1JHJ | pdb_00001jhj

Crystal structure of the APC10/Doc1 subunit of the human anaphase-promoting complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.244 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.214 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1JHJ

This is version 1.6 of the entry. See complete history

Literature

Crystal structure of the APC10/DOC1 subunit of the human anaphase-promoting complex

Wendt, K.S.Vodermaier, H.C.Jacob, U.Gieffers, C.Gmachl, M.Peters, J.M.Huber, R.Sondermann, P.

(2001) Nat Struct Biol 8: 784-788

  • DOI: https://doi.org/10.1038/nsb0901-784
  • Primary Citation Related Structures: 
    1JHJ

  • PubMed Abstract: 

    The anaphase-promoting complex (APC), or cyclosome, is a cell cycle-regulated ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC is composed of at least 11 subunits; no structure has been determined for any of these subunits. The subunit APC10/DOC1, a one-domain protein consisting of 185 amino acids, has a conserved core (residues 22-161) that is homologous to domains found in several other putative ubiquitin ligases and, therefore, may play a role in ubiquitination reactions. Here we report the crystal structure of human APC10 at 1.6 A resolution. The core of the protein is formed by a beta-sandwich that adopts a jellyroll fold. Unexpectedly, this structure is highly similar to ligand-binding domains of several bacterial and eukaryotic proteins, such as galactose oxidase and coagulation factor Va, raising the possibility that APC10 may function by binding a yet unidentified ligand. We further provide biochemical evidence that the C-terminus of APC10 binds to CDC27/APC3, an APC subunit that contains multiple tetratrico peptide repeats.


  • Organizational Affiliation
    • Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. wendt@biochem.mpg.de

Macromolecule Content 

  • Total Structure Weight: 19.56 kDa 
  • Atom Count: 1,450 
  • Modeled Residue Count: 161 
  • Deposited Residue Count: 171 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
APC10171Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM13 (Homo sapiens)
Explore Q9UM13 
Go to UniProtKB:  Q9UM13
PHAROS:  Q9UM13
GTEx:  ENSG00000164162 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM13
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI

Query on NI



Download:Ideal Coordinates CCD File
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.244 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.664α = 90
b = 97.664β = 90
c = 67.769γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-03-29
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.5: 2022-04-13
    Changes: Database references
  • Version 1.6: 2024-05-29
    Changes: Data collection