]189Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U5 snRNAB [auth 5]116Homo sapiens
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Entity ID: 3
MoleculeChainsLengthOrganismImage
U6 snRNAC [auth 6]106Homo sapiens
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  • Entity ID: 11
    MoleculeChainsLengthOrganismImage
    Ligated exons: MINX mRNAK [auth E]14Human adenovirus 2
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    Entity ID: 15
    MoleculeChainsLengthOrganismImage
    Intron lariat: MINX RNAO [auth I]113Human adenovirus 2
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    Small Molecules
    Ligands 6 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    IHP (Subject of Investigation/LOI)
    Query on IHP

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    SB [auth c]INOSITOL HEXAKISPHOSPHATE
    C6 H18 O24 P6
    IMQLKJBTEOYOSI-GPIVLXJGSA-N
     Ligand Interaction
    GTP (Subject of Investigation/LOI)
    Query on GTP

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    KB [auth C]GUANOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O14 P3
    XKMLYUALXHKNFT-UUOKFMHZSA-N
     Ligand Interaction
    ATP (Subject of Investigation/LOI)
    Query on ATP

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    JB [auth 7]ADENOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O13 P3
    ZKHQWZAMYRWXGA-KQYNXXCUSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    MB [auth L], NB [auth L], OB [auth L], PB [auth M], QB [auth M], RB [auth M], TB [auth c]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

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    HB [auth 6]POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    CB [auth 6], DB [auth 6], EB [auth 6], FB [auth 6], GB [auth 6], IB [auth 7], LB [auth C]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    SEP
    Query on SEP
    Q [auth K]L-PEPTIDE LINKINGC3 H8 N O6 PSER
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.30 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Medical Research Council (United Kingdom)United KingdomMC_U105184330
    European Research CouncilAdG-693087-SPLICE3D

    Revision History  (Full details and data files)

    • Version 1.0: 2019-02-20
      Type: Initial release
    • Version 1.1: 2019-02-27
      Changes: Data collection, Database references
    • Version 2.0: 2020-10-07
      Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary