ISDA: 9ZED

Deposition Date 2025-11-29

Release Date 2026-04-15

Last Version Date 2026-04-15

Entry Detail

PDB ID:

9ZED

Keywords:

SPLICING

Title:

Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 2)

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.94 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:U2 snRNA
Chain IDs:A (auth: 2)
Chain Length:37
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA-binding protein 5
Gene (Uniprot):RBM5
Chain IDs:B (auth: A)
Chain Length:824
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52756 Pfam ID:PF00076, PF00641, PF17780, PF01585

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3A subunit 1
Gene (Uniprot):SF3A1
Chain IDs:C (auth: A1)
Chain Length:793
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15459 Pfam ID:PF01805, PF12230, PF00240

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3A subunit 2
Gene (Uniprot):SF3A2
Chain IDs:D (auth: A2)
Chain Length:464
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15428 Pfam ID:PF12874, PF16835

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3A subunit 3
Gene (Uniprot):SF3A3
Chain IDs:E (auth: A3)
Chain Length:501
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q12874 Pfam ID:PF12108, PF16837, PF13297, PF11931

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 1
Gene (Uniprot):SF3B1
Chain IDs:F (auth: B1)
Chain Length:1304
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75533 Pfam ID:PF08920, PF22646

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 2
Gene (Uniprot):SF3B2
Chain IDs:G (auth: B2)
Chain Length:895
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13435 Pfam ID:PF02037, PF04037, PF04046

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 3
Gene (Uniprot):SF3B3
Chain IDs:H (auth: B3)
Chain Length:1217
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15393 Pfam ID:PF10433, PF23726, PF03178

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 4
Gene (Uniprot):SF3B4
Chain IDs:I (auth: B4)
Chain Length:424
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15427 Pfam ID:PF00076

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 5
Gene (Uniprot):SF3B5
Chain IDs:J (auth: B5)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BWJ5 Pfam ID:PF07189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 6
Gene (Uniprot):SF3B6
Chain IDs:K (auth: B6)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3B4 Pfam ID:PF00076

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PHD finger-like domain-contai
Gene (Uniprot):PHF5A
Chain IDs:L (auth: H)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q7RTV0 Pfam ID:PF03660

Polymer Type:polyribonucleotide
Molecule:pre-mRNA
Chain IDs:M (auth: R)
Chain Length:42
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

Primary Citation

The tumour suppressor RBM5 activates the helicase DHX15 to regulate splicing.

Liu, S, Su, T, Huang, J, Lin, C.H, Black, D.L, Damianov, A, Zhou, Z.H.Show

Biorxiv ? ? ? (2026)

PMID: 41929118 DOI: 10.64898/2026.03.26.714623

Primary Citation of related structures

Feedback Form