5ZWN image
Deposition Date 2018-05-16
Release Date 2018-08-29
Last Version Date 2024-03-27
Entry Detail
PDB ID:
5ZWN
Keywords:
SPLICING
Title:
Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region)
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae S288c (Taxon ID: 559292)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.40 Å
Aggregation State:
CELL
Reconstruction Method:
SINGLE PARTICLE
5ZWN validation report missing
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:pre-mRNA
Chain IDs:A (auth: G)
Chain Length:77
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Molecule:U1 snRNA
Chain IDs:B (auth: P)
Chain Length:568
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleopr
Gene (Uniprot):SNP1
Chain IDs:C (auth: Q)
Chain Length:300
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q00916 Pfam ID:PF12220, PF00076
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleopr
Gene (Uniprot):YHC1
Chain IDs:D (auth: R)
Chain Length:231
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q05900 Pfam ID:PF06220
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleopr
Gene (Uniprot):MUD1
Chain IDs:E (auth: S)
Chain Length:298
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P32605 Pfam ID:PF00076
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleopr
Gene (Uniprot):PRP42
Chain IDs:F (auth: T)
Chain Length:544
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q03776 Pfam ID:PF23240, PF23241
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 39
Gene (Uniprot):PRP39
Chain IDs:G (auth: U)
Chain Length:629
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P39682 Pfam ID:PF23240, PF23241
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein NAM8
Gene (Uniprot):NAM8
Chain IDs:H (auth: V)
Chain Length:523
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q00539 Pfam ID:PF00076
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:56 kDa U1 small nuclear ribon
Gene (Uniprot):SNU56
Chain IDs:I (auth: W)
Chain Length:492
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q03782 Pfam ID:PF19097
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U1 small nuclear ribonucleopr
Gene (Uniprot):SNU71
Chain IDs:Q (auth: X)
Chain Length:49
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P53207 Pfam ID:PF24826, PF24825
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein LUC7
Gene (Uniprot):LUC7
Chain IDs:R (auth: Y)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q07508 Pfam ID:PF03194
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SMB1
Chain IDs:J (auth: a)
Chain Length:196
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40018 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SMD1
Chain IDs:K (auth: b)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q02260 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SMD2
Chain IDs:L (auth: c)
Chain Length:110
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q06217 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SMD3
Chain IDs:M (auth: d)
Chain Length:101
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P43321 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SME1
Chain IDs:N (auth: e)
Chain Length:94
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q12330 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SMX3
Chain IDs:O (auth: f)
Chain Length:86
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P54999 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SMX2
Chain IDs:P (auth: g)
Chain Length:77
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40204 Pfam ID:PF01423
Polymer Type:polypeptide(L)
Molecule:U1 snRNP
Chain IDs:S (auth: x)
Chain Length:49
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing ATP-depende
Gene (Uniprot):PRP28
Chain IDs:T (auth: y)
Chain Length:261
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P23394 Pfam ID:PF00270, PF00271 EC:3.6.4.13
Ligand Molecules
ZN
Primary Citation
Structures of the fully assembledSaccharomyces cerevisiaespliceosome before activation
Science 360 1423 1429 (2018)
PMID: 29794219 DOI: 10.1126/science.aau0325

Abstact

The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.

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Primary Citation of related structures
5ZWM
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