› 5hpk

X-ray diffraction
2.43Å resolution

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L and UbV NL.1

Released:
DOI: 10.2210/pdb5hpk/pdb
PDB entry 5hpk coloured by chain, front view.
PDB entry 5hpk coloured by chain, side view.
PDB entry 5hpk 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
[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-S-ubiquitinyl-L-cysteine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158839 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase NEDD4-like Chain: A
Molecule details ›
Chain: A
Length: 383 amino acids
Theoretical weight: 45.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96PU5 (Residues: 594-975; Coverage: 39%)
Gene names: KIAA0439, NEDD4L, NEDL3
Sequence domains: HECT-domain (ubiquitin-transferase)
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 86 amino acids
Theoretical weight: 10.05 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

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P4212
Unit cell:
a: 151.306Å b: 151.306Å c: 85.952Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.211 0.227
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

34 review citations

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

6 mentions without citation

Specific targeting of the deubiquitinase and E3 ligase families with engineered ubiquitin variants.
Gorelik et al. (2017)
5 more