ISDA

Entry Detail

PDB ID:

8Q7W

EMDB ID:

EMD-18235

Keywords:

SPLICING

Title:

Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 3)

Biological Source:

Source Organism:

Homo sapiens

Host Organism:

Homo sapiens

PDB Version:

Deposition Date:

2023-08-17

Release Date:

2024-04-17

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Description:U5 snRNA
Chain IDs:A (auth: 5)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Description:Pre-mRNA-processing-splicing factor 8
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 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:U5 small nuclear ribonucleoprotein 200 kDa helicase
Chain IDs:C (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

Protein Blast

Polymer Type:polypeptide(L)
Description:116 kDa U5 small nuclear ribonucleoprotein component
Chain IDs:D (auth: C)
Chain Length:972
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15029 Pfam ID:PF16004, PF00009, PF03144, PF14492, PF03764, PF00679 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:U5 small nuclear ribonucleoprotein 40 kDa protein
Chain IDs:E (auth: D)
Chain Length:126
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96DI7 Pfam ID:PF00400 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Probable ATP-dependent RNA helicase DDX23
Chain IDs:F (auth: E)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BUQ8 Pfam ID:PF00270, PF00271 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Pre-mRNA-processing factor 6
Chain IDs:G (auth: F)
Chain Length:941
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O94906 Pfam ID:PF06424, PF14559, PF13432 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:CD2 antigen cytoplasmic tail-binding protein 2
Chain IDs:H (auth: G)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O95400 Pfam ID:PF02213 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Small nuclear ribonucleoprotein Sm D1
Chain IDs:I (auth: a)
Chain Length:2335
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62314 Pfam ID:PF01423 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Small nuclear ribonucleoprotein-associated proteins B and B'
Chain IDs:J (auth: b)
Chain Length:2136
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P14678 Pfam ID:PF01423 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Small nuclear ribonucleoprotein Sm D2
Chain IDs:K (auth: c)
Chain Length:972
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62316 Pfam ID:PF01423 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Small nuclear ribonucleoprotein Sm D3
Chain IDs:L (auth: d)
Chain Length:126
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62318 Pfam ID:PF01423 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Small nuclear ribonucleoprotein E
Chain IDs:M (auth: e)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62304 Pfam ID:PF01423 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Small nuclear ribonucleoprotein F
Chain IDs:N (auth: f)
Chain Length:941
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62306 Pfam ID:PF01423 EC:3.6.4.13

Protein Blast

Polymer Type:polypeptide(L)
Description:Small nuclear ribonucleoprotein G
Chain IDs:O (auth: g)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62308 Pfam ID:PF01423 EC:3.6.4.13

Ligand Molecules

GTP

Primary Citation

Structural basis of human U5 snRNP late biogenesis and recycling.

Riabov Bassat, D, Visanpattanasin, S, Vorlander, M.K, Fin, L, Phillips, A.W, Plaschka, C.Show

Nat.Struct.Mol.Biol. 31 747 751 (2024)

PMID: 38467876 DOI: 10.1038/s41594-024-01243-4

Abstact

Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP is the ~1 MDa 'heart' of the spliceosome and is recycled through an unknown mechanism involving major architectural rearrangements and the dedicated chaperones CD2BP2 and TSSC4. Late steps in U5 snRNP biogenesis similarly involve these chaperones. Here we report cryo-electron microscopy structures of four human U5 snRNP-CD2BP2-TSSC4 complexes, revealing how a series of molecular events primes the U5 snRNP to generate the ~2 MDa U4/U6.U5 tri-snRNP, the largest building block of the spliceosome.

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Disease

Primary Citation of related structures