5ZWM image
Deposition Date 2018-05-16
Release Date 2018-08-29
Last Version Date 2024-11-13
Entry Detail
PDB ID:
5ZWM
Keywords:
SPLICING
Title:
Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part)
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
5ZWM validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 snRNP component HSH155
Gene (Uniprot):HSH155
Chain IDs:TA (auth: 1)
Chain Length:971
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P49955 Pfam ID:PF22646
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cold sensitive U2 snRNA suppr
Gene (Uniprot):CUS1
Chain IDs:UA (auth: 2)
Chain Length:436
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q02554 Pfam ID:PF04037, PF04046
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor RSE1
Gene (Uniprot):RSE1
Chain IDs:VA (auth: 3)
Chain Length:1361
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q04693 Pfam ID:PF10433, PF03178, PF23726
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein HSH49
Gene (Uniprot):HSH49
Chain IDs:WA (auth: 4)
Chain Length:213
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q99181 Pfam ID:PF00076
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor RDS3
Gene (Uniprot):RDS3
Chain IDs:XA (auth: 5)
Chain Length:107
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q06835 Pfam ID:PF03660
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:RDS3 complex subunit 10
Gene (Uniprot):YSF3
Chain IDs:YA (auth: 6)
Chain Length:85
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P0C074 Pfam ID:PF07189
Structures with similar UniProt ID
Structural Superimposition 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, PF10597, PF10596, PF12134, PF08083, PF10598, PF08084 EC:3.1.13.2
Polymer Type:polyribonucleotide
Molecule:U5 snRNA
Chain IDs:R (auth: B)
Chain Length:146
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 factor SNU1
Gene (Uniprot):SNU114
Chain IDs:H (auth: C)
Chain Length:1008
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P36048 Pfam ID:PF16004, PF00009, PF03764, PF00679
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing helicase BR
Gene (Uniprot):BRR2
Chain IDs:AA (auth: D)
Chain Length:101
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P32639 Pfam ID:PF21188, PF18149, PF00270, PF00271, PF02889, PF23445 EC:3.6.4.13
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spliceosomal protein DIB1
Gene (Uniprot):DIB1
Chain IDs:F (auth: E)
Chain Length:94
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q06819 Pfam ID:PF02966
Polymer Type:polyribonucleotide
Molecule:U6 snRNA
Chain IDs:P (auth: F)
Chain Length:112
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Molecule:Pre-mRNA-BPS
Chain IDs:IA (auth: G)
Chain Length:77
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Molecule:U2 snRNA
Chain IDs:JA (auth: H)
Chain Length:196
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polyribonucleotide
Molecule:U4 snRNA
Chain IDs:Q (auth: I)
Chain Length:94
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6 small nuclear ribonucle
Gene (Uniprot):PRP3
Chain IDs:E (auth: J)
Chain Length:86
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q03338 Pfam ID:PF08572, PF06544
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U4/U6 small nuclear ribonucle
Gene (Uniprot):PRP4
Chain IDs:B (auth: K)
Chain Length:465
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P20053 Pfam ID:PF00400
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-processing factor 31
Gene (Uniprot):PRP31
Chain IDs:C (auth: L)
Chain Length:101
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P49704 Pfam ID:PF01798, PF09785
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:13 kDa ribonucleoprotein-asso
Gene (Uniprot):SNU13
Chain IDs:G (auth: M)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P39990 Pfam ID:PF01248
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor 6
Gene (Uniprot):PRP6
Chain IDs:D (auth: N)
Chain Length:899
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P19735 Pfam ID:PF06424
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:66 kDa U4/U6.U5 small nuclear
Gene (Uniprot):SNU66
Chain IDs:S (auth: O)
Chain Length:587
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q12420 Pfam ID:PF19252, PF03343
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 snRNP component IST3
Gene (Uniprot):IST3
Chain IDs:ZA (auth: X)
Chain Length:86
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40565 Pfam ID:PF00076
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor CWC2
Gene (Uniprot):BUD13
Chain IDs:AB (auth: Y)
Chain Length:115
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P46947 Pfam ID:PF09736
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA leakage protein 1
Gene (Uniprot):PML1
Chain IDs:BB (auth: Z)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q07930 Pfam ID:PF00498
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small nuclear ribonucleoprote
Gene (Uniprot):SMB1
Chain IDs:U (auth: a), BA (auth: P), KA (auth: h)
Chain Length:196
Number of Molecules:3
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:V (auth: b), CA (auth: Q), PA (auth: m)
Chain Length:146
Number of Molecules:3
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:W (auth: c), DA (auth: R), QA (auth: n)
Chain Length:1008
Number of Molecules:3
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:T (auth: d), EA (auth: S), OA (auth: l)
Chain Length:187
Number of Molecules:3
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:X (auth: e), FA (auth: T), LA (auth: i)
Chain Length:94
Number of Molecules:3
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:Y (auth: f), GA (auth: U), MA (auth: j)
Chain Length:112
Number of Molecules:3
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:Z (auth: g), HA (auth: V), NA (auth: k)
Chain Length:77
Number of Molecules:3
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40204 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleopr
Gene (Uniprot):LEA1
Chain IDs:RA (auth: o)
Chain Length:587
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q08963 Pfam ID:PF14580
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U2 small nuclear ribonucleopr
Gene (Uniprot):MSL1
Chain IDs:SA (auth: p)
Chain Length:196
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40567 Pfam ID:PF13893
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM2
Chain IDs:J (auth: q)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P38203 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM3
Chain IDs:K (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P57743 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM4
Chain IDs:O (auth: s)
Chain Length:187
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40070 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM5
Chain IDs:M (auth: t)
Chain Length:94
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P40089 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor PRP9
Gene (Uniprot):PRP9
Chain IDs:CB (auth: u)
Chain Length:530
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P19736 Pfam ID:PF16958, PF16837, PF11931, PF12171
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor PRP1
Gene (Uniprot):PRP11
Chain IDs:EB (auth: v)
Chain Length:266
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q07350 Pfam ID:PF12874, PF16835
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-mRNA-splicing factor PRP2
Gene (Uniprot):PRP21
Chain IDs:DB (auth: w)
Chain Length:280
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P32524 Pfam ID:PF01805, PF12230
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM6
Chain IDs:L (auth: x)
Chain Length:86
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:Q06406 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM7
Chain IDs:N (auth: y)
Chain Length:115
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P53905 Pfam ID:PF01423
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:U6 snRNA-associated Sm-like p
Gene (Uniprot):LSM8
Chain IDs:I (auth: z)
Chain Length:204
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
UniProt ID:P47093 Pfam ID:PF01423
Ligand Molecules
GTP
MG
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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Disease

Primary Citation of related structures
5ZWN
5ZWO
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