8Y7E image
Deposition Date 2024-02-04
Release Date 2024-03-13
Last Version Date 2024-10-23
Entry Detail
PDB ID:
8Y7E
Keywords:
SPLICING/RNA
Title:
Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U12 snRNP part
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Homo sapiens
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.66 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8Y7E validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 1
Gene (Uniprot):SF3B1
Chain IDs:B (auth: 1)
Chain Length:1304
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75533 Pfam ID:PF08920, PF22646
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 2
Gene (Uniprot):SF3B2
Chain IDs:C (auth: 2)
Chain Length:895
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13435 Pfam ID:PF02037, PF04037, PF04046
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 3
Gene (Uniprot):SF3B3
Chain IDs:D (auth: 3)
Chain Length:1217
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15393 Pfam ID:PF10433, PF03178
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 4
Gene (Uniprot):SF3B4
Chain IDs:E (auth: 4)
Chain Length:424
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15427 Pfam ID:PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 6
Gene (Uniprot):SF3B6
Chain IDs:F (auth: 5)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y3B4 Pfam ID:PF00076
Protein Blast
Polymer Type:polypeptide(L)
Molecule:PHD finger-like domain-containing protein 5A
Gene (Uniprot):PHF5A
Chain IDs:G (auth: 6)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7RTV0 Pfam ID:PF03660
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 5
Gene (Uniprot):SF3B5
Chain IDs:H (auth: 7)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BWJ5 Pfam ID:PF07189
Polymer Type:polyribonucleotide
Molecule:pre-mRNA
Chain IDs:A
Chain Length:280
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U12 snRNA
Chain IDs:I (auth: H)
Chain Length:126
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D3
Gene (Uniprot):SNRPD3
Chain IDs:J (auth: h)
Chain Length:126
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62318 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein-associated proteins B and B'
Gene (Uniprot):SNRPB
Chain IDs:K (auth: i)
Chain Length:240
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P14678 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D1
Gene (Uniprot):SNRPD1
Chain IDs:L (auth: j)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62314 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D2
Gene (Uniprot):SNRPD2
Chain IDs:M (auth: k)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62316 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein E
Gene (Uniprot):SNRPE
Chain IDs:N (auth: l)
Chain Length:92
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62304 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein F
Gene (Uniprot):SNRPF
Chain IDs:O (auth: m)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62306 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein G
Gene (Uniprot):SNRPG
Chain IDs:P (auth: n)
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62308 Pfam ID:PF01423
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sodium channel modifier 1
Gene (Uniprot):SCNM1
Chain IDs:Q (auth: v)
Chain Length:230
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BWG6 Pfam ID:PF15803, PF15805
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP B SER modified residue
TPO D THR modified residue
Ligand Molecules
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
8Y7E