6J6N image
Deposition Date 2019-01-15
Release Date 2019-04-24
Last Version Date 2024-11-06
Entry Detail
PDB ID:
6J6N
Keywords:
SPLICING
Title:
Cryo-EM structure of the yeast B*-b1 complex at an average resolution of 3.86 angstrom
Biological Source:
Source Organism:
Saccharomyces cerevisiae S288c (Taxon ID: 559292)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.86 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6J6N validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor 8
Gene (Uniprot):PRP8
Chain IDs:A
Chain Length:2413
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P33334 Pfam ID:PF08082, PF08083, PF10598, PF10597, PF10596, PF12134, PF08084 EC:3.1.13.2
Polymer Type:polyribonucleotide
Molecule:UBC4 pre-mRNA
Chain IDs:P (auth: B)
Chain Length:246
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SNU114
Gene (Uniprot):SNU114
Chain IDs:B (auth: C)
Chain Length:590
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P36048 Pfam ID:PF16004, PF00009, PF03764, PF00679
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:Q (auth: D)
Chain Length:687
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Molecule:U6 snRNA
Chain IDs:R (auth: E)
Chain Length:110
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor ISY1
Gene (Uniprot):ISY1
Chain IDs:O (auth: H)
Chain Length:86
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P21374 Pfam ID:PF06246
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SYF2
Gene (Uniprot):SYF2
Chain IDs:M (auth: I)
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P53277 Pfam ID:PF08231
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC21
Gene (Uniprot):CWC21
Chain IDs:C (auth: J)
Chain Length:77
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q03375 Pfam ID:PF08312
Polymer Type:polyribonucleotide
Molecule:U2 snRNA
Chain IDs:S (auth: L)
Chain Length:101
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor PRP46
Gene (Uniprot):PRP46
Chain IDs:D (auth: O)
Chain Length:503
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q12417 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing protein 45
Gene (Uniprot):PRP45
Chain IDs:E (auth: P)
Chain Length:503
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P28004 Pfam ID:PF02731
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SLT11
Gene (Uniprot):ECM2
Chain IDs:F (auth: Q)
Chain Length:364
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P38241 Pfam ID:PF21369
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC2
Gene (Uniprot):CWC2
Chain IDs:G (auth: R)
Chain Length:503
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q12046 Pfam ID:PF16131, PF00076
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC15
Gene (Uniprot):CWC15
Chain IDs:H (auth: S)
Chain Length:175
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q03772 Pfam ID:PF04889
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor BUD31
Gene (Uniprot):BUD31
Chain IDs:I (auth: T)
Chain Length:157
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P25337 Pfam ID:PF01125
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC22
Gene (Uniprot):CWC22
Chain IDs:J (auth: Z)
Chain Length:577
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P53333 Pfam ID:PF02847
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleoprotein B''
Gene (Uniprot):MSL1
Chain IDs:U (auth: a)
Chain Length:2413
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40567 Pfam ID:PF13893
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleoprotein A'
Gene (Uniprot):LEA1
Chain IDs:V (auth: b)
Chain Length:246
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q08963 Pfam ID:PF14580
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CEF1
Gene (Uniprot):CEF1
Chain IDs:K (auth: c)
Chain Length:590
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q03654 Pfam ID:PF00249, PF11831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CLF1
Gene (Uniprot):CLF1
Chain IDs:L (auth: d)
Chain Length:687
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q12309 Pfam ID:PF05843
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D2
Gene (Uniprot):SMD2
Chain IDs:BA (auth: g), DA (auth: e)
Chain Length:110
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q06217 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein F
Gene (Uniprot):SMX3
Chain IDs:AA (auth: h), HA (auth: w)
Chain Length:86
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P54999 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein G
Gene (Uniprot):SMX2
Chain IDs:Z (auth: j), IA (auth: x)
Chain Length:77
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40204 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein-associated protein B
Gene (Uniprot):SMB1
Chain IDs:CA (auth: k), EA (auth: s)
Chain Length:196
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40018 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D3
Gene (Uniprot):SMD3
Chain IDs:FA (auth: l), JA (auth: y)
Chain Length:101
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P43321 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein Sm D1
Gene (Uniprot):SMD1
Chain IDs:Y (auth: m), KA (auth: z)
Chain Length:146
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q02260 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 17
Gene (Uniprot):CDC40
Chain IDs:N (auth: n)
Chain Length:455
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40968 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 19
Gene (Uniprot):PRP19
Chain IDs:LA (auth: r), MA (auth: p), NA (auth: q), OA (auth: o)
Chain Length:503
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P32523 Pfam ID:PF08606 EC:2.3.2.27
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SNT309
Gene (Uniprot):SNT309
Chain IDs:W (auth: t)
Chain Length:157
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q06091
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprotein E
Gene (Uniprot):SME1
Chain IDs:X (auth: u), GA (auth: i)
Chain Length:215
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q12330 Pfam ID:PF01423
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor SYF1
Gene (Uniprot):SYF1
Chain IDs:T (auth: v)
Chain Length:859
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q04048 Pfam ID:PF05843
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP N SER modified residue
Ligand Molecules
GTP
IHP
MG
ZN
Primary Citation
Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
Cell 177 339 351.e13 (2019)
PMID: 30879786 DOI: 10.1016/j.cell.2019.02.006

Abstact

Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B∗) is pivotal for understanding the branching reaction. In this study, we assembled the B∗ complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B∗ complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B∗ complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state.

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Primary Citation of related structures
6J6N
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