PDB entry 4p5o

View 4p5o on RCSB PDB site
Description: Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action
Class: ligase
Keywords: Nedd8, Cullin, Neddylation, Complex, Ubc12, Dcn1, ubiquitin, LIGASE
Deposited on 2014-03-18, released 2014-07-02
The last revision prior to the SCOPe 2.06 freeze date was dated 2014-07-02, with a file datestamp of 2014-06-27.
Experiment type: XRAY
Resolution: 3.11 Å
R-factor: 0.23
AEROSPACI score: 0.14 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Cullin-1
    Species: Homo sapiens [TaxId:9606]
    Gene: CUL1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d4p5oa1, d4p5oa2
  • Chain 'B':
    Compound: E3 ubiquitin-protein ligase RBX1
    Species: Homo sapiens [TaxId:9606]
    Gene: RBX1, RNF75, ROC1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d4p5ob_
  • Chain 'C':
    Compound: Cullin-1
    Species: Homo sapiens [TaxId:9606]
    Gene: CUL1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d4p5oc1, d4p5oc2
  • Chain 'D':
    Compound: E3 ubiquitin-protein ligase RBX1
    Species: Homo sapiens [TaxId:9606]
    Gene: RBX1, RNF75, ROC1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d4p5od_
  • Chain 'E':
    Compound: DCN1-like protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: DCUN1D1, DCUN1L1, RP42, SCCRO
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: DCN1-like protein 1
    Species: Homo sapiens [TaxId:9606]
    Gene: DCUN1D1, DCUN1L1, RP42, SCCRO
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: NEDD8-conjugating enzyme Ubc12
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2M, UBC12
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61081 (1-182)
      • expression tag (0)
      • engineered mutation (102)
      • engineered mutation (110)
      • expression tag (183)
    Domains in SCOPe 2.06: d4p5og1, d4p5og2, d4p5og3
  • Chain 'H':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d4p5oh_
  • Chain 'I':
    Compound: NEDD8-conjugating enzyme Ubc12
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2M, UBC12
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61081 (1-182)
      • expression tag (0)
      • engineered mutation (102)
      • engineered mutation (110)
      • expression tag (183)
    Domains in SCOPe 2.06: d4p5oi1, d4p5oi2, d4p5oi3
  • Chain 'K':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d4p5ok_
  • Heterogens: ZN

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4p5oA (A:)
    gsmaqssskspeelarycdsllkkssknpeeaeledtlnqvmekfkkiedkdvfqkfyak
    mlakrlvhqnsasddaeasmisklkqacgfeytsklqrmfqdigvskdlneqfkkhltns
    epldldfsiqvlssgswpfqqsctfalpselersyqrftafyasrhsgrkltwlyqlskg
    elvtncfknrytlqastfqmaillqyntedaytvqqltdstqikmdilaqvlqillkskl
    lvledenanvdevelkpdtliklylgyknkklrvninvpmkteqkqeqetthknieedrk
    lliqaaivrimrmrkvlkhqqllgevltqlssrfkprvpvikkcidiliekeylervdge
    kdtysyla
    

    Sequence, based on observed residues (ATOM records): (download)
    >4p5oA (A:)
    skspeelarycdsllkkssknpeeaeledtlnqvmekfkkiedkdvfqkfyakmlakrlv
    hqnsasddaeasmisklkqacgfeytsklqrmfqdigvskdlneqfkkhltnsepldldf
    siqvlssgswpfqqsctfalpselersyqrftafyasrhsgrkltwlyqlskgelvtncf
    knrytlqastfqmaillytvqqltdstqikmdilaqvlqillksklpdtlirvninvpmk
    teqkqeqetthknieedrklliqaaivrimrmrkvlkhqqllgevltqlssrfkprvpvi
    kkcidiliekeylervdgekdtysyla
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4p5oB (B:)
    gsmdvdtpsgtnsgagkkrfevkkwnavalwawdivvdncaicrnhimdlciecqanqas
    atseectvawgvcnhafhfhcisrwlktrqvcpldnrewefqkygh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4p5oB (B:)
    evkkwnavalwawdivvdncaicrnhimdlciecqanectvawgvcnhafhfhcisrwlk
    trqvcpldnrewefq
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4p5oC (C:)
    gsmaqssskspeelarycdsllkkssknpeeaeledtlnqvmekfkkiedkdvfqkfyak
    mlakrlvhqnsasddaeasmisklkqacgfeytsklqrmfqdigvskdlneqfkkhltns
    epldldfsiqvlssgswpfqqsctfalpselersyqrftafyasrhsgrkltwlyqlskg
    elvtncfknrytlqastfqmaillqyntedaytvqqltdstqikmdilaqvlqillkskl
    lvledenanvdevelkpdtliklylgyknkklrvninvpmkteqkqeqetthknieedrk
    lliqaaivrimrmrkvlkhqqllgevltqlssrfkprvpvikkcidiliekeylervdge
    kdtysyla
    

    Sequence, based on observed residues (ATOM records): (download)
    >4p5oC (C:)
    skspeelarycdsllkkssknpeeaeledtlnqvmekfkkiedkdvfqkfyakmlakrlv
    hqnsasddaeasmisklkqacgfeytsklqrmfqdigvskdlneqfkkhltnsepldldf
    siqvlssgswpfqqsctfalpselersyqrftafyasrhsgrkltwlyqlskgelvtncf
    ktlqastfqmaiytvqqltdstqikmdilaqvlqillkskllpdtlivninvpmkteqkq
    eqetthknieedrklliqaaivrimrmrkvlkhqqllgevltqlssrfkprvpvikkcid
    iliekeylervdgekdtysyla
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4p5oD (D:)
    gsmdvdtpsgtnsgagkkrfevkkwnavalwawdivvdncaicrnhimdlciecqanqas
    atseectvawgvcnhafhfhcisrwlktrqvcpldnrewefqkygh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4p5oD (D:)
    evkkwnavalwawdivvdncaicrnhimdlciecqanectvawgvcnhafhfhcisrwlk
    trqvcpldnrewefqk
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4p5oG (G:)
    xiklfslkqqkkeeesaggtkgsskkasaaqlriqkdinelnlpktcdisfsdpddllnf
    klvicpdegfyksgkfvfsfkvgqgyphdppkvkcetmvyhpsidlegnvslnilredwk
    pvltinsiiyglqylflepnpedplnkeaaevlqnnrrlfeqnvqrsmrggyigstyfer
    clkhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4p5oG (G:)
    xiklfslkqqkkeeeaaqlriqkdinelnlpktcdisfsdpddllnfklvicpdegfyks
    gkfvfsfkvgqgyphdppkvkcetmvyhpsidlegnvslnilredwkpvltinsiiyglq
    ylflepnpedplnkeaaevlqnnrrlfeqnvqrsmrggyigstyferclkh
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >4p5oH (H:)
    gsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndekt
    aadykilggsvlhlvlalrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >4p5oH (H:)
    mlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaadyk
    ilggsvlhlvlalrgg
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >4p5oI (I:)
    xiklfslkqqkkeeesaggtkgsskkasaaqlriqkdinelnlpktcdisfsdpddllnf
    klvicpdegfyksgkfvfsfkvgqgyphdppkvkcetmvyhpsidlegnvslnilredwk
    pvltinsiiyglqylflepnpedplnkeaaevlqnnrrlfeqnvqrsmrggyigstyfer
    clkhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4p5oI (I:)
    xiklfslkqqkkeaaqlriqkdinelnlpktcdisfsdpddllnfklvicpdegfyksgk
    fvfsfkvgqgyphdppkvkcetmvyhpsidlegnvslnilredwkpvltinsiiyglqyl
    flepnpedplnkeaaevlqnnrrlfeqnvqrsmrggyigstyferclkh
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >4p5oK (K:)
    gsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndekt
    aadykilggsvlhlvlalrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >4p5oK (K:)
    mlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaadyk
    ilggsvlhlvlalrgg