› 5khu

Electron Microscopy
4.8Å resolution

Model of human Anaphase-promoting complex/Cyclosome (APC15 deletion mutant), in complex with the Mitotic checkpoint complex (APC/C-CDC20-MCC) based on cryo EM data at 4.8 Angstrom resolution

Released:
DOI: 10.2210/pdb5khu/pdb
PDB entry 5khu coloured by chain, front view.
PDB entry 5khu coloured by chain, side view.
PDB entry 5khu coloured by chain, top view.
Source organism: Homo sapiens
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-4021

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 23-mer (preferred)
PDBe Complex ID:
PDB-CPX-130029 (preferred)
Entry contents:
17 distinct polypeptide molecules
Macromolecules (17 distinct):
Anaphase-promoting complex subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 1944 amino acids
Theoretical weight: 217.58 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: 69.08 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: 92.52 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: 9.92 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: 808 amino acids
Theoretical weight: 92.3 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: 71.93 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: 21.31 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: 94.15 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: 85.45 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UJX4 (Residues: 1-755; Coverage: 100%)
Gene names: ANAPC5, APC5
Sequence domains:
Mitotic checkpoint serine/threonine-protein kinase BUB1 beta Chain: Q
Molecule details ›
Chain: Q
Length: 1050 amino acids
Theoretical weight: 120 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O60566 (Residues: 1-1050; Coverage: 100%)
Gene names: BUB1B, BUBR1, MAD3L, SSK1
Sequence domains: Mad3/BUB1 homology region 1
Cell division cycle protein 20 homolog Chains: R, S
Molecule details ›
Chains: R, S
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:
Mitotic spindle assembly checkpoint protein MAD2A Chain: T
Molecule details ›
Chain: T
Length: 205 amino acids
Theoretical weight: 23.53 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13257 (Residues: 1-205; Coverage: 100%)
Gene names: MAD2, MAD2L1
Sequence domains: HORMA domain
unknown Chain: U
Molecule details ›
Chain: U
Length: 9 amino acids
Theoretical weight: 786 Da
Source organism: Homo sapiens
Expression system: Trichoplusia ni
Anaphase-promoting complex subunit 7 Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 565 amino acids
Theoretical weight: 63.39 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: 4.8Å
Relevant EMDB volumes: EMD-4021
Expression system: Trichoplusia ni

Quick links

Citations

21 review citations

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

5 mentions without citation

Cryo-EM of Mitotic Checkpoint Complex-Bound APC/C Reveals Reciprocal and Conformational Regulation of Ubiquitin Ligation.
Yamaguchi et al. (2016)
4 more