› 5khr

Electron Microscopy
6.1Å resolution

Model of human Anaphase-promoting complex/Cyclosome complex (APC15 deletion mutant) in complex with the E2 UBE2C/UBCH10 poised for ubiquitin ligation to substrate (APC/C-CDC20-substrate-UBE2C)

Released:
DOI: 10.2210/pdb5khr/pdb
PDB entry 5khr coloured by chain, front view.
PDB entry 5khr coloured by chain, side view.
PDB entry 5khr coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM of Mitotic Checkpoint Complex-Bound APC/C Reveals Reciprocal and Conformational Regulation of Ubiquitin Ligation.
Yamaguchi M, VanderLinden R, Weissmann F, Qiao R, Dube P, Brown NG, Haselbach D, Zhang W, Sidhu SS, Peters JM, Stark H, Schulman BA
Mol Cell 63 593-607 (2016)
PMID: 27522463
Related structures: EMD-4025

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 21-mer (preferred)
PDBe Complex ID:
PDB-CPX-126385 (preferred)
Entry contents:
16 distinct polypeptide molecules
Macromolecules (16 distinct):
Anaphase-promoting complex subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 1944 amino acids
Theoretical weight: 216.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9H1A4 (Residues: 1-1944; Coverage: 100%)
Gene names: ANAPC1, TSG24
Sequence domains:
Anaphase-promoting complex subunit 11 Chain: B
Molecule details ›
Chain: B
Length: 84 amino acids
Theoretical weight: 9.85 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9NYG5 (Residues: 1-84; Coverage: 100%)
Gene names: ANAPC11, HSPC214
Sequence domains: Anaphase-promoting complex subunit 11 RING-H2 finger
Cell division cycle protein 23 homolog Chains: C, P
Molecule details ›
Chains: C, P
Length: 597 amino acids
Theoretical weight: 68.92 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UJX2 (Residues: 1-597; Coverage: 100%)
Gene names: ANAPC8, CDC23
Sequence domains: Anaphase promoting complex subunit 8 / Cdc23
Anaphase-promoting complex subunit 16 Chain: E
Molecule details ›
Chain: E
Length: 110 amino acids
Theoretical weight: 11.68 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96DE5 (Residues: 1-110; Coverage: 100%)
Gene names: ANAPC16, C10orf104, CENP-27
Sequence domains: Anaphase-promoting complex, subunit 16
Cell division cycle protein 27 homolog Chains: F, H
Molecule details ›
Chains: F, H
Length: 824 amino acids
Theoretical weight: 91.97 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P30260 (Residues: 1-824; Coverage: 100%)
Gene names: ANAPC3, CDC27, D0S1430E, D17S978E
Sequence domains:
Anaphase-promoting complex subunit CDC26 Chains: G, W
Molecule details ›
Chains: G, W
Length: 85 amino acids
Theoretical weight: 9.79 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8NHZ8 (Residues: 1-85; Coverage: 100%)
Gene names: ANAPC12, C9orf17, CDC26
Sequence domains: Anaphase-promoting complex APC subunit CDC26
Anaphase-promoting complex subunit 4 Chain: I
Molecule details ›
Chain: I
Length: 818 amino acids
Theoretical weight: 93.21 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UJX5 (Residues: 1-808; Coverage: 100%)
Gene names: ANAPC4, APC4
Sequence domains:
Cell division cycle protein 16 homolog Chains: J, K
Molecule details ›
Chains: J, K
Length: 620 amino acids
Theoretical weight: 71.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13042 (Residues: 1-620; Coverage: 100%)
Gene names: ANAPC6, CDC16
Sequence domains:
Anaphase-promoting complex subunit 10 Chain: L
Molecule details ›
Chain: L
Length: 185 amino acids
Theoretical weight: 21.28 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UM13 (Residues: 1-185; Coverage: 100%)
Gene names: ANAPC10, APC10
Sequence domains: Anaphase-promoting complex, subunit 10 (APC10)
Anaphase-promoting complex subunit 13 Chain: M
Molecule details ›
Chain: M
Length: 74 amino acids
Theoretical weight: 8.53 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BS18 (Residues: 1-74; Coverage: 100%)
Gene name: ANAPC13
Sequence domains: Apc13p protein
Anaphase-promoting complex subunit 2 Chain: N
Molecule details ›
Chain: N
Length: 822 amino acids
Theoretical weight: 94.02 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UJX6 (Residues: 1-822; Coverage: 100%)
Gene names: ANAPC2, APC2, KIAA1406
Sequence domains:
Anaphase-promoting complex subunit 5 Chain: O
Molecule details ›
Chain: O
Length: 755 amino acids
Theoretical weight: 85.25 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UJX4 (Residues: 1-755; Coverage: 100%)
Gene names: ANAPC5, APC5
Sequence domains:
Ubiquitin-conjugating enzyme E2 C Chain: Q
Molecule details ›
Chain: Q
Length: 190 amino acids
Theoretical weight: 20.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O00762 (Residues: 1-179; Coverage: 100%)
Gene names: UBCH10, UBE2C
Sequence domains: Ubiquitin-conjugating enzyme
Cell division cycle protein 20 homolog Chain: R
Molecule details ›
Chain: R
Length: 499 amino acids
Theoretical weight: 54.8 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q12834 (Residues: 1-499; Coverage: 100%)
Gene name: CDC20
Sequence domains:
Probable serine/threonine-protein kinase HSL1 Chain: S
Molecule details ›
Chain: S
Length: 33 amino acids
Theoretical weight: 3.78 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
UniProt:
  • Canonical: P34244 (Residues: 774-837; Coverage: 2%)
Gene names: HSL1, YKL101W, YKL453
Anaphase-promoting complex subunit 7 Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 565 amino acids
Theoretical weight: 63.2 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UJX3 (Residues: 1-565; Coverage: 100%)
Gene names: ANAPC7, APC7
Sequence domains: Tetratricopeptide repeat

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.1Å
Relevant EMDB volumes: EMD-4025
Expression systems:
  • Trichoplusia ni
  • Not provided

Quick links

Citations

21 review citations

Cell cycle control in cancer.
Matthews et al. (2022)
20 more

1 mention without citation

Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands.
Perez et al. (2019)