PDB entry 3jcm

View 3jcm on RCSB PDB site
Description: Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP
Class: transcription
Keywords: U4/U6.U5 tri-snRNP, pre-mRNA, TRANSCRIPTION
Deposited on 2015-12-23, released 2016-02-24
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-10-16, with a file datestamp of 2019-10-11.
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 S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P33334
• Chain 'B':
  Compound: U4/U6 small nuclear ribonucleoprotein PRP4
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P20053 (Start-464)
• Chain 'C':
  Compound: pre-mRNA
  Species: synthetic construct, synthetic [TaxId:32630]
  
• Chain 'D':
  Compound: SNR6 snRNA
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  
• Chain 'E':
  Compound: SNR14 snRNA
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  
• Chain 'F':
  Compound: SNR7-L snRNA
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  
• Chain 'G':
  Compound: Pre-mRNA-splicing factor 6
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P19735 (Start-898)
• Chain 'H':
  Compound: Pre-mRNA-splicing factor SNU114
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P36048
• Chain 'I':
  Compound: Pre-mRNA-processing factor 31
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P49704
• Chain 'J':
  Compound: Small nuclear ribonucleoprotein Sm D3
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P43321
  Domains in SCOPe 2.08: d3jcmj_
• Chain 'K':
  Compound: U4/U6 small nuclear ribonucleoprotein Prp3
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q03338
• Chain 'L':
  Compound: Spliceosomal protein DIB1
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06819
• Chain 'M':
  Compound: 13 kDa ribonucleoprotein-associated protein
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P39990 (0-125)
• Chain 'N':
  Compound: Pre-mRNA-splicing helicase BRR2
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P32639 (Start-2162)
• Chain 'O':
  Compound: Small nuclear ribonucleoprotein-associated protein B
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40018
  Domains in SCOPe 2.08: d3jcmo_
• Chain 'P':
  Compound: Small nuclear ribonucleoprotein Sm D1
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q02260 (0-End)
  Domains in SCOPe 2.08: d3jcmp_
• Chain 'Q':
  Compound: Small nuclear ribonucleoprotein Sm D2
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06217
  Domains in SCOPe 2.08: d3jcmq_
• Chain 'R':
  Compound: Small nuclear ribonucleoprotein Sm D3
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P43321
  Domains in SCOPe 2.08: d3jcmr_
• Chain 'S':
  Compound: Small nuclear ribonucleoprotein-associated protein B
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40018
  Domains in SCOPe 2.08: d3jcms_
• Chain 'T':
  Compound: Small nuclear ribonucleoprotein Sm D1
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q02260 (0-End)
  Domains in SCOPe 2.08: d3jcmt_
• Chain 'U':
  Compound: Small nuclear ribonucleoprotein Sm D2
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06217 (Start-109)
  Domains in SCOPe 2.08: d3jcmu_
• Chain 'V':
  Compound: Small nuclear ribonucleoprotein E
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12330
  Domains in SCOPe 2.08: d3jcmv_
• Chain 'W':
  Compound: Small nuclear ribonucleoprotein F
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P54999
  Domains in SCOPe 2.08: d3jcmw_
• Chain 'X':
  Compound: Small nuclear ribonucleoprotein G
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40204 (0-End)
  Domains in SCOPe 2.08: d3jcmx_
• Chain 'Y':
  Compound: Small nuclear ribonucleoprotein E
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12330
  Domains in SCOPe 2.08: d3jcmy_
• Chain 'Z':
  Compound: Small nuclear ribonucleoprotein F
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P54999
  Domains in SCOPe 2.08: d3jcmz_
• Chain 'a':
  Compound: Small nuclear ribonucleoprotein G
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40204 (0-End)
• Chain 'b':
  Compound: U6 snRNA-associated Sm-like protein LSm8
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P47093
• Chain 'c':
  Compound: u6 snrna-associated sm-like protein lsm2
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P38203 (0-End)
• Chain 'd':
  Compound: U6 snRNA-associated Sm-like protein LSm3
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P57743
• Chain 'e':
  Compound: U6 snRNA-associated Sm-like protein LSm6
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06406
• Chain 'f':
  Compound: U6 snRNA-associated Sm-like protein LSm5
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40089
• Chain 'g':
  Compound: U6 snRNA-associated Sm-like protein LSm7
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P53905
• Chain 'h':
  Compound: u6 snrna-associated sm-like protein lsm4
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40070 (0-End)
• Heterogens: GTP, M7M

PDB Chain Sequences:

• Chain 'A':
  No sequence available.
  
  
• Chain 'B':
  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':
  Sequence, based on SEQRES records: (download)
  

  >3jcmJ (J:)
  mtmngipvkllneaqghivslelttgatyrgklvesedsmnvqlrdviatepqgavthmd
  qifvrgsqikfivvpdllknaplfkknssrpmppirgpkrr
  

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

  >3jcmJ (J:)
  gipvkllneaqghivslelttgatyrgklvesedsmnvqlrdviatepqgavthmdqifv
  rgsqikfivvpdllknapl
  

  
  
• Chain 'K':
  No sequence available.
  
  
• Chain 'L':
  No sequence available.
  
  
• Chain 'M':
  No sequence available.
  
  
• Chain 'N':
  No sequence available.
  
  
• Chain 'O':
  Sequence, based on SEQRES records: (download)
  

  >3jcmO (O:)
  mskiqvahssrlanlidyklrvltqdgrvyigqlmafdkhmnlvlnecieervpktqldk
  lrprkdskdgttlnikvekrvlgltilrgeqilstvvedkpllskkerlvrdkkekkqaq
  kqtklrkekekkpgkiakpntanakhtssnsreiaqpsssrynggndniganrsrfnnea
  ppqtrkfqpppgfkrk
  

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

  >3jcmO (O:)
  hssrlanlidyklrvltqdgrvyigqlmafdkhmnlvlnecieervvekrvlgltilrge
  qilstvvedkpll
  

  
  
• Chain 'P':
  Sequence, based on SEQRES records: (download)
  

  >3jcmP (P:)
  mklvnflkklrneqvtielkngttvwgtlqsvspqmnailtdvkltlpqprlnklnsngi
  amaslyltggqqptasdniaslqyinirgntirqiilpdslnldsllvdqkqlnslrrsg
  qiandpskkrrrdfgapankrprrgl
  

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

  >3jcmP (P:)
  mklvnflkklrneqvtielkngttvwgtlqsvspqmnailtdvkltlqqptasdnianti
  rqiilpdslnldsllvd
  

  
  
• Chain 'Q':
  Sequence, based on SEQRES records: (download)
  

  >3jcmQ (Q:)
  mssqiidrpkhelsraeleeleefefkhgpmslindamvtrtpviislrnnhkiiarvka
  fdrhcnmvlenvkelwtekkgknvinrerfisklflrgdsvivvlktpve
  

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

  >3jcmQ (Q:)
  eleefefkhgpmslindamvtrtpviislrnnhkiiarvkafdrhcnmvlenvkelwtek
  kknvinrerfisklflrgdsvivvlktpv
  

  
  
• Chain 'R':
  Sequence, based on SEQRES records: (download)
  

  >3jcmR (R:)
  mtmngipvkllneaqghivslelttgatyrgklvesedsmnvqlrdviatepqgavthmd
  qifvrgsqikfivvpdllknaplfkknssrpmppirgpkrr
  

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

  >3jcmR (R:)
  gipvkllneaqghivslelttgatyrgklvesedsmnvqlrdviatepqgavthmdqifv
  rgsqikfivvpdllknapl
  

  
  
• Chain 'S':
  Sequence, based on SEQRES records: (download)
  

  >3jcmS (S:)
  mskiqvahssrlanlidyklrvltqdgrvyigqlmafdkhmnlvlnecieervpktqldk
  lrprkdskdgttlnikvekrvlgltilrgeqilstvvedkpllskkerlvrdkkekkqaq
  kqtklrkekekkpgkiakpntanakhtssnsreiaqpsssrynggndniganrsrfnnea
  ppqtrkfqpppgfkrk
  

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

  >3jcmS (S:)
  hssrlanlidyklrvltqdgrvyigqlmafdkhmnlvlnecieervvekrvlgltilrge
  qilstvvedkpll
  

  
  
• Chain 'T':
  Sequence, based on SEQRES records: (download)
  

  >3jcmT (T:)
  mklvnflkklrneqvtielkngttvwgtlqsvspqmnailtdvkltlpqprlnklnsngi
  amaslyltggqqptasdniaslqyinirgntirqiilpdslnldsllvdqkqlnslrrsg
  qiandpskkrrrdfgapankrprrgl
  

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

  >3jcmT (T:)
  mklvnflkklrneqvtielkngttvwgtlqsvspqmnailtdvkltlqqptasdnianti
  rqiilpdslnldsllvd
  

  
  
• Chain 'U':
  Sequence, based on SEQRES records: (download)
  

  >3jcmU (U:)
  mssqiidrpkhelsraeleeleefefkhgpmslindamvtrtpviislrnnhkiiarvka
  fdrhcnmvlenvkelwtekkgknvinrerfisklflrgdsvivvlktpve
  

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

  >3jcmU (U:)
  eleefefkhgpmslindamvtrtpviislrnnhkiiarvkafdrhcnmvlenvkelwtek
  kknvinrerfisklflrgdsvivvlktpve
  

  
  
• Chain 'V':
  Sequence, based on SEQRES records: (download)
  

  >3jcmV (V:)
  msnkvktkamvppincifnflqqqtpvtiwlfeqigirikgkivgfdefmnvvideavei
  pvnsadgkedvekgtplgkillkgdnitlitsad
  

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

  >3jcmV (V:)
  mvppincifnflqqqtpvtiwlfeqigirikgkivgfdefmnvvideaveikedvekkil
  lkgdnitlitsa
  

  
  
• Chain 'W':
  Sequence, based on SEQRES records: (download)
  

  >3jcmW (W:)
  msessdisamqpvnpkpflkglvnhrvgvklkfnsteyrgtlvstdnyfnlqlneaeefv
  agvshgtlgeifircnnvlyirelpn
  

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

  >3jcmW (W:)
  qpvnpkpflkglvnhrvgvklkteyrgtlvstdnyfnlqlneaeefvagvshgtlgeifi
  rcnnvlyire
  

  
  
• Chain 'X':
  Sequence, based on SEQRES records: (download)
  

  >3jcmX (X:)
  mvstpelkkymdkkillningsrkvagilrgydiflnvvlddameingedpannhqlglq
  tvirgnsiislealdai
  

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

  >3jcmX (X:)
  mvstpelkkymdkkillningsrkvagilrgydiflnvvlddameinannhqlgtvirgn
  siislealda
  

  
  
• Chain 'Y':
  Sequence, based on SEQRES records: (download)
  

  >3jcmY (Y:)
  msnkvktkamvppincifnflqqqtpvtiwlfeqigirikgkivgfdefmnvvideavei
  pvnsadgkedvekgtplgkillkgdnitlitsad
  

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

  >3jcmY (Y:)
  mvppincifnflqqqtpvtiwlfeqigirikgkivgfdefmnvvideaveikedvekkil
  lkgdnitlitsa
  

  
  
• Chain 'Z':
  Sequence, based on SEQRES records: (download)
  

  >3jcmZ (Z:)
  msessdisamqpvnpkpflkglvnhrvgvklkfnsteyrgtlvstdnyfnlqlneaeefv
  agvshgtlgeifircnnvlyirelpn
  

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

  >3jcmZ (Z:)
  qpvnpkpflkglvnhrvgvklkteyrgtlvstdnyfnlqlneaeefvagvshgtlgeifi
  rcnnvlyire
  

  
  
• Chain 'a':
  No sequence available.
  
  
• Chain 'b':
  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.