PDB entry 2gyc

View 2gyc on RCSB PDB site
Description: Structure of the 50S subunit of a SecM-stalled E. coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-EM map EMD-1143
Class: ribosome
Keywords: SecM; nascent chain, signal transduction, RNA world, polypeptide exit tunnel, translocation, ribosome, elongation arrest, protein-conducting channel
Deposited on 2006-05-09, released 2006-09-26
The last revision prior to the SCOPe 2.08 freeze date was dated 2014-12-10, with a file datestamp of 2014-12-05.
Experiment type: EM
Resolution: 15 Å
R-factor: N/A
AEROSPACI score: -0.15 (click here for full SPACI score report)

Chains and heterogens:

• Chain '0':
  Compound: 23S ribosomal RNA
  Species: Escherichia coli [TaxId:562]
  
• Chain '1':
  Compound: 50S ribosomal protein L33
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7N9 (0-51)
  Domains in SCOPe 2.08: d2gyc11
• Chain '2':
  Compound: 50s ribosomal protein l1
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7L0 (0-221)
• Chain '3':
  Compound: 50S ribosomal protein L7/L12
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7K2 (0-118)
  Domains in SCOPe 2.08: d2gyc31, d2gyc32
• Chain '5':
  Compound: 50S ribosomal protein L7/L12
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7K2 (0-118)
  Domains in SCOPe 2.08: d2gyc51, d2gyc52
• Chain '9':
  Compound: 5S ribosomal RNA
  Species: Escherichia coli [TaxId:562]
  
• Chain 'A':
  Compound: 50S ribosomal protein L2
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P60422 (0-226)
• Chain 'B':
  Compound: 50S ribosomal protein L3
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P60438 (0-208)
  Domains in SCOPe 2.08: d2gycb1
• Chain 'C':
  Compound: 50S ribosomal protein L4
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P60723 (0-197)
  Domains in SCOPe 2.08: d2gycc1
• Chain 'D':
  Compound: 50S ribosomal protein L5
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P62399 (0-176)
  Domains in SCOPe 2.08: d2gycd1
• Chain 'E':
  Compound: 50S ribosomal protein L6
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0AG55 (0-166)
• Chain 'F':
  Compound: 50S ribosomal protein L9
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7R1 (0-148)
  Domains in SCOPe 2.08: d2gycf1, d2gycf2
• Chain 'G':
  Compound: 50S ribosomal protein L11
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7J7 (0-138)
  Domains in SCOPe 2.08: d2gycg1, d2gycg2
• Chain 'H':
  Compound: 50S ribosomal protein L13
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0AA10 (0-141)
  Domains in SCOPe 2.08: d2gych1
• Chain 'I':
  Compound: 50S ribosomal protein L14
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0ADY3 (0-121)
  Domains in SCOPe 2.08: d2gyci1
• Chain 'J':
  Compound: 50S ribosomal protein L15
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P02413 (0-139)
  Domains in SCOPe 2.08: d2gycj1
• Chain 'K':
  Compound: 50S ribosomal protein L16
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0ADY7 (0-130)
  Domains in SCOPe 2.08: d2gyck1
• Chain 'L':
  Compound: 50S ribosomal protein L17
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0AG44 (0-113)
• Chain 'M':
  Compound: 50S ribosomal protein L18
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0C018 (0-112)
  Domains in SCOPe 2.08: d2gycm1
• Chain 'N':
  Compound: 50S ribosomal protein L19
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7K6 (0-113)
  Domains in SCOPe 2.08: d2gycn1
• Chain 'O':
  Compound: 50S ribosomal protein L20
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7L3 (0-114)
  Domains in SCOPe 2.08: d2gyco1
• Chain 'Q':
  Compound: 50S ribosomal protein L22
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P61175 (0-105)
  Domains in SCOPe 2.08: d2gycq1
• Chain 'R':
  Compound: 50S ribosomal protein L23
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0ADZ0 (0-91)
• Chain 'S':
  Compound: 50S ribosomal protein L24
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P60624 (0-98)
  Domains in SCOPe 2.08: d2gycs1
• Chain 'T':
  Compound: 50S ribosomal protein L25
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P68919 (0-93)
  Domains in SCOPe 2.08: d2gyct1
• Chain 'U':
  Compound: 50S ribosomal protein L27
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7L8 (0-83)
  Domains in SCOPe 2.08: d2gycu1
• Chain 'W':
  Compound: 50S ribosomal protein L29
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7M6 (0-59)
  Domains in SCOPe 2.08: d2gycw1
• Chain 'X':
  Compound: 50S ribosomal protein L30
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0AG51 (0-55)
  Domains in SCOPe 2.08: d2gycx1
• Chain 'Z':
  Compound: 50S ribosomal protein L32
  Species: Escherichia coli [TaxId:562]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P0A7N4 (0-28)

PDB Chain Sequences:

• Chain '0':
  No sequence available.
  
  
• Chain '1':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gyc1 (1:)
  akgirekiklvssagtghfytttknkrtkpeklelkkfdpvvrqhviykeak
  

  
  
• Chain '2':
  No sequence available.
  
  
• Chain '3':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gyc3 (3:)
  itkdqiieavaamsvmdvvelisameekfgvsaaaavavaagpveaaeektefdvilkaa
  gankvavikavrgatglglkeakdlvesapaalkegvskddaealkkaleeagaevevk
  

  
  
• Chain '5':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gyc5 (5:)
  itkdqiieavaamsvmdvvelisameekfgvsaaaavavaagpveaaeektefdvilkaa
  gankvavikavrgatglglkeakdlvesapaalkegvskddaealkkaleeagaevevk
  

  
  
• Chain '9':
  No sequence available.
  
  
• Chain 'A':
  No sequence available.
  
  
• Chain 'B':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycB (B:)
  miglvgkkvgmtriftedgvsipvtvieveanrvtqvkdlandgyraiqvttgakkanrv
  tkpeaghfakagveagrglwefrlaegeeftvgqsisvelfadvkkvdvtgtskgkgfag
  tvkrwnfrtqdathgnslshrvpgsigqnqtpgkvfkgkkmagqmgnervtvqsldvvrv
  daernlllvkgavpgatgsdlivkpavka
  

  
  
• Chain 'C':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycC (C:)
  melvlkdaqsaltvsettfgrdfnealvhqvvvayaagarqgtraqktraevtgsgkkpw
  rqkgtgrarsgsikspiwrsggvtfaarpqdhsqkvnkkmyrgalksilselvrqdrliv
  vekfsveapktkllaqklkdmaledvliitgeldenlflaarnlhkvdvrdatgidpvsl
  iafdkvvmtadavkqvee
  

  
  
• Chain 'D':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycD (D:)
  klhdyykdevvkklmtefnynsvmqvprvekitlnmgvgeaiadkklldnaaadlaaisg
  qkplitkarksvagfkirqgypigckvtlrgermwefferlitiavprirdfrglsaksf
  dgrgnysmgvreqiifpeidydkvdrvrgldititttaksdeegrallaafdfpfrk
  

  
  
• Chain 'E':
  No sequence available.
  
  
• Chain 'F':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycF (F:)
  mqvilldkvanlgslgdqvnvkagyarnflvpqgkavpatkknieffearraeleaklae
  vlaaanaraekinaletvtiaskagdegklfgsigtrdiadavtaagvevaksevrlpng
  vlrttgehevsfqvhsevfakvivnvvae
  

  
  
• Chain 'G':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycG (G:)
  kkvqayvklqvaagmanpsppvgpalgqqgvnimefckafnaktdsiekglpipvvitvy
  adrsftfvtktppaavllkkaagiksgsgkpnkdkvgkisraqlqeiaqtkaadmtgadi
  eamtrsiegtarsmglvve
  

  
  
• Chain 'H':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycH (H:)
  mktftakpetvkrdwyvvdatgktlgrlatelarrlrgkhkaeytphvdtgdyiivlnad
  kvavtgnkrtdkvyyhhtghiggikqatfeemiarrpervieiavkgmlpkgplgramfr
  klkvyagnehnhaaqqpqvldi
  

  
  
• Chain 'I':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycI (I:)
  iqeqtmlnvadnsgarrvmcikvlggshrryagvgdiikitikeaiprgkvkkgdvlkav
  vvrtkkgvrrpdgsvirfdgnacvllnnnseqpigtrifgpvtrelrsekfmkiislape
  vl
  

  
  
• Chain 'J':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycJ (J:)
  ntlspaegskkagkrlgrgigsglgktggrghkgqksrsgggvrrgfeggqmplyrrlpk
  fgftsrkaaitaeirlsdlakveggvvdlntlkaaniigiqiefakvilagevttpvtvr
  glrvtkgaraaieaaggkie
  

  
  
• Chain 'K':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycK (K:)
  qpkrtkfrkmhkgrnrglaqgtdvsfgsfglkavgrgrltarqieaarramtravkrqgk
  iwirvfpdkpitekplavrmgkgkgnveywvaliqpgkvlyemdgvpeelareafklaaa
  klpikttfvtk
  

  
  
• Chain 'L':
  No sequence available.
  
  
• Chain 'M':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycM (M:)
  kksarirratrarrklqelgatrlvvhrtprhiyaqviapngsevlvaastvekaiaeql
  kytgnkdaaaavgkavaeralekgikdvsfdrsgfqyhgrvqaladaareagl
  

  
  
• Chain 'N':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycN (N:)
  sniikqleqeqmkqdvpsfrpgdtvevkvwvvegskkrlqafegvviairnrglhsaftv
  rkisngegvervfqthspvvdsisvkrrgavrkaklyylrertgkaarikerln
  

  
  
• Chain 'O':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycO (O:)
  rvkrgviararhkkilkqakgyygarsrvyrvafqavikagqyayrdrrqrkrqfrqlwi
  arinaaarqngisyskfinglkkasveidrkiladiavfdkvaftalvekakaal
  

  
  
• Chain 'Q':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycQ (Q:)
  akhrharssaqkvrlvadlirgkkvsqaldiltytnkkaavlvkkvlesaianaehndga
  diddlkvtkifvdegpsmkrimprakgradrilkrtshitvvvsdr
  

  
  
• Chain 'R':
  No sequence available.
  
  
• Chain 'S':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycS (S:)
  kirrddevivltgkdkgkrgkvknvlssgkviveginlvkkhqkpvpalnqpggivekea
  aiqvsnvaifnaatgkadrvgfrfedgkkvrffksnset
  

  
  
• Chain 'T':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycT (T:)
  mftinaevrkeqgkgasrrlraankfpaiiyggkeaplaieldhdkvmnmqakaefysev
  ltivvdgkeikvkaqdvqrhpykpklqhidfvra
  

  
  
• Chain 'U':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycU (U:)
  ahkkaggstrngrdseakrlgvkrfggesvlagsiivrqrgtkfhaganvgcgrdhtlfa
  kadgkvkfevkgpknrkfisieae
  

  
  
• Chain 'W':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycW (W:)
  mkakelreksveelntellnllreqfnlrmqaasgqlqqshllkqvrrdvarvktllnek
  

  
  
• Chain 'X':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >2gycX (X:)
  tikitqtrsaigrlpkhkatllglglrrightveredtpairgminavsfmvkvee
  

  
  
• Chain 'Z':
  No sequence available.