6FF4 image
Deposition Date 2018-01-03
Release Date 2018-08-29
Last Version Date 2025-07-02
Entry Detail
PDB ID:
6FF4
Keywords:
Title:
human Bact spliceosome core structure
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:RNA-binding motif protein, X-linked 2
Gene (Uniprot):RBMX2
Chain IDs:A (auth: 1)
Chain Length:322
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U2 snRNA
Chain IDs:B (auth: 2)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BUD13 homolog
Gene (Uniprot):BUD13
Chain IDs:C (auth: 3)
Chain Length:619
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:D (auth: 5)
Chain Length:116
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:U6 snRNA
Chain IDs:E (auth: 6)
Chain Length:107
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3A subunit 2
Gene (Uniprot):SF3A2
Chain IDs:F (auth: 7)
Chain Length:464
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 2
Gene (Uniprot):SF3B2
Chain IDs:G (auth: 8)
Chain Length:895
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing-splicing factor 8
Gene (Uniprot):PRPF8
Chain IDs:H (auth: A)
Chain Length:2335
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:116 kDa U5 small nuclear ribonucleoprotein component
Gene (Uniprot):EFTUD2
Chain IDs:I (auth: B)
Chain Length:972
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:SNW domain-containing protein 1
Gene (Uniprot):SNW1
Chain IDs:J (auth: C)
Chain Length:536
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Pleiotropic regulator 1
Gene (Uniprot):PLRG1
Chain IDs:K (auth: D)
Chain Length:514
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 17
Gene (Uniprot):CDC40
Chain IDs:L (auth: E)
Chain Length:579
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Cell division cycle 5-like protein
Gene (Uniprot):CDC5L
Chain IDs:M (auth: L)
Chain Length:802
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Crooked neck-like protein 1
Gene (Uniprot):CRNKL1
Chain IDs:N (auth: O)
Chain Length:848
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor RBM22
Gene (Uniprot):RBM22
Chain IDs:O (auth: P)
Chain Length:420
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Protein BUD31 homolog
Gene (Uniprot):BUD31
Chain IDs:P (auth: Q)
Chain Length:144
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Spliceosome-associated protein CWC15 homolog
Gene (Uniprot):CWC15
Chain IDs:Q (auth: R)
Chain Length:229
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Serine/arginine repetitive matrix protein 2
Gene (Uniprot):SRRM2
Chain IDs:R (auth: S)
Chain Length:2752
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans isomerase-like 1
Gene (Uniprot):PPIL1
Chain IDs:S (auth: V)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Serine/arginine repetitive matrix protein 1
Gene (Uniprot):SRRM1
Chain IDs:T (auth: Y)
Chain Length:904
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:pre mRNA
Chain IDs:U (auth: Z)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans isomerase CWC27 homolog
Gene (Uniprot):CWC27
Chain IDs:V (auth: s)
Chain Length:2752
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:RING finger protein 113A
Gene (Uniprot):RNF113A
Chain IDs:W (auth: t)
Chain Length:343
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 1
Gene (Uniprot):SF3B1
Chain IDs:X (auth: u)
Chain Length:1304
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 3
Gene (Uniprot):SF3B3
Chain IDs:Y (auth: v)
Chain Length:166
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 5
Gene (Uniprot):SF3B5
Chain IDs:Z (auth: x)
Chain Length:86
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:PHD finger-like domain-containing protein 5A
Gene (Uniprot):PHF5A
Chain IDs:AA (auth: y)
Chain Length:904
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Splicing factor 3B subunit 6
Gene (Uniprot):SF3B6
Chain IDs:BA (auth: z)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Structure and Conformational Dynamics of the Human Spliceosomal BactComplex.
Cell 172 454 464.e11 (2018)
PMID: 29361316 DOI: 10.1016/j.cell.2018.01.010

Abstact

The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human Bact spliceosome at 3.4 Å resolution. In the Bact state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast Bact spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation.

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Primary Citation of related structures