8Y6O image
Deposition Date 2024-02-02
Release Date 2024-03-20
Last Version Date 2024-03-27
Entry Detail
PDB ID:
8Y6O
Keywords:
SPLICING/RNA
Title:
Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.38 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8Y6O validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:pre-mRNA
Chain IDs:A
Chain Length:280
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:B
Chain Length:119
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:C
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P2Q9 Pfam ID:PF08082, PF10596, PF12134, PF01398, PF08084, PF10597, PF10598, PF08083
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:116 kDa U5 small nuclear ribonucleoprotein component
Gene (Uniprot):EFTUD2
Chain IDs:D
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:U5 small nuclear ribonucleoprotein 200 kDa helicase
Gene (Uniprot):SNRNP200
Chain IDs:E
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:U5 small nuclear ribonucleoprotein 40 kDa protein
Gene (Uniprot):SNRNP40
Chain IDs:F
Chain Length:86
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:Pre-mRNA-processing factor 6
Gene (Uniprot):PRPF6
Chain IDs:G
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O94906 Pfam ID:PF14559, PF06424, PF13432
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Thioredoxin-like protein 4B
Gene (Uniprot):TXNL4B
Chain IDs:H
Chain Length:240
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NX01 Pfam ID:PF02966
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable ATP-dependent RNA helicase DDX23
Gene (Uniprot):DDX23
Chain IDs:I
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BUQ8 Pfam ID:PF00270, PF00271
Polymer Type:polyribonucleotide
Molecule:U4atac snRNA
Chain IDs:Q (auth: J)
Chain Length:131
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U6atac snRNA
Chain IDs:R (auth: K)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6 small nuclear ribonucleoprotein Prp31
Gene (Uniprot):PRPF31
Chain IDs:S (auth: L)
Chain Length:499
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WWY3 Pfam ID:PF01798, PF09785
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6 small nuclear ribonucleoprotein Prp4
Gene (Uniprot):PRPF4
Chain IDs:T (auth: M)
Chain Length:522
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43172 Pfam ID:PF00400, PF08799
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6 small nuclear ribonucleoprotein Prp3
Gene (Uniprot):PRPF3
Chain IDs:U (auth: N)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43395 Pfam ID:PF01480, PF08572, PF06544
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:NHP2-like protein 1
Gene (Uniprot):SNU13
Chain IDs:V (auth: O)
Chain Length:240
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P55769 Pfam ID:PF01248
Polymer Type:polyribonucleotide
Molecule:U11 snRNA
Chain IDs:EA (auth: P)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein kinase PRP4 homolog
Gene (Uniprot):PRP4K
Chain IDs:TA (auth: Q)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13523 Pfam ID:PF00069 EC:2.7.11.1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Centrosomal AT-AC splicing factor
Gene (Uniprot):CENATAC
Chain IDs:W (auth: R)
Chain Length:332
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q86UT8 Pfam ID:PF14968
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6.U5 tri-snRNP-associated protein 1
Gene (Uniprot):SART1
Chain IDs:RA (auth: S)
Chain Length:800
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O43290 Pfam ID:PF19252, PF03343
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6.U5 tri-snRNP-associated protein 2
Gene (Uniprot):USP39
Chain IDs:SA (auth: U)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q53GS9 Pfam ID:PF00443, PF02148
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Zinc finger matrin-type protein 5
Gene (Uniprot):ZMAT5
Chain IDs:FA (auth: V)
Chain Length:170
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9UDW3 Pfam ID:PF06220, PF00642
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U11/U12 small nuclear ribonucleoprotein 35 kDa protein
Gene (Uniprot):SNRNP35
Chain IDs:GA (auth: W)
Chain Length:246
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q16560 Pfam ID:PF00076
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U11/U12 small nuclear ribonucleoprotein 25 kDa protein
Gene (Uniprot):SNRNP25
Chain IDs:HA (auth: X)
Chain Length:132
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BV90 Pfam ID:PF18036
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U11/U12 small nuclear ribonucleoprotein 48 kDa protein
Gene (Uniprot):SNRNP48
Chain IDs:IA (auth: Y)
Chain Length:339
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6IEG0 Pfam ID:PF05253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Programmed cell death protein 7
Gene (Uniprot):PDCD7
Chain IDs:JA (auth: Z)
Chain Length:485
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N8D1 Pfam ID:PF16021
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:J (auth: a), X (auth: h), KA (auth: o)
Chain Length:280
Number of Molecules:3
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:K (auth: b), Y (auth: i), LA (auth: p)
Chain Length:119
Number of Molecules:3
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:L (auth: c), Z (auth: j), MA (auth: q)
Chain Length:118
Number of Molecules:3
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:M (auth: d), AA (auth: k), NA (auth: r)
Chain Length:972
Number of Molecules:3
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:N (auth: e), BA (auth: l), OA (auth: s)
Chain Length:2136
Number of Molecules:3
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:O (auth: f), CA (auth: m), PA (auth: t)
Chain Length:86
Number of Molecules:3
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:P (auth: g), DA (auth: n), QA (auth: u)
Chain Length:76
Number of Molecules:3
Biological Source:Homo sapiens
UniProt ID:P62308 Pfam ID:PF01423
Ligand Molecules
GTP
IHP
MG
ZN
Primary Citation
Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome.
Science 383 1245 1252 (2024)
PMID: 38484052 DOI: 10.1126/science.adn7272

Abstact

The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly.

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Disease

Primary Citation of related structures
8Y6O