PDB entry 5gmk

View 5gmk on RCSB PDB site
Description: Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution
Class: RNA binding protein/RNA
Keywords: RNA splicing, Spliceosome, Catalytic Step I, Intron lariat, RNA BINDING PROTEIN-RNA complex
Deposited on 2016-07-14, released 2016-08-17
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-12-21, with a file datestamp of 2016-12-16.
Experiment type: EM
Resolution: 3.4 Å
R-factor: N/A
AEROSPACI score: 0.11 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: Pre-mRNA-splicing factor 8
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P33334
• Chain 'B':
  Compound: 5'-Exon
  Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
  
• Chain 'C':
  Compound: Pre-mRNA-splicing factor SNU114
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P36048
• Chain 'D':
  Compound: U5 snRNA
  Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
  
• Chain 'E':
  Compound: U6 snRNA
  Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
  
• Chain 'F':
  Compound: Protein CWC16
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P28320
  Domains in SCOPe 2.07: d5gmkf_
• Chain 'G':
  Compound: Pre-mRNA-splicing factor CWC25
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P53854
  Domains in SCOPe 2.07: d5gmkg_
• Chain 'H':
  Compound: Pre-mRNA-splicing factor ISY1
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P21374
  Domains in SCOPe 2.07: d5gmkh_
• Chain 'I':
  Compound: Pre-mRNA-splicing factor SYF2
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P53277
  Domains in SCOPe 2.07: d5gmki_
• Chain 'J':
  Compound: Pre-mRNA-splicing factor CWC21
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q03375
• Chain 'L':
  Compound: U2 snRNA
  Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
  
• Chain 'M':
  Compound: Intron_BPS
  Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
  
• Chain 'N':
  Compound: 5'-Splicing Site
  Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
  
• Chain 'O':
  Compound: Pre-mRNA-splicing factor PRP46
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12417
• Chain 'P':
  Compound: Pre-mRNA-processing protein 45
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P28004
• Chain 'Q':
  Compound: Pre-mRNA-splicing factor SLT11
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P38241
• Chain 'R':
  Compound: Pre-mRNA-splicing factor CWC2
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12046 (0-End)
• Chain 'S':
  Compound: Pre-mRNA-splicing factor CWC15
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q03772 (Start-174)
• Chain 'T':
  Compound: Pre-mRNA-splicing factor BUD31
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P25337 (0-156)
• Chain 'Z':
  Compound: Pre-mRNA-splicing factor CWC22
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P53333
• Chain 'a':
  Compound: U2 small nuclear ribonucleoprotein B''
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40567 (Start-110)
  Domains in SCOPe 2.07: d5gmka_
• Chain 'b':
  Compound: U2 small nuclear ribonucleoprotein A'
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q08963 (0-End)
  Domains in SCOPe 2.07: d5gmkb_
• Chain 'c':
  Compound: Pre-mRNA-splicing factor CEF1
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q03654 (Start-252)
  • PDB 5GMK
  • Uniprot Q03654 (481-586)
• Chain 'd':
  Compound: Pre-mRNA-splicing factor CLF1
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12309 (Start-274)
  • PDB 5GMK
  Domains in SCOPe 2.07: d5gmkd_
• Chain 'e':
  Compound: Small nuclear ribonucleoprotein Sm D2
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06217
• Chain 'g':
  Compound: Small nuclear ribonucleoprotein Sm D2
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06217
• Chain 'h':
  Compound: Small nuclear ribonucleoprotein F
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P54999
• Chain 'i':
  Compound: Small nuclear ribonucleoprotein E
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12330
• Chain 'j':
  Compound: Small nuclear ribonucleoprotein G
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40204
• Chain 'k':
  Compound: Small nuclear ribonucleoprotein-associated protein B
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40018
• Chain 'l':
  Compound: Small nuclear ribonucleoprotein Sm D3
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P43321
• Chain 'm':
  Compound: Small nuclear ribonucleoprotein Sm D1
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q02260 (0-End)
• Chain 'n':
  Compound: Pre-mRNA-processing factor 17
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40968 (Start-454)
  Domains in SCOPe 2.07: d5gmkn1, d5gmkn2
• Chain 'o':
  Compound: Pre-mRNA-processing factor 19
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P32523 (0-End)
• Chain 'p':
  Compound: Pre-mRNA-processing factor 19
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P32523 (0-End)
• Chain 'q':
  Compound: Pre-mRNA-processing factor 19
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P32523 (0-End)
• Chain 'r':
  Compound: Pre-mRNA-processing factor 19
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P32523 (0-End)
• Chain 's':
  Compound: Small nuclear ribonucleoprotein-associated protein B
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40018
• Chain 't':
  Compound: Pre-mRNA-splicing factor SNT309
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q06091 (0-174)
• Chain 'u':
  Compound: Small nuclear ribonucleoprotein E
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q12330
• Chain 'v':
  Compound: Pre-mRNA-splicing factor SYF1
  Species: Saccharomyces cerevisiae S288c [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • PDB 5GMK
  • Uniprot Q04048 (568-733)
  • PDB 5GMK
  Domains in SCOPe 2.07: d5gmkv_
• Chain 'w':
  Compound: Small nuclear ribonucleoprotein F
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P54999
• Chain 'x':
  Compound: Small nuclear ribonucleoprotein G
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P40204
• Chain 'y':
  Compound: Small nuclear ribonucleoprotein Sm D3
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P43321
• Chain 'z':
  Compound: Small nuclear ribonucleoprotein Sm D1
  Species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) [TaxId:559292]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q02260 (0-End)
• Heterogens: GTP, MG, ZN

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':
  Sequence, based on SEQRES records: (download)
  

  >5gmkF (F:)
  mserkainkyyppdynpleaeklsrkmakklktmnkshasirlmtpfsmrclecneyipk
  srkfngkkellkekyldsikiyrltiscprcansiafrtdpgnsdyvmevggvrnyvpqk
  pnddlnaktavesidetlqrlvrekemeqnekmgikeqaddkmdllekrlakiqqeqedd
  eelenlrkknlemsqraeminrskhaqqekavttddldnlvdqvfdnhrqrtnkpgnnnd
  ekrtplfnptstkgkiqkkssvrtnplgivikrgkslk
  

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

  >5gmkF (F:)
  serkainkyyppdynpleaeklsrkmakklktmnkshasirlmtpfsmrclecneyipks
  rkfngkkellkekyldsikiyrltiscprcansiafrtdpgnsdyvmevggvrny
  

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

  >5gmkG (G:)
  mgsgdlnllkswnpklmknrkkvweteqdliteqqklntrlkeiekerelnellnesskd
  kpetlkndlalkksglewmyqdaklsdekedyllgkkkldssilnqpatppvraattisa
  sgaatsissqkkkskllkddpmskfkvtkqqrrtpdstkkramsqrgkplskpapdldy
  

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

  >5gmkG (G:)
  gsgdlnllkswnpklmknrkkvweteqdliteqqklntrlk
  

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

  >5gmkH (H:)
  msrnvdkansvlvrfqeqqaesaggykdysryqrprnvskvksikeanewkrqvskeikq
  kstriydpslnemqiaelndelnnlfkewkrwqwhidhtlmekktkrkrledshvlmnsg
  klingkryfgralelpevkewlkqsqrqndggsintkcipkdrndfyyhgkvtaaltefe
  anwtsilkahynvpvnedeeemsrqtqeihvptladmehwlvqrrkkklmdelnl
  

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

  >5gmkH (H:)
  srnvdkansvlvrfqeqqaesaggykdysryqrprnvskvksikeanewkrqvskeikqk
  striydpslnemqiaelndelnnlfkewkrwqwhi
  

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

  >5gmkI (I:)
  mdfykldeklkelkrkrvdvsiksrkladreiqevsanrkprvysmedvndadesvgdte
  spekekafhytvqeydawerrhpqgktgqsqrggisydqlaklsyektlrnlatqtqnss
  kqdssadeednknvpkkgrigkvqkdtktgkitiadddklvnklavslqseskkryeark
  rqmqnaktlygvesfindknkqfneklsreskgse
  

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

  >5gmkI (I:)
  rggisydqlaklsyektlrnlatqtqnsskqdkvqkdtktgkitiadddklvnklavslq
  seskkryearkrqmqnaktlygvesfindknkqfneklsres
  

  
  
• Chain 'J':
  No sequence available.
  
  
• Chain 'L':
  No sequence available.
  
  
• Chain 'M':
  No sequence available.
  
  
• Chain 'N':
  No sequence available.
  
  
• Chain 'O':
  No sequence available.
  
  
• Chain 'P':
  No sequence available.
  
  
• Chain 'Q':
  No sequence available.
  
  
• Chain 'R':
  No sequence available.
  
  
• Chain 'S':
  No sequence available.
  
  
• Chain 'T':
  No sequence available.
  
  
• Chain 'Z':
  No sequence available.
  
  
• Chain 'a':
  Sequence, based on SEQRES records: (download)
  

  >5gmka (a:)
  mveparkkqridrdthhtvaepvteakntlyvsqlnekinmqrlrvnlfllfatfgevlk
  vsmnfkkqrgqafitmrtidqaslaqislngerffgkplkvefsksetktl
  

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

  >5gmka (a:)
  tlyvsqlnekinmqrlrvnlfllfatfgevvsmnfkkqrgqafitmrtidqaslaqisln
  gerffgkplkvefsksetktl
  

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

  >5gmkb (b:)
  mkftpsividapqyyvdhfngkynvdkcvilrdlqletdsesmpsslkhltkpthildlt
  nndlimipdlsrrddihtlllgrnnivevdgrllpmnvqnltlsnnsirrfedlqrlrra
  prtlknltlignqvchlanyrehvlrlvphletldfqnvtaeerksamsfprqadgdtlg
  pvntairdngsrdktmeimnlvvskmtverrnelkkqlaeatsleeiarlekllsggv
  

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

  >5gmkb (b:)
  mkftpsividapqyyvddlqletesmpsslkhltkpthildltnndlimipdlsrrddih
  tlllgrnnivevdvqnltlsnnsirrfedlqrlrralknltlignqvchlanyrehvlrl
  vphletldfqnvtae
  

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

  >5gmkd (d:)
  mdtleptavdthvsaeqilrdvykkgqkargstnidildleelreyqrrkrteyegylkr
  nrldmgqwiryaqfeieqhdmrrarsiferallvdssfiplwiryidaelkvkcinharn
  lmnraistlprvdklwykyliveeslnnveivrslytkwcslepgvnawnsfvdfeirqk
  nwngvreiyskyvmahpqmqtwlkwvrfenrhgnteftrsvyslaidtvanlqnlqiwsd
  mevaklvnsfahweaaqqeyerssalyqiaiekwpxxxxxxxxxxxxxxxxxxxxxxxxx
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  Sequence, based on observed residues (ATOM records): (download)
  

  >5gmkd (d:)
  dildleelreyqrrkrteyegylkrnrldmgqwiryaqfeieqhdmrrarsiferallvd
  ssfiplwiryidaelkvkcinharnlmnraistlprvdklwykyliveeslnnveivrsl
  ytkwcslepgvnawnsfvdfeirqknwngvreiyskyvmahpqmqtwlkwvrfenrhgnt
  eftrsvyslaidtvanlqnlqiwsdmevaklvnsfahweaaqqeyerssalyqiaiekwp
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  xxxxxxxxx
  

  
  
• Chain 'e':
  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)
  

  >5gmkn (n:)
  mglvdgydtssdsdlnfdegksvhekkngnlhedtsyepssnnihkrkshftkselkrrr
  ktrkgdgpwgswsssddetsqasetqkedqdifvhalaednldseqieveevshfygkse
  kdyqgrgylyppndvdvdlreerisfrcylpkkvirnypghpegttalkflpktghlils
  ggndhtikiwdfyhdyeclrdfqghnkpikalrftedcqsflsssfdrsvkiwdtetgkv
  ktrlhlnstpadvesrptnphefivglsnskilhyddrvsenqglvqtydhhlssilalk
  yfpdgskfisssedktvriwenqinvpikqisdtaqhsmpflnvhpsqnyfcaqsmdnri
  ysfslkpkykrhpkkifkghssagygislafsgdgryicsgdsksrlftwdwntsrllnn
  ikipgnkpitqvdwhpqetskvicsgaagkiyvcd
  

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

  >5gmkn (n:)
  ftkselkrrrktrkgdgpwgswspkkvirnypghpegttalkflpktghlilsggndhti
  kiwdfeclrdfqghnkpikalrftedcqsflsssfdrsvkiwdtetgkvktrlhlnstpa
  dvesrptnphefivglsnskilhyddvqtydhhlssilalkyfpdgskfisssedktvri
  wenqinvpikqisdtasmpflnvhpnyfcaqsmdnriysfskykrhpkkihssagygisl
  afsgdgryicsgdsksrlftwdwntsrllipgnkpitqvdwhpskvicsgaagkiyvcd
  

  
  
• Chain 'o':
  No sequence available.
  
  
• Chain 'p':
  No sequence available.
  
  
• Chain 'q':
  No sequence available.
  
  
• Chain 'r':
  No sequence available.
  
  
• Chain 's':
  No sequence available.
  
  
• Chain 't':
  No sequence available.
  
  
• Chain 'u':
  No sequence available.
  
  
• Chain 'v':
  Sequence, based on SEQRES records: (download)
  

  >5gmkv (v:)
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  xxxxxxxxxxxxxxxxxxxxxxxxxxxxktkmayntvidlrlitpamaenfalflqnhye
  vmesfqvyektiplfppeiqyelwieylevatshqlsslspehirflfekalknlcsngi
  dcktifiaysvfeerisglisksieilrrgavigtvsvsthlesrlqlwrmciskaestl
  gpsvtrelyqeciqxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
  xxxxxxxxxxxxxxxxxxx
  

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

  >5gmkv (v:)
  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxktkmayntvidltpama
  enfalflqnhyevmesfqvyektiplfppeiqyelwieylevatshqlspehirflfeka
  lkktifiaysvfeerilisksieilrrlqlwrmciskaestlgpsvtrelyqeciqxxxx
  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
  xxxxxxxxxxxxx
  

  
  
• Chain 'w':
  No sequence available.
  
  
• Chain 'x':
  No sequence available.
  
  
• Chain 'y':
  No sequence available.
  
  
• Chain 'z':
  No sequence available.