› 5hpl

X-ray diffraction
2.31Å resolution

System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: Rsp5 and UbV R5.4

Released:
DOI: 10.2210/pdb5hpl/pdb
PDB entry 5hpl coloured by chain, front view.
PDB entry 5hpl coloured by chain, side view.
PDB entry 5hpl coloured by chain, top view.
Source organisms:
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

Reaction 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
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-153984 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase RSP5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 380 amino acids
Theoretical weight: 44.86 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P39940 (Residues: 430-809; Coverage: 47%)
Gene names: MDP1, NPI1, RSP5, SYGP-ORF41, YER125W
Sequence domains: HECT-domain (ubiquitin-transferase)
Ubiquitin Chains: C, D
Molecule details ›
Chains: C, D
Length: 86 amino acids
Theoretical weight: 9.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62987 (Residues: 1-77; Coverage: 60%)
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 24-ID-C
Spacegroup: P21
Unit cell:
a: 72.486Å b: 92.352Å c: 82.161Å
α: 90° β: 101.6° γ: 90°
R-values:
R R work R free
0.194 0.191 0.254
Expression system: Escherichia coli

Quick links

Citations

36 review citations

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

3 mentions without citation

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