RCSB PDB - 3HM3: The Structure and conformation of Lys-63 linked tetra-ubiquitin (original) (raw)
3HM3 | pdb_00003hm3
The Structure and conformation of Lys-63 linked tetra-ubiquitin
This is version 1.4 of the entry. See complete history.
The structure and conformation of Lys63-linked tetraubiquitin.
[Datta, A.B.](/search?q=citation.rcsb%5Fauthors:Datta, A.B.), [Hura, G.L.](/search?q=citation.rcsb%5Fauthors:Hura, G.L.), [Wolberger, C.](/search?q=citation.rcsb%5Fauthors:Wolberger, C.)
(2009) J Mol Biology 392: 1117-1124
PubMed Abstract:
Ubiquitination involves the covalent attachment of the ubiquitin (Ub) C-terminus to the lysine side chain of a substrate protein by an isopeptide bond. The modification can comprise a single Ub moiety or a chain of Ub molecules joined by isopeptide bonds between the C-terminus of one Ub with one of the seven lysine residues in the next Ub. Modification of substrate proteins with Lys63-linked poly-Ub plays a key nondegradative signaling role in many biological processes, including DNA repair and nuclear factor-kappaB activation, whereas substrates modified by Lys48-linked chains are targeted to the proteasome for degradation. The distinct signaling properties of alternatively linked Ub chains presumably stem from structural differences that can be distinguished by effector proteins. We have determined the crystal structure of Lys63 tetra-Ub at a resolution of 1.96 A and performed small-angle X-ray scattering experiments and molecular dynamics simulations to probe the conformation of Lys63 tetra-Ub in solution. The chain adopts a highly extended conformation in the crystal, in contrast with the compact globular fold of Lys48 tetra-Ub. Small-angle X-ray scattering experiments show that the Lys63 tetra-Ub chain is dynamic in solution, adopting an ensemble of conformations that are more compact than the extended form in the crystal. The results of these studies provide a basis for understanding the differences in the behavior and recognition of Lys63 poly-Ub chains.
Organizational Affiliation:
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Macromolecule Content
- Total Structure Weight: 34.7 kDa
- Atom Count: 2,759
- Modelled Residue Count: 304
- Deposited Residue Count: 304
- Unique protein chains: 1
Find similar proteins by:
(by identity cutoff) | 3D Structure
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.96 Å
- R-Value Free: 0.236 (Depositor), 0.240 (DCC)
- R-Value Work: 0.186 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.188 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 105.882 | α = 90 |
| b = 105.882 | β = 90 |
| c = 105.882 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data scaling |
Revision History (Full details and data files)
- Version 1.0: 2009-08-25
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.4: 2024-11-27
Changes: Structure summary