8RC0 image
Deposition Date 2023-12-05
Release Date 2024-03-27
Last Version Date 2025-07-02
Entry Detail
PDB ID:
8RC0
Keywords:
SPLICING
Title:
Structure of the human 20S U5 snRNP
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8RC0 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:C (auth: 5)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing-splicing factor 8
Gene (Uniprot):PRPF8
Chain IDs:B (auth: A)
Chain Length:2335
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P2Q9 Pfam ID:PF08082, PF08083, PF10598, PF10597, PF10596, PF12134, PF01398, PF08084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U5 small nuclear ribonucleoprotein 200 kDa helicase
Gene (Uniprot):SNRNP200
Chain IDs:G (auth: B)
Chain Length:2136
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75643 Pfam ID:PF21188, PF18149, PF00270, PF00271, PF02889 EC:3.6.4.13
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:116 kDa U5 small nuclear ribonucleoprotein component
Gene (Uniprot):EFTUD2
Chain IDs:O (auth: C)
Chain Length:972
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15029 Pfam ID:PF16004, PF00009, PF03144, PF14492, PF03764, PF00679
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable ATP-dependent RNA helicase DDX23
Gene (Uniprot):DDX23
Chain IDs:E (auth: D)
Chain Length:820
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BUQ8 Pfam ID:PF00270, PF00271
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 6
Gene (Uniprot):PRPF6
Chain IDs:D (auth: E)
Chain Length:941
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O94906 Pfam ID:PF06424, PF14559, PF13432
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CD2 antigen cytoplasmic tail-binding protein 2
Gene (Uniprot):CD2BP2
Chain IDs:A (auth: F)
Chain Length:341
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O95400 Pfam ID:PF02213
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U5 small nuclear ribonucleoprotein 40 kDa protein
Gene (Uniprot):SNRNP40
Chain IDs:F (auth: G)
Chain Length:357
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96DI7 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein-associated proteins B and B'
Gene (Uniprot):SNRPB
Chain IDs:N (auth: h)
Chain Length:240
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P14678 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D1
Gene (Uniprot):SNRPD1
Chain IDs:H (auth: i)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62314 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D2
Gene (Uniprot):SNRPD2
Chain IDs:M (auth: j)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62316 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D3
Gene (Uniprot):SNRPD3
Chain IDs:I (auth: k)
Chain Length:126
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62318 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein E
Gene (Uniprot):SNRPE
Chain IDs:J (auth: l)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62304 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein F
Gene (Uniprot):SNRPF
Chain IDs:K (auth: m)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62306 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein G
Gene (Uniprot):SNRPG
Chain IDs:L (auth: n)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62308 Pfam ID:PF01423
Ligand Molecules
GTP
Primary Citation
Structure of the human 20S U5 snRNP.
Nat.Struct.Mol.Biol. 31 752 756 (2024)
PMID: 38467877 DOI: 10.1038/s41594-024-01250-5

Abstact

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.

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Primary Citation of related structures
8RC0
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