PDB entry 5lj3

View 5lj3 on RCSB PDB site
Description: Structure of the core of the yeast spliceosome immediately after branching
Class: splicing
Keywords: spliceosome, snRNP, pre-mRNA splicing, trans-esterification, lariat intermediate, complex C, splicing
Deposited on 2016-07-17, released 2016-08-03
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-10-23, with a file datestamp of 2019-10-18.
Experiment type: EM
Resolution: 3.8 Å
R-factor: N/A
AEROSPACI score: 0.05 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: Pre-mRNA-splicing factor 8
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P33334
• Chain 'C':
  Compound: Pre-mRNA-splicing factor SNU114
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P36048
• Chain 'D':
  Compound: Protein CWC16
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P28320
• Chain 'E':
  Compound: Exon 1 (5' exon) of UBC4 pre-mRNA
  Species: Saccharomyces cerevisiae [TaxId:4932]
  
• Chain 'F':
  Compound: Pre-mRNA-splicing factor CWC25
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P53854
• Chain 'G':
  Compound: isy1
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A165UGV0 (0-End)
• Chain 'H':
  Compound: cwc22
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A162ERE7
• Chain 'I':
  Compound: Intron of UBC4 pre-mRNA
  Species: Saccharomyces cerevisiae [TaxId:4932]
  
• Chain 'J':
  Compound: prp46
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A162HKW4
• Chain 'K':
  Compound: Pre-mRNA-processing protein 45
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P28004
• Chain 'L':
  Compound: Pre-mRNA-splicing factor BUD31
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P25337
• Chain 'M':
  Compound: cwc2
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A162HWE4
• Chain 'N':
  Compound: Pre-mRNA-splicing factor SLT11
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P38241
  Domains in SCOPe 2.08: d5lj3n1, d5lj3n2
• Chain 'O':
  Compound: cef1
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A165TLN2
• Chain 'P':
  Compound: cwc15
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A162GIZ3
• Chain 'R':
  Compound: Pre-mRNA-splicing factor CWC21
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q03375
  Domains in SCOPe 2.08: d5lj3r_
• Chain 'S':
  Compound: clf1
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A165TU20
• Chain 'T':
  Compound: syf1
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot A0A165VVY6
• Chain 'U':
  Compound: U5 snRNA (small nuclear RNA)
  Species: Saccharomyces cerevisiae [TaxId:4932]
  
• Chain 'V':
  Compound: U6 snRNA (small nuclear RNA)
  Species: Saccharomyces cerevisiae [TaxId:4932]
  
• Chain 'W':
  Compound: U2 small nuclear ribonucleoprotein A'
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q08963 (0-End)
• Chain 'Y':
  Compound: U2 small nuclear ribonucleoprotein B''
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40567 (Start-110)
• Chain 'Z':
  Compound: U2 snRNA (small nuclear RNA)
  Species: Saccharomyces cerevisiae [TaxId:4932]
  
• Chain 'b':
  Compound: Small nuclear ribonucleoprotein-associated protein B
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40018
• Chain 'd':
  Compound: Small nuclear ribonucleoprotein Sm D3
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P43321
• Chain 'e':
  Compound: Small nuclear ribonucleoprotein E
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12330
• Chain 'f':
  Compound: Small nuclear ribonucleoprotein F
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P54999
• Chain 'g':
  Compound: Small nuclear ribonucleoprotein G
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40204
• Chain 'h':
  Compound: Small nuclear ribonucleoprotein Sm D1
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q02260 (0-End)
• Chain 'j':
  Compound: Small nuclear ribonucleoprotein Sm D2
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06217
• Chain 'k':
  Compound: Small nuclear ribonucleoprotein-associated protein B
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40018
• Chain 'l':
  Compound: Small nuclear ribonucleoprotein Sm D1
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q02260 (0-End)
• Chain 'm':
  Compound: Small nuclear ribonucleoprotein Sm D2
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06217
• Chain 'n':
  Compound: Small nuclear ribonucleoprotein Sm D3
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P43321
• Chain 'p':
  Compound: Small nuclear ribonucleoprotein E
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12330
• Chain 'q':
  Compound: Small nuclear ribonucleoprotein F
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P54999
• Chain 'r':
  Compound: Small nuclear ribonucleoprotein G
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40204
• Chain 'x':
  Compound: unknown
  Species: Saccharomyces cerevisiae [TaxId:4932]
  Database cross-references and differences (RAF-indexed):
  • PDB 5LJ3 (0-131)
• Heterogens: MG, ZN, GTP

PDB Chain Sequences:

• Chain 'A':
  No sequence available.
  
  
• Chain 'C':
  No sequence available.
  
  
• Chain 'D':
  No sequence available.
  
  
• Chain 'E':
  No sequence available.
  
  
• Chain 'F':
  No sequence available.
  
  
• Chain 'G':
  No sequence available.
  
  
• Chain 'H':
  No sequence available.
  
  
• Chain 'I':
  No sequence available.
  
  
• Chain 'J':
  No sequence available.
  
  
• Chain 'K':
  No sequence available.
  
  
• Chain 'L':
  No sequence available.
  
  
• Chain 'M':
  No sequence available.
  
  
• Chain 'N':
  Sequence, based on SEQRES records: (download)
  

  >5lj3N (N:)
  mndeinepppniceqclgdeanirmtkipqgseckictlpftlyhfktskrsnniiktli
  cvrcatqrnicqccmldsrwhipiqlrdhlislvneenvmteeakndmmkrflslknvkl
  ggaqitsdpseadnivdklknillratsdgpstpliknttalyknekganevknlekyas
  vdishilkklplnesflknpstksfflynidasipewkitdtvsqllgikkwkdgnslsl
  ivnhkakcgglrfqsselgerfvskisetlvtpkglkrgvllidrfrifiipwssgfsaa
  sfgtntaeniklslslnkliqlelglsfptkstdnakndkkktskkvhkdrskkskpran
  klti
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5lj3N (N:)
  nepppniceqclgdeanirmtkipqgseckictlpftlyhfktskrsnniiktlicvrca
  tqrnicqccmldsrwhipiqlrdhlislvvmteeakndmmkrflslknvklggaqitsdp
  seadnivdklknillsfflynsipewkitdtvsqllslivnhkakcgglrfqsselgerf
  vskifiipwstaeniklslslnkliqlel
  

  
  
• Chain 'O':
  No sequence available.
  
  
• Chain 'P':
  No sequence available.
  
  
• Chain 'R':
  Sequence, based on SEQRES records: (download)
  

  >5lj3R (R:)
  msyngiglksakgsstsghvqrslasnnrrrpqgsqqqrqqrqnaikkashdkasrplav
  qkqiethmekreievqvselrdrleeeetlseeqidkkcealrakltnewqeqqrmssly
  tprkarlteeqhrhe
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >5lj3R (R:)
  syngiglksakgsstsghvqrslasnnrrrpqgsqqqrqqrqnaikkasiethmekreie
  vqvselrdrleeeetlseeqidkkcealrakltnewq
  

  
  
• Chain 'S':
  No sequence available.
  
  
• Chain 'T':
  No sequence available.
  
  
• Chain 'U':
  No sequence available.
  
  
• Chain 'V':
  No sequence available.
  
  
• Chain 'W':
  No sequence available.
  
  
• Chain 'Y':
  No sequence available.
  
  
• Chain 'Z':
  No sequence available.
  
  
• Chain 'b':
  No sequence available.
  
  
• Chain 'd':
  No sequence available.
  
  
• Chain 'e':
  No sequence available.
  
  
• Chain 'f':
  No sequence available.
  
  
• Chain 'g':
  No sequence available.
  
  
• Chain 'h':
  No sequence available.
  
  
• Chain 'j':
  No sequence available.
  
  
• Chain 'k':
  No sequence available.
  
  
• Chain 'l':
  No sequence available.
  
  
• Chain 'm':
  No sequence available.
  
  
• Chain 'n':
  No sequence available.
  
  
• Chain 'p':
  No sequence available.
  
  
• Chain 'q':
  No sequence available.
  
  
• Chain 'r':
  No sequence available.
  
  
• Chain 'x':
  No sequence available.