PDB entry 3u5i

View 3u5i on RCSB PDB site
Description: The structure of the eukaryotic ribosome at 3.0 A resolution. This entry contains proteins of the 60S subunit, ribosome B
Class: ribosome
Keywords: Translation, ribosome, 40S, 60S, 80S, ribosomal, ribosomal RNA, rRNA, ribosomal protein, STM1, eukaryotic ribosome, RNA-protein complex
Deposited on 2011-10-11, released 2011-12-21
The last revision prior to the SCOPe 2.07 freeze date was dated 2014-12-10, with a file datestamp of 2014-12-05.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.182
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 60S ribosomal protein L2-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: 60S Ribosomal protein L3
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: 60S ribosomal protein L4-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 60S Ribosomal protein L5
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: 60S ribosomal protein L6-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: 60S ribosomal protein L7-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: 60S ribosomal protein L8-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: 60S ribosomal protein L9-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: 60S ribosomal protein L10
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: 60S ribosomal protein L11-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: Ribosomal protein L12
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • PDB 3U5I (0-154)
  • Chain 'L':
    Compound: 60S ribosomal protein L13-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: 60S ribosomal protein L14-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: 60S ribosomal protein L15-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'O':
    Compound: 60S ribosomal protein L16-A, 60S ribosomal protein L16-B
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'P':
    Compound: 60S ribosomal protein L17-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Q':
    Compound: 60S ribosomal protein L18-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'R':
    Compound: 60S ribosomal protein L19-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'S':
    Compound: 60S ribosomal protein L20-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: 60S ribosomal protein L21-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'U':
    Compound: 60S ribosomal protein L22-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'V':
    Compound: 60S ribosomal protein L23-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'W':
    Compound: 60S ribosomal protein L24-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'X':
    Compound: 60S ribosomal protein L25
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Y':
    Compound: 60S ribosomal protein L26-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Z':
    Compound: 60S ribosomal protein L27-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
  • Chain 'a':
    Compound: 60S ribosomal protein L28
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ia_
  • Chain 'b':
    Compound: 60S ribosomal protein L29
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ib_
  • Chain 'c':
    Compound: 60s ribosomal protein l30
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ic_
  • Chain 'd':
    Compound: 60s ribosomal protein l31-a
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5id_
  • Chain 'e':
    Compound: 60S Ribosomal protein L32
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ie_
  • Chain 'f':
    Compound: 60S ribosomal protein L33-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5if_
  • Chain 'g':
    Compound: 60S ribosomal protein L34-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ig_
  • Chain 'h':
    Compound: 60S ribosomal protein L35-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ih_
  • Chain 'i':
    Compound: 60S ribosomal protein L36-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ii_
  • Chain 'j':
    Compound: 60S ribosomal protein L37-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ij_
  • Chain 'k':
    Compound: 60S ribosomal protein L38
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ik_
  • Chain 'l':
    Compound: 60S ribosomal protein L39
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5il_
  • Chain 'm':
    Compound: 60S ribosomal protein L40
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5im_
  • Chain 'n':
    Compound: 60S ribosomal protein L41-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5in_
  • Chain 'o':
    Compound: 60S ribosomal protein L42-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5io_
  • Chain 'p':
    Compound: 60S ribosomal protein L43-A
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3u5ip_
  • Chain 'q':
    Compound: 60S acidic ribosomal protein P0
    Species: Saccharomyces cerevisiae [TaxId:559292]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P05317
      • see remark 999 (198-220)
    Domains in SCOPe 2.07: d3u5iq_
  • Chain 'r':
    Compound: Ribosomal protein P1 alpha
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • PDB 3U5I (0-46)
    Domains in SCOPe 2.07: d3u5ir_
  • Chain 's':
    Compound: Ribosomal protein P2 beta
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • PDB 3U5I (0-45)
    Domains in SCOPe 2.07: d3u5is_
  • Heterogens: 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':
    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':
    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 'U':
    No sequence available.

  • Chain 'V':
    No sequence available.

  • Chain 'W':
    No sequence available.

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    No sequence available.

  • Chain 'Z':
    No sequence available.

  • Chain 'a':
    Sequence, based on SEQRES records: (download)
    >3u5ia (a:)
    mpsrftktrkhrghvsagkgrigkhrkhpggrgmaggqhhhrinmdkyhpgyfgkvgmry
    fhkqqahfwkpvlnldklwtlipedkrdqylksasketapvidtlaagygkilgkgripn
    vpvivkarfvsklaeekiraaggvvelia
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ia (a:)
    psrftktrkhrghvsagkgrigkhrkhpggrgmaggqhhhrinmdkyhpgyfgkvgmryf
    hkqqahfwkpvlnldklwtlipedkrdqylksasketapvidtlaagygkilgkgripnv
    pvivkarfvsklaeekiraaggvvelia
    

  • Chain 'b':
    Sequence, based on SEQRES records: (download)
    >3u5ib (b:)
    maksknhtahnqtrkahrngikkpktykypslkgvdpkfrrnhkhalhgtakalaaakk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ib (b:)
    aksknhtahnqtrkahrngikkpktykypslkgvdpkfrrnhkhalhgtakalaaakk
    

  • Chain 'c':
    Sequence, based on SEQRES records: (download)
    >3u5ic (c:)
    mapvksqesinqklalviksgkytlgykstvkslrqgkskliiiaantpvlrkseleyya
    mlsktkvyyfqggnnelgtavgklfrvgvvsileagdsdilttla
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ic (c:)
    sqesinqklalviksgkytlgykstvkslrqgkskliiiaantpvlrkseleyyamlskt
    kvyyfqggnnelgtavgklfrvgvvsileagdsdilttla
    

  • Chain 'd':
    Sequence, based on SEQRES records: (download)
    >3u5id (d:)
    maglkdvvtreytinlhkrlhgvsfkkrapravkeikkfaklhmgtddvrlapelnqaiw
    krgvkgveyrlrlrisrkrneeedaknplfsyvepvlvasakglqtvvveeda
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5id (d:)
    lkdvvtreytinlhkrlhgvsfkkrapravkeikkfaklhmgtddvrlapelnqaiwkrg
    vkgveyrlrlrisrkrneeedaknplfsyvepvlvasakglqtvvveed
    

  • Chain 'e':
    Sequence, based on SEQRES records: (download)
    >3u5ie (e:)
    maslphpkivkkhtkkfkrhhsdryhrvaenwrkqkgidsvvrrrfrgnisqpkigygsn
    kktkflspsghktflvanvkdletltmhtktyaaeiahnisaknrvvilarakalgikvt
    npkgrlalea
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ie (e:)
    aslphpkivkkhtkkfkrhhsdryhrvaenwrkqkgidsvvrrrfrgnisqpkigygsnk
    ktkflspsghktflvanvkdletltmhtktyaaeiahnisaknrvvilarakalgikvtn
    pkgrlal
    

  • Chain 'f':
    Sequence, based on SEQRES records: (download)
    >3u5if (f:)
    maeshrlyvkgkhlsyqrskrvnnpnvslikiegvatpqdaqfylgkriayvyraskevr
    gskirvmwgkvtrthgnsgvvratfrnnlpaktfgasvriflypsni
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5if (f:)
    aeshrlyvkgkhlsyqrskrvnnpnvslikiegvatpqdaqfylgkriayvyraskevrg
    skirvmwgkvtrthgnsgvvratfrnnlpaktfgasvriflypsni
    

  • Chain 'g':
    Sequence, based on SEQRES records: (download)
    >3u5ig (g:)
    maqrvtfrrrnpyntrsnkikvvktpggilraqhvkklatrpkcgdcgsalqgistlrpr
    qyatvskthktvsrayggsrcancvkeriiraflieeqkivkkvvkeqteaakksekkak
    k
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ig (g:)
    aqrvtfrrrnpyntrsnkikvvktpggilraqhvkklatrpkcgdcgsalqgistlrprq
    yatvskthktvsrayggsrcancvkeriiraflieeqkivkkvvkeqteaak
    

  • Chain 'h':
    Sequence, based on SEQRES records: (download)
    >3u5ih (h:)
    magvkayelrtkskeqlasqlvdlkkelaelkvqklsrpslpkiktvrksiacvltvine
    qqreavrqlykgkkyqpkdlrakktralrraltkfeasqvtekqrkkqiafpqrkyaika
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ih (h:)
    agvkayelrtkskeqlasqlvdlkkelaelkvqklsrpslpkiktvrksiacvltvineq
    qreavrqlykgkkyqpkdlrakktralrraltkfeasqvtekqrkkqiafpqrkyaika
    

  • Chain 'i':
    Sequence, based on SEQRES records: (download)
    >3u5ii (i:)
    mtvktgiaiglnkgkkvtsmtpapkisykkgaasnrtkfvrslvreiaglspyerrlidl
    irnsgekrarkvakkrlgsftrakakveemnniiaasrrh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ii (i:)
    tvktgiaiglnkgkkvtsmtpapkisykkgaasnrtkfvrslvreiaglspyerrlidli
    rnsgekrarkvakkrlgsftrakakveemnniiaasrrh
    

  • Chain 'j':
    Sequence, based on SEQRES records: (download)
    >3u5ij (j:)
    mgkgtpsfgkrhnkshtlcnrcgrrsfhvqkktcsscgypaaktrsynwgakakrrhttg
    tgrmrylkhvsrrfkngfqtgsaskasa
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ij (j:)
    gkgtpsfgkrhnkshtlcnrcgrrsfhvqkktcsscgypaaktrsynwgakakrrhttgt
    grmrylkhvsrrfkngfqtgsaskasa
    

  • Chain 'k':
    Sequence, based on SEQRES records: (download)
    >3u5ik (k:)
    mareitdikqfleltrradvktatvkinkklnkagkpfrqtkfkvrgssslytlvindag
    kakkliqslpptlkvnrl
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ik (k:)
    areitdikqfleltrradvktatvkinkklnkagkpfrqtkfkvrgssslytlvindagk
    akkliqslpptlkvnrl
    

  • Chain 'l':
    Sequence, based on SEQRES records: (download)
    >3u5il (l:)
    maaqksfrikqkmakakkqnrplpqwirlrtnntirynakrrnwrrtkmni
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5il (l:)
    aaqksfrikqkmakakkqnrplpqwirlrtnntirynakrrnwrrtkmni
    

  • Chain 'm':
    Sequence, based on SEQRES records: (download)
    >3u5im (m:)
    mqifvktltgktitlevessdtidnvkskiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrggiiepslkalaskyncdksvcrkcyarlppratncrkrkcghtnq
    lrpkkklk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5im (m:)
    iiepslkalaskyncdksvcrkcyarlppratncrkrkcghtnqlrpkkklk
    

  • Chain 'n':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3u5in (n:)
    mrakwrkkrtrrlkrkrrkvrarsk
    

  • Chain 'o':
    Sequence, based on SEQRES records: (download)
    >3u5io (o:)
    mvnvpktrktyckgktcrkhtqhkvtqykagkaslfaqgkrrydrkqsgfggqtkpvfhk
    kakttkkvvlrlecvkcktraqltlkrckhfelggekkqkgqalqf
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5io (o:)
    vnvpktrktyckgktcrkhtqhkvtqykagkaslfaqgkrrydrkqsgfggqtkpvfhkk
    akttkkvvlrlecvkcktraqltlkrckhfelggekkqkgqalqf
    

  • Chain 'p':
    Sequence, based on SEQRES records: (download)
    >3u5ip (p:)
    makrtkkvgitgkygvrygsslrrqvkkleiqqharydcsfcgkktvkrgaagiwtcscc
    kktvaggaytvstaaaatvrstirrlremvea
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5ip (p:)
    akrtkkvgitgkygvrygsslrrqvkkleiqqharydcsfcgkktvkrgaagiwtcscck
    ktvaggaytvstaaaatvrstirrlremvea
    

  • Chain 'q':
    Sequence, based on SEQRES records: (download)
    >3u5iq (q:)
    mggirekkaeyfaklreyleeykslfvvgvdnvssqqmhevrkelrgravvlmgkntmvr
    rairgflsdlpdfekllpfvkgnvgfvftneplteiknvivsnrvaaparagavapediw
    vravntgmepgktsffqalgvptkiargtieivsdvkvvdagnkvgqseasllnllnisp
    ftfgltvvqvydngqvfpxxxxxxxxxxxxxxxxxxxxxxxsislaigyptlpsvghtli
    nnykdllavaiaasyhypeiedlvdrienpekyaaaapaatsaasgdaapaeeaaaeeee
    esdddmgfglfd
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u5iq (q:)
    girekkaeyfaklreyleeykslfvvgvdnvssqqmhevrkelrgravvlmgkntmvrra
    irgflsdlpdfekllpfvkgnvgfvftneplteiknvivsnrvaagltvvqvydngqvfp
    xxxxxxxxxxxxxxxxxxxxxxx
    

  • Chain 'r':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3u5ir (r:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    

  • Chain 's':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3u5is (s:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx