› 5hpt

X-ray diffraction
2.84Å resolution

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1, Ubv P2.3 and UBCH7

Released:
DOI: 10.2210/pdb5hpt/pdb
PDB entry 5hpt coloured by chain, front view.
PDB entry 5hpt coloured by chain, side view.
PDB entry 5hpt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.
Zhang W, Wu KP, Sartori MA, Kamadurai HB, Ordureau A, Jiang C, Mercredi PY, Murchie R, Hu J, Persaud A, Mukherjee M, Li N, Doye A, Walker JR, Sheng Y, Hao Z, Li Y, Brown KR, Lemichez E, Chen J, Tong Y, Harper JW, Moffat J, Rotin D, Schulman BA, Sidhu SS
Mol Cell 62 121-36 (2016)
PMID: 26949039

Function and Biology Details

Reactions catalysed: 
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero dimer
PDBe Complex ID:
PDB-CPX-158834 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
NEDD4-like E3 ubiquitin-protein ligase WWP1 Chains: A, D, G
Molecule details ›
Chains: A, D, G
Length: 383 amino acids
Theoretical weight: 45.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H0M0 (Residues: 537-917; Coverage: 41%)
Gene name: WWP1
Sequence domains: HECT-domain (ubiquitin-transferase)
Ubiquitin Chains: B, E, H
Molecule details ›
Chains: B, E, H
Length: 83 amino acids
Theoretical weight: 9.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62987 (Residues: 1-75; Coverage: 59%)
Gene names: UBA52, UBCEP2
Sequence domains: Ubiquitin family
Ubiquitin-conjugating enzyme E2 L3 Chains: C, F
Molecule details ›
Chains: C, F
Length: 161 amino acids
Theoretical weight: 18.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P68036 (Residues: 2-154; Coverage: 99%)
Gene names: UBCE7, UBCH7, UBE2L3
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 114.005Å b: 118.897Å c: 158.663Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.218 0.237
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

35 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
34 more

6 mentions without citation

Emerging drug development technologies targeting ubiquitination for cancer therapeutics.
Veggiani et al. (2019)
5 more