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 2.06 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): Domains in SCOPe 2.06: d2gyc11
  • Chain '2':
    Compound: 50s ribosomal protein l1
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
  • Chain '3':
    Compound: 50S ribosomal protein L7/L12
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gyc31, d2gyc32
  • Chain '5':
    Compound: 50S ribosomal protein L7/L12
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: 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):
  • Chain 'B':
    Compound: 50S ribosomal protein L3
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycb1
  • Chain 'C':
    Compound: 50S ribosomal protein L4
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycc1
  • Chain 'D':
    Compound: 50S ribosomal protein L5
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycd1
  • Chain 'E':
    Compound: 50S ribosomal protein L6
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: 50S ribosomal protein L9
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycf1, d2gycf2
  • Chain 'G':
    Compound: 50S ribosomal protein L11
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycg1, d2gycg2
  • Chain 'H':
    Compound: 50S ribosomal protein L13
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gych1
  • Chain 'I':
    Compound: 50S ribosomal protein L14
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gyci1
  • Chain 'J':
    Compound: 50S ribosomal protein L15
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycj1
  • Chain 'K':
    Compound: 50S ribosomal protein L16
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gyck1
  • Chain 'L':
    Compound: 50S ribosomal protein L17
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: 50S ribosomal protein L18
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycm1
  • Chain 'N':
    Compound: 50S ribosomal protein L19
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycn1
  • Chain 'O':
    Compound: 50S ribosomal protein L20
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gyco1
  • Chain 'Q':
    Compound: 50S ribosomal protein L22
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycq1
  • Chain 'R':
    Compound: 50S ribosomal protein L23
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
  • Chain 'S':
    Compound: 50S ribosomal protein L24
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycs1
  • Chain 'T':
    Compound: 50S ribosomal protein L25
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gyct1
  • Chain 'U':
    Compound: 50S ribosomal protein L27
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycu1
  • Chain 'W':
    Compound: 50S ribosomal protein L29
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycw1
  • Chain 'X':
    Compound: 50S ribosomal protein L30
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2gycx1
  • Chain 'Z':
    Compound: 50S ribosomal protein L32
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):

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.