› 5l9u

Electron Microscopy
6.4Å resolution

Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with a cross linked Ubiquitin variant-substrate-UBE2C (UBCH10) complex representing key features of multiubiquitination

Released:
DOI: 10.2210/pdb5l9u/pdb
PDB entry 5l9u coloured by chain, front view.
PDB entry 5l9u coloured by chain, side view.
PDB entry 5l9u coloured by chain, top view.
Source organisms:
Primary publication:
Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C.
Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA
Cell 165 1440-1453 (2016)
PMID: 27259151
Related structures: EMD-3432

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 22-mer (preferred)
PDBe Complex ID:
PDB-CPX-126384 (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: 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 15 Chain: D
Molecule details ›
Chain: D
Length: 121 amino acids
Theoretical weight: 14.29 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P60006 (Residues: 1-121; Coverage: 100%)
Gene names: ANAPC15, C11orf51, HSPC020
Sequence domains: Anaphase-promoting complex subunit 15
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: 93.94 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: 85.18 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UJX4 (Residues: 1-755; Coverage: 100%)
Gene names: ANAPC5, APC5
Sequence domains:
Fizzy-related protein homolog Chain: R
Molecule details ›
Chain: R
Length: 493 amino acids
Theoretical weight: 54.84 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UM11 (Residues: 1-496; Coverage: 99%)
Gene names: CDH1, FYR, FZR, FZR1, KIAA1242
Sequence domains:
Probable serine/threonine-protein kinase HSL1; Ubiquitin Chain: S
Molecule details ›
Chain: S
Length: 157 amino acids
Theoretical weight: 17.06 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: P34244 (Residues: 768-842; Coverage: 3%)
  • Canonical: Q63429 (Residues: 685-762; Coverage: 10%)
Gene names: HSL1, Ubc, YKL101W, YKL453
Sequence domains: Ubiquitin family
Ubiquitin-conjugating enzyme E2 C Chain: U
Molecule details ›
Chain: U
Length: 188 amino acids
Theoretical weight: 20.77 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
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: 6.4Å
Relevant EMDB volumes: EMD-3432
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

31 review citations

Breaking the chains: deubiquitylating enzyme specificity begets function.
Clague et al. (2019)
30 more

2 mentions without citation

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