PDB entry 7b5l

View 7b5l on RCSB PDB site
Description: ubiquitin ligation to f-box protein substrates by scf-rbr e3-e3 super- assembly: nedd8-cul1-rbx1-skp1-skp2-ckshs1-cyclin a-cdk2-p27- ube2l3~ub~arih1. transition state 1
Deposited on 2020-12-04, released 2021-02-10
The last revision was dated 2021-03-10, with a file datestamp of 2021-03-05.
Experiment type: EM
Resolution: 3.8 Å
R-factor: N/A
AEROSPACI score: 0.12 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'C':
    Compound: Cullin-1
    Species: Homo sapiens [TaxId:9606]
    Gene: CUL1
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Ubiquitin-conjugating enzyme E2 L3
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2L3, UBCE7, UBCH7
    Database cross-references and differences (RAF-indexed):
    • Uniprot P68036 (0-End)
      • engineered mutation (16)
      • engineered mutation (136)
  • Chain 'H':
    Compound: E3 ubiquitin-protein ligase ARIH1
    Species: Homo sapiens [TaxId:9606]
    Gene: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: Cyclin-dependent kinases regulatory subunit 1
    Species: Homo sapiens [TaxId:9606]
    Gene: CKS1B, CKS1, PNAS-143, PNAS-16
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: cyclin-dependent kinase 2
    Species: Homo sapiens [TaxId:9606]
    Gene: CDK2, CDKN2
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
  • Chain 'P':
    Compound: Cyclin-dependent kinase inhibitor 1B
    Species: Homo sapiens [TaxId:9606]
    Gene: CDKN1B, KIP1
    Database cross-references and differences (RAF-indexed):
  • Chain 'R':
    Compound: E3 ubiquitin-protein ligase RBX1
    Species: Homo sapiens [TaxId:9606]
    Gene: RBX1, RNF75, ROC1
    Database cross-references and differences (RAF-indexed):
  • Chain 'S':
    Compound: S-phase kinase-associated protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: S-phase kinase-associated protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: SKP2, FBXL1
    Database cross-references and differences (RAF-indexed):
  • Chain 'U':
    Compound: Polyubiquitin-C
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
  • Chain 'Y':
    Compound: Cyclin-A2
    Species: Homo sapiens [TaxId:9606]
    Gene: CCNA2, CCN1, CCNA
    Database cross-references and differences (RAF-indexed):
  • Heterogens: ZN, SY8

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 'C':
    Sequence, based on SEQRES records:
    >7b5lC (C:)
    msstrsqnphglkqigldqiwddlragiqqvytrqsmaksrymelythvynyctsvhqsn
    qargagvppskskkgqtpggaqfvglelykrlkeflknyltnllkdgedlmdesvlkfyt
    qqwedyrfsskvlngicaylnrhwvrrecdegrkgiyeiyslalvtwrdclfrplnkqvt
    navlkliekerngetintrlisgvvqsyvelglneddafakgptltvykesfesqfladt
    erfytresteflqqnpvteymkkaearlleeqrrvqvylhestqdelarkceqvliekhl
    eifhtefqnlldadknedlgrmynlvsriqdglgelkkllethihnqglaaiekcgeaal
    ndpkmyvqtvldvhkkynalvmsafnndagfvaaldkacgrfinnnavtkmaqssskspe
    llarycdsllkkssknpeeaeledtlnqvmvvfkyiedkdvfqkfyakmlakrlvhqnsa
    sddaeasmisklkqacgfeytsklqrmfqdigvskdlneqfkkhltnsepldldfsiqvl
    ssgswpfqqsctfalpselersyqrftafyasrhsgrkltwlyqlskgelvtncfknryt
    lqastfqmaillqyntedaytvqqltdstqikmdilaqvlqillkskllvledenanvde
    velkpdtliklylgyknkklrvninvpmkteqkqeqetthknieedrklliqaaivrimk
    mrkvlkhqqllgevltqlssrfkprvpvikkcidiliekeylervdgekdtysyla
    

    Sequence, based on observed residues (ATOM records):
    >7b5lC (C:)
    ldqiwddlragiqqvytrqsmaksrymelythvynyctsvglelykrlkeflknyltnll
    kdgedlmdesvlkfytqqwedyrfsskvlngicaylnrhwvrreyeiyslalvtwrdclf
    rplnkqvtnavlkliekerngetintrlisgvvqsyvelglneddafakgptltvykesf
    esqfladterfytresteflqqnpvteymkkaearlleeqrrvqvylhestqdelarkce
    qvliekhleifhtefqnlldadknedlgrmynlvsriqdglgelkkllethihnqglaai
    ekcgeaalndpkmyvqtvldvhkkynalvmsafnndagfvaaldkacgrfinnnavtkma
    qssskspellarycdsllkkssknpeeaeledtlnqvmvvfkyiedkdvfqkfyakmlak
    rlvhqnsasddaeasmisklkqacgfeytsklqrmfqdigvskdlneqfkkhltnsepld
    ldfsiqvlssgswpfqqsctfalpselersyqrftafyasrhsgrkltwlyqlskgelvt
    ncfknrytlqastfqmaillqyntedaytvqqltdstqikmdilaqvlqillkskllvle
    denanvdevelkpdtliklylgyknkklrvninvedrklliqaaivrimkmrkvlkhqql
    lgevltqlssrfkprvpvikkcidiliekeylervdgekdtysyla
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >7b5lD (D:)
    maasrrlmkeleeirkagmknfrniqvdeanlltwqglivpdnppydkgafrieinfpae
    ypfkppkitfktkiyhpnidekgqvclpvisaenwkpatktdqviqslialvndpqpehp
    lradlaeeyskdrkkfaknaeeftkkygekrpvd
    

    Sequence, based on observed residues (ATOM records):
    >7b5lD (D:)
    maasrrlmkeleeirkagmknfrniqvdeanlltwqglivpdnppydkgafrieinfpae
    ypfkppkitfktkiyhpnidekgqvclpvisaenwkpatktdqviqslialvndpqpehp
    lradlaeeyskdrkkfaknaeeftkkygekr
    

  • Chain 'H':
    Sequence, based on SEQRES records:
    >7b5lH (H:)
    mdsdegynyefdedeecseedsgaeeeededddepdddtldlgevelvepglgvggerdg
    llcgetgggggsalgpggggggggggggggpgheqeedyryevltaeqilqhmvecirev
    neviqnpatitrillshfnwdkeklmeryfdgnleklfaechvinpskksrtrqmntrss
    aqdmpcqicylnypnsyftglecghkfcmqcwseylttkimeegmgqtiscpahgcdilv
    ddntvmrlitdskvklkyqhlitnsfvecnrllkwcpapdchhvvkvqypdakpvrckcg
    rqfcfncgenwhdpvkckwlkkwikkcdddsetsnwiaantkecpkchvtiekdggcnhm
    vcrnqnckaefcwvclgpwephgsawyncnryneddakaardaqersraalqrylfycnr
    ymnhmqslrfehklyaqvkqkmeemqqhnmswievqflkkavdvlcqcratlmytyvfaf
    ylkknnqsiifennqadlenatevlsgylerdisqdslqdikqkvqdkyrycesrrrvll
    qhvhegyekdlweyied
    

    Sequence, based on observed residues (ATOM records):
    >7b5lH (H:)
    dyryevltaeqilqhmvecirevneviqnpatitrillshfnwdkeklmeryfdgnlekl
    faechvimpcqicylnypnsyftglecghkfcmqcwseylttkimeegmgqtiscpahgc
    dilvddntvmrlitdskvklkyqhlitnsfvecnrllkwcpapdchhvvkvqypdakpvr
    ckcgrqfcfncgenwhdpvkckwlkkwikkcdddsetsnwiaantkecpkchvtiekdgg
    cnhmvcrnqnckaefcwvclgpwephgsawyncnrsraalqrylfycnrymnhmqslrfe
    hklyaqvkqkmeemqqhnmswievqflkkavdvlcqcratlmytyvfafylkknnqsiif
    ennqadlenatevlsgylerdisqdslqdikqkvqdkyrycesrrrvllqhvhegyekdl
    wey
    

  • Chain 'K':
    Sequence, based on SEQRES records:
    >7b5lK (K:)
    mshkqiyysdkyddeefeyrhvmlpkdiaklvpkthlmsesewrnlgvqqsqgwvhymih
    epephillfrrpl
    

    Sequence, based on observed residues (ATOM records):
    >7b5lK (K:)
    qiyysdkyddeefeyrhvmlpkdiaklvpkthlmsesewrnlgvqqsqgwvhymihepep
    hillfrrpl
    

  • Chain 'L':
    Sequence, based on SEQRES records:
    >7b5lL (L:)
    menfqkvekigegtygvvykarnkltgevvalkkirldtetegvpstaireisllkelnh
    pnivklldvihtenklylvfeflhqdlkkfmdasaltgiplpliksylfqllqglafchs
    hrvlhrdlkpqnllintegaikladfglarafgvpvrtythevvtlwyrapeillgckyy
    stavdiwslgcifaemvtrralfpgdseidqlfrifrtlgtpdevvwpgvtsmpdykpsf
    pkwarqdfskvvppldedgrsllsqmlhydpnkrisakaalahpffqdvtkpvphlrl
    

    Sequence, based on observed residues (ATOM records):
    >7b5lL (L:)
    gtygvvykarnkltgevvalkkirldtetegvpstaireisllkelnhpnivklldviht
    enklylvfeflhqdlkkfmdasaltgiplpliksylfqllqglafchshrvlhrdlkpqn
    llintegaikladfglarafgvrtythevvtlwyrapeillgckyystavdiwslgcifa
    emvtrralfpgdseidqlfrifrtlgtpdevvwpgvtsmpdykpsfpkwarqdfskvvpp
    ldedgrsllsqmlhydpnkrisakaalahpffqdvtkpvphlrl
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records:
    >7b5lN (N:)
    mlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaadyk
    ilggsvlhlvlalrgg
    

  • Chain 'P':
    Sequence, based on SEQRES records:
    >7b5lP (P:)
    msnvrvsngspslermdarqaehpkpsacrnlfgpvdheeltrdlekhcrdmeeasqrkw
    nfdfqnhkplegkyewqevekgslpefyyrpprppkgackvpaqesqdvsgsrpaaplig
    apansedthlvdpktdpsdsqtglaeqcagirkrpatddsstqnkranrteenvsdgspn
    agsveqtpkkpglrrrqt
    

    Sequence, based on observed residues (ATOM records):
    >7b5lP (P:)
    sacrnlfgpvdheeltrdlekhcrdmeeasqrkwnfdfqnhkplegkyewqevekgslpe
    fyyrppragsveqtpkk
    

  • Chain 'R':
    Sequence, based on SEQRES records:
    >7b5lR (R:)
    maaamdvdtpsgtnsgagkkrfevkkwnavalwawdivvdncaicrnhimdlciecqanq
    asatseectvawgvcnhafhfhcisrwlktrqvcpldnrewefqkygh
    

    Sequence, based on observed residues (ATOM records):
    >7b5lR (R:)
    rfevkkwnavalwawdivvdncaicrnhimdlciecqanectvawgvcnhafhfhcisrw
    lktrqvcpldnrewefqkygh
    

  • Chain 'S':
    Sequence, based on SEQRES records:
    >7b5lS (S:)
    mpsiklqssdgeifevdveiakqsvtiktmledlgmddegdddpvplpnvnaailkkviq
    wcthhkddppppeddenkekrtddipvwdqeflkvdqgtlfelilaanyldikglldvtc
    ktvanmikgktpeeirktfnikndfteeeeaqvrkenqwceek
    

    Sequence, based on observed residues (ATOM records):
    >7b5lS (S:)
    psiklqssdgeifevdveiakqsvtiktmledpvplpnvnaailkkviqwcthhkddppt
    ddipvwdqeflkvdqgtlfelilaanyldikglldvtcktvanmikgktpeeirktfnik
    ndfteeeeaqvrkenqwc
    

  • Chain 'T':
    Sequence, based on SEQRES records:
    >7b5lT (T:)
    mhrkhlqeipdlssnvatsftwgwdssktsellsgmgvsalekeepdsenipqellsnlg
    hpespprkrlkskgsdkdfvivrrpklnrenfpgvswdslpdelllgifsclclpellkv
    sgvckrwyrlasdeslwqtldltgknlhpdvtgrllsqgviafrcprsfmdqplaehfsp
    frvqhmdlsnsvievstlhgilsqcsklqnlsleglrlsdpivntlaknsnlvrlnlsgc
    sgfsefalqtllsscsrldelnlswcfdftekhvqvavahvsetitqlnlsgyrknlqks
    dlstlvrrcpnlvhldlsdsvmlkndcfqeffqlnylqhlslsrcydiipetllelgeip
    tlktlqvfgivpdgtlqllkealphlqincshfttiarptignkknqeiwgikcrltlqk
    pscl
    

    Sequence, based on observed residues (ATOM records):
    >7b5lT (T:)
    vswdslpdelllgifsclclpellkvsgvckrwyrlasdeslwqtldltgknlhpdvtgr
    llsqgviafrcprsfmdqplaehfspfrvqhmdlsnsvievstlhgilsqcsklqnlsle
    glrlsdpivntlaknsnlvrlnlsgcsgfsefalqtllsscsrldelnlswcfdftekhv
    qvavahvsetitqlnlsgyrknlqksdlstlvrrcpnlvhldlsdsvmlkndcfqeffql
    nylqhlslsrcydiipetllelgeiptlktlqvfgivpdgtlqllkealphlqincshft
    tiarptinqeiwgikcrltlq
    

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records:
    >7b5lU (U:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrg
    

  • Chain 'Y':
    Sequence, based on SEQRES records:
    >7b5lY (Y:)
    mlgnsapgpatreagsallalqqtalqedqeninpekaapvqqprtraalavlksgnprg
    laqqqrpktrrvaplkdlpvndehvtvppwkanskqpaftihvdeaekeaqkkpaesqki
    eredalafnsaislpgprkplvpldypmdgsfesphtmdmsiiledekpvsvnevpdyhe
    dihtylremevkckpkvgymkkqpditnsmrailvdwlvevgeeyklqnetlhlavnyid
    rflssmsvlrgklqlvgtaamllaskfeeiyppevaefvyitddtytkkqvlrmehlvlk
    vltfdlaaptvnqfltqyflhqqpanckveslamflgelslidadpylkylpsviagaaf
    hlalytvtgqswpeslirktgytleslkpclmdlhqtylkapqhaqqsirekyknskyhg
    vsllnppetlnl
    

    Sequence, based on observed residues (ATOM records):
    >7b5lY (Y:)
    vpdyhedihtylremevkckpkvgymkkqpditnsmrailvdwlvevgeeyklqnetlhl
    avnyidrflssmsvlrgklqlvgtaamllaskfeeiyppevaefvyitddtytkkqvlrm
    ehlvlkvltfdlaaptvnqfltqyflhanckveslamflgelslidpylkylpsviagaa
    fhlalytvtgqswpeslirktgytleslkpclmdlhqtylkapqhaqqsirekyknskyh
    gvsllnppetlnl