RCSB PDB - 5AIU: A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink) (original) (raw)
5AIU | pdb_00005aiu
A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)
This is version 1.5 of the entry. See complete history.
Structural Basis for the Ring Catalyzed Synthesis of K63 Linked Ubiquitin Chains
[Branigan, E.](/search?q=citation.rcsb%5Fauthors:Branigan, E.), [Plechanovova, A.](/search?q=citation.rcsb%5Fauthors:Plechanovova, A.), [Jaffray, E.](/search?q=citation.rcsb%5Fauthors:Jaffray, E.), [Naismith, J.H.](/search?q=citation.rcsb%5Fauthors:Naismith, J.H.), [Hay, R.T.](/search?q=citation.rcsb%5Fauthors:Hay, R.T.)
(2015) Nat Struct Mol Biol 22: 597
PubMed Abstract:
RING E3 ligase-catalyzed formation of K63-linked ubiquitin chains by the Ube2V2-Ubc13 E2 complex is required in many important biological processes. Here we report the structure of the RING-domain dimer of rat RNF4 in complex with a human Ubc13∼Ub conjugate and Ube2V2. The structure has captured Ube2V2 bound to the acceptor (priming) ubiquitin with K63 in a position favorable for attack on the linkage between Ubc13 and the donor (second) ubiquitin held in the active 'folded back' conformation by the RING domain of RNF4. We verified the interfaces identified in the structure by in vitro ubiquitination assays of site-directed mutants. To our knowledge, this represents the first view of synthesis of K63-linked ubiquitin chains in which both substrate ubiquitin and ubiquitin-loaded E2 are juxtaposed to allow E3 ligase-mediated catalysis.
Organizational Affiliation:
Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK.
Macromolecule Content
- Total Structure Weight: 67.05 kDa
- Atom Count: 4,591
- Modelled Residue Count: 575
- Deposited Residue Count: 593
- Unique protein chains: 3
Find similar proteins by:
(by identity cutoff) | 3D Structure
Find similar proteins by:
(by identity cutoff) | 3D Structure
Find similar proteins by:
(by identity cutoff) | 3D Structure
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.21 Å
- R-Value Free: 0.255 (Depositor), 0.260 (DCC)
- R-Value Work: 0.217 (Depositor), 0.230 (DCC)
- R-Value Observed: 0.219 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 69.19 | α = 90 |
| b = 169.21 | β = 90 |
| c = 52.62 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
Revision History (Full details and data files)
- Version 1.0: 2015-07-08
Type: Initial release - Version 1.1: 2015-07-15
Changes: Database references, Structure summary - Version 1.2: 2015-08-19
Changes: Database references - Version 1.3: 2017-06-28
Changes: Data collection - Version 1.4: 2019-07-31
Changes: Advisory, Data collection, Derived calculations - Version 1.5: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description