PDB entry 6gyp

View 6gyp on RCSB PDB site
Description: cryo-em structure of the cbf3-core-ndc10-dbd complex of the budding yeast kinetochore
Deposited on 2018-07-01, released 2018-12-05
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: EM
Resolution: 3.6 Å
R-factor: N/A
AEROSPACI score: 0.09 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Centromere DNA-binding protein complex CBF3 subunit C
    Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
    Gene: CTF13, CBF3C, YMR094W, YM6543.01, YM9582.19
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Centromere DNA-binding protein complex CBF3 subunit B
    Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
    Gene: CEP3, CBF3, CBF3B, CSL1, YMR168C, YM8520.17C
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Centromere DNA-binding protein complex CBF3 subunit B
    Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
    Gene: CEP3, CBF3, CBF3B, CSL1, YMR168C, YM8520.17C
    Database cross-references and differences (RAF-indexed):
    • Uniprot P40969 (4-563)
      • initiating methionine (0)
      • expression tag (1-3)
  • Chain 'D':
    Compound: Suppressor of kinetochore protein 1
    Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
    Gene: SKP1, CBF3D, YDR328C, D9798.14
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: centromere DNA-binding protein complex cbf3 subunit a
    Species: SACCHAROMYCES CEREVISIAE S288C [TaxId:559292]
    Gene: CBF2, CBF3A, CEP2, CTF14, NDC10, YGR140W
    Database cross-references and differences (RAF-indexed):
  • Heterogens: MET, PHE, ASN, ARG, THR, GLN

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6gypA (A:)
    mpsfnpvrflelpidirkevyfhldgnfcgahpypidilyksndvelpgkpsykrskrsk
    kllrymypvfatylnifeyspqliekwleyafwlrydclvldcfkvnhlydgtlidalew
    tyldnelrlayfnkasmlevwytfkeykkwvidsvafdeldllnvsniqfnidnltpqlv
    dkclsileqkdlfatigevqfgqdeevgeekdvdvsgansdensspsstiknkkrsaskr
    shsdngnvgathnqltsisvirtirsmesmkslrkitvrgeklyellinfhgfrdnpgkt
    isyivkrrineirlsrmnqisrtgladftrwdnlqklvlsrvayidlnsivfpknfkslt
    mkrvskikwwnieenilkelkvdkrtfkslyikeddskftkffnlrhtrikeldkseinq
    itylrcqaivwlsfrtlnhiklqnvsevfnniivpralfdskrveiyrcekisqvlvi
    

    Sequence, based on observed residues (ATOM records):
    >6gypA (A:)
    sfnpvrflelpidirkevyfhldgnfcgahpypidilyksndvelpgrskrskkllrymy
    pvfatylnifeyspqliekwleyafwlrydclvldcfkvnhlydgtlidalewtyldnel
    rlayfnkasmlevwytfkeykkwvidsvafdeldllnvsniqfnidnltpqlvdkclsil
    eqkdlfatigevqfgqdnqltsisvirtirsmesmkslrkitvrgeklyellinfhgfrd
    npgktisyivkrrineirlsrmnqisrtgladftrwdnlqklvlsrvayidlnsivfpkn
    fksltmkrvskikwwnieenilkelkvdkrtfkslyikeddskftkffnlrhtrikeldk
    seinqitylrcqaivwlsfrtlnhiklqnvsevfnniivpralfdskrveiyrcekisqv
    lvi
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6gypB (B:)
    mfnrttqlkskhpcsvctrrkvkcdrmipcgncrkrgqdsecmkstklitassskeylpd
    lllfwqnyeywitniglyktkqrdltrtpanldtdteecmfwmnylqkdqsfqlmnfame
    nlgalyfgsigdiselylrveqywdrradknhsvdgkywdaliwsvftmciyympvekla
    eifsvyplheylgsnkrlnwedgmqlvmcqnfarcslfqlkqcdfmahpdirlvqaylil
    atttfpydepllanslltqcihtfknfhvddfrpllnddpvesiakvtlgrifyrlcgcd
    ylqsgprkpialhtevssllqhaaylqdlpnvdvyreenstevlywkiisldrdldqyln
    ksskpplktldairreldifqykvdsleedfrsnnsrfqkfialfqistvswklfkmyli
    yydtadsllkvihyskviislivnnfhakseffnrhpmvmqtitrvvsfisfyqifvesa
    avkqllvdlteltanlptifgskldklvylterlsklkllwdkvqlldsgdsfyhpvfki
    lqndikiielkndemfslikglgslvplnklrqeslleeedenntepsdfrtiveefqse
    ynisdils
    

    Sequence, based on observed residues (ATOM records):
    >6gypB (B:)
    sskeylpdlllfwqnyeywitniglyktkqrdltrtpanldtdteecmfwmnylqkdqsf
    qlmnfamenlgalyfgsigdiselylrveqywdrradknhsvdgkywdaliwsvftmciy
    ympveklaeifsvyplheylgsnkrlnwedgmqlvmcqnfarcslfqlkqcdfmahpdir
    lvqaylilatttfpydepllanslltqcihtfknfhvddfrpllnddpvesiakvtlgri
    fyrlcgcdylqsgprkpialhtevsslnvdvyreenstevlywkiisldrdldqylnkss
    kpplktldairreldifqykvdsleedfrsnnsrfqkfialfqistvswklfkmyliyyd
    tadsllkvihyskviislivnnfhakseffnrhpmvmqtitrvvsfisfyqifvesaavk
    qllvdlteltanlptifgskldklvylterlsklkllwdkvqlldsgdsfyhpvfkilqn
    dikiielkndemfslikglgslvplnsdfrtiveefqseynisdils
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6gypC (C:)
    mfnritassskeylpdlllfwqnyeywitniglyktkqrdltrtpanldtdteecmfwmn
    ylqkdqsfqlmnfamenlgalyfgsigdiselylrveqywdrradknhsvdgkywdaliw
    svftmciyympveklaeifsvyplheylgsnkrlnwedgmqlvmcqnfarcslfqlkqcd
    fmahpdirlvqaylilatttfpydepllanslltqcihtfknfhvddfrpllnddpvesi
    akvtlgrifyrlcgcdylqsgprkpialhtevssllqhaaylqdlpnvdvyreenstevl
    ywkiisldrdldqylnksskpplktldairreldifqykvdsleedfrsnnsrfqkfial
    fqistvswklfkmyliyydtadsllkvihyskviislivnnfhakseffnrhpmvmqtit
    rvvsfisfyqifvesaavkqllvdlteltanlptifgskldklvylterlsklkllwdkv
    qlldsgdsfyhpvfkilqndikiielkndemfslikglgslvplnklrqeslleeedenn
    tepsdfrtiveefqseynisdils
    

    Sequence, based on observed residues (ATOM records):
    >6gypC (C:)
    mfnritassskeylpdlllfwqnyeywitniglyktkqrdltrtpanldtdteecmfwmn
    ylqkdqsfqlmnfamenlgalyfgsigdiselylrveqywdrradknhsvdgkywdaliw
    svftmciyympveklaeifsvyplheylgsnkrlnwedgmqlvmcqnfarcslfqlkqcd
    fmahpdirlvqaylilatttfpydepllanslltqcihtfknfhvddfrpllnddpvesi
    akvtlgrifyrlcgcdylqsgprkpialhtevssllnstevlywkiisldrdldqylnks
    skpplktldairreldifqykvdsleedfrsnnsrfqkfialfqistvswklfkmyliyy
    dtadsllkvihyskviislivnnfhakseffnrhpmvmqtitrvvsfisfyqifvesaav
    kqllvdlteltanlptifgskldklvylterlsklkllwdkvqlldsgdsfyhpvfkilq
    ndikiielkndemfslikglgslvplnsdfrtiveefqseynisdils
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6gypD (D:)
    mvtsnvvlvsgegerftvdkkiaerslllknylndmhdsnlqnnsdsesdsdsetnhksk
    dnnngddddedddeivmpvpnvrssvlqkviewaehhrdsnfpdeddddsrksapvdswd
    reflkvdqemlyeiilaanylnikplldagckvvaemirgrspeeirrtfnivndftpee
    eaairrenewaedr
    

    Sequence, based on observed residues (ATOM records):
    >6gypD (D:)
    snvvlvsgegerftvdkkiaerslllknylndeivmpvpnvrssvlqkviewaehhrdsn
    fpdeddddsrksapvdswdreflkvdqemlyeiilaanylnikplldagckvvaemirgr
    speeirrtfnivndftpeeeaairrenewae
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6gypE (E:)
    mrssilfllklmkimdvqqqqeamssedrfqelvdslkprtahqyktyytkyiqwcqlnq
    iiptpednsvnsvpykdlpisaelihwflldtlitddkpgekreetedldeeeensfkia
    tlkkiigslnflsklckvhenpnanidtkylesvtklhthwidsqkaittnetnntntqv
    lcppllkvslnlwnpetnhlsekffktcseklrflvdfqlrsylnlsfeerskirfgslk
    lgkrdrdaiiyhkvthsaekkdtpghhqllallpqdcpficpqttlaaylylrfygipsv
    skgdgfpnlnadengsllqdipilrgkslttypreetfsnyyttvfrychlpykrreyfn
    kcnlvyptwdedtfrtffneenhgnwleqpeafafpdkipfdfkkimnfkspytsystna
    kkdpfpppkdllvqifpeideykrhdyeglsqnsrdfldlmevlrerflsnlpwiykffp
    nhdifqdpifgnsdfqsyfndktihskgspilsfdilpgfnkiyknktnfysllierpsq
    ltfasshnpdthptqkqesegplqmsqldttqlnellkqqsfeyvqfqtlsnfqillsvf
    nkifeklemkkssrgyilhqlnlfkitlderikkskiddadkfirdnqpikkeenivned
    gpntsrrtkrpkqirllsiadssdesstedsnvfkkdgesiedgaygenedendsemqeq
    lksminelinskistflrdqmdqfelkinalldkileekvtriieqklgshtgkfstlkr
    pqlymteehnvgfdmevpkklrtsgkyaetvkdnddhqamsttaspspeqdqeaksytde
    qefmldksidsiegiilewftpnakyanqcvhsmnksgnkswrancealykerksivefy
    iylvnhesldrykavdiceklrdqnegsfsrlakflrkwrhdhqnsfdgllvylsn
    

    Sequence, based on observed residues (ATOM records):
    >6gypE (E:)
    edrfqelvdslkprtahqyktyytkyiqwcqlnqiiptpednsvnsvpykdlpisaelih
    wflldtlitddkpgekreetedldeeeensfkiatlkkiigslnflsklckvhenpnani
    dtkylesvtklhthwidsqkaittnetnntntqvlcppllkvslnlwnpetnhlsekffk
    tcseklrflvdfqlrsylnlsfeerskirfgslklgkrdrdaiiyhkvthsaekkdtpgh
    hqllallpqdcpficpqttlaaylylrfygipsvskgdgfpnlnadengsllqdipilrg
    kslttypreetfsnyyttvfrychlpykrreyfnkcnlvyptwdedtfrtffneenhgnw
    leqpeafafpdkipfdfkkimnfkspytsystnakkdpfpppkdllvqifpeideykrhd
    yeglsqnsrdfldlmevlrerflsnlpwiykffpnhdifqdpifgnsdfqsyfndktihs
    kgspilsfdilpgfnkiyknktnfysllierp