8Q91

Structure of the human 20S U5 snRNP core

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Structure of the human 20S U5 snRNP.

Schneider, S., Brandina, I., Peter, D., Lagad, S., Fraudeau, A., Portell-Montserrat, J., Tholen, J., Zhao, J., Galej, W.P.

(2024) Nat Struct Mol Biol 31: 752-756

  • DOI: https://doi.org/10.1038/s41594-024-01250-5
  • Primary Citation of Related Structures:  
    8Q91, 8RC0

  • PubMed Abstract: 

    The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. CD2BP2 is a hallmark protein of the 20S U5 snRNP, absent from the mature tri-snRNP. Here we report a high-resolution cryogenic electron microscopy structure of the 20S U5 snRNP, shedding light on the mutually exclusive interfaces utilized during tri-snRNP assembly and the role of the CD2BP2 in facilitating this process.

    • Organizational Affiliation: 

    European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CD2 antigen cytoplasmic tail-binding protein 2A [auth F]341Homo sapiensMutation(s): 0 
Gene Names: CD2BP2
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PHAROS:  O95400
GTEx:  ENSG00000169217 
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UniProt GroupO95400
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8B [auth A]2,335Homo sapiensMutation(s): 0 
Gene Names: PRPF8, PRPC8
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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
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 6D [auth E]941Homo sapiensMutation(s): 0 
Gene Names: PRPF6
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Find proteins for O94906 (Homo sapiens)
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PHAROS:  O94906
GTEx:  ENSG00000101161 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX23E [auth D]820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
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Find proteins for Q9BUQ8 (Homo sapiens)
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GTEx:  ENSG00000174243 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentF [auth C]972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2, KIAA0031, SNRP116
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GTEx:  ENSG00000108883 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseG [auth B]2,136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200, ASCC3L1, HELIC2, KIAA0788
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FH [auth m]86Homo sapiensMutation(s): 0 
Gene Names: SNRPF, PBSCF
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PHAROS:  P62306
GTEx:  ENSG00000139343 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GI [auth n]76Homo sapiensMutation(s): 0 
Gene Names: SNRPG, PBSCG
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GTEx:  ENSG00000143977 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1J [auth i]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Find proteins for P62314 (Homo sapiens)
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PHAROS:  P62314
GTEx:  ENSG00000167088 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2K [auth j]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2, SNRPD1
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GTEx:  ENSG00000125743 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3L [auth k]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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GTEx:  ENSG00000100028 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'M [auth h]240Homo sapiensMutation(s): 0 
Gene Names: SNRPB, COD, SNRPB1
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Find proteins for P14678 (Homo sapiens)
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GTEx:  ENSG00000125835 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EN [auth l]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Find proteins for P62304 (Homo sapiens)
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GTEx:  ENSG00000182004 
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Entity ID: 3
MoleculeChains LengthOrganismImage
U5 snRNAC [auth 5]117Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP
Download Ideal Coordinates CCD File 
O [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union950278

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary