RCSB PDB - 2XEW: Crystal structure of K11-linked diubiquitin (original) (raw)
2XEW | pdb_00002xew
Crystal structure of K11-linked diubiquitin
This is version 1.4 of the entry. See complete history.
Lys11-Linked Ubiquitin Chains Adopt Compact Conformations and are Preferentially Hydrolyzed by the Deubiquitinase Cezanne
[Bremm, A.](/search?q=citation.rcsb%5Fauthors:Bremm, A.), [Freund, S.M.V.](/search?q=citation.rcsb%5Fauthors:Freund, S.M.V.), [Komander, D.](/search?q=citation.rcsb%5Fauthors:Komander, D.)
(2010) Nat Struct Mol Biol 17: 939
PubMed Abstract:
Ubiquitin is a versatile cellular signaling molecule that can form polymers of eight different linkages, and individual linkage types have been associated with distinct cellular functions. Though little is currently known about Lys11-linked ubiquitin chains, recent data indicate that they may be as abundant as Lys48 linkages and may be involved in vital cellular processes. Here we report the generation of Lys11-linked polyubiquitin in vitro, for which the Lys11-specific E2 enzyme UBE2S was fused to a ubiquitin binding domain. Crystallographic and NMR analyses of Lys11-linked diubiquitin reveal that Lys11-linked chains adopt compact conformations in which Ile44 is solvent exposed. Furthermore, we identify the OTU family deubiquitinase Cezanne as the first deubiquitinase with Lys11-linkage preference. Our data highlight the intrinsic specificity of the ubiquitin system that extends to Lys11-linked chains and emphasize that differentially linked polyubiquitin chains must be regarded as independent post-translational modifications.
Organizational Affiliation:
Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
Macromolecule Content
- Total Structure Weight: 104.6 kDa
- Atom Count: 7,921
- Modelled Residue Count: 908
- Deposited Residue Count: 912
- Unique protein chains: 1
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| UBIQUITIN | A, B, C, D, EA, B, C, D, E, F, G, H, I, J, K, L | 76 | [Homo sapiens](/search?q=rcsb%5Fentity%5Fsource%5Forganism.taxonomy%5Flineage.name:Homo sapiens) | Mutation(s): 0 |  |
| UniProt & NIH Common Fund Data Resources | |||||
| Find proteins for [P0CG48](/search?q=rcsb%5Fpolymer%5Fentity%5Fcontainer%5Fidentifiers.reference%5Fsequence%5Fidentifiers.database%5Faccession:P0CG48 AND rcsb%5Fpolymer%5Fentity%5Fcontainer%5Fidentifiers.reference%5Fsequence%5Fidentifiers.database%5Fname:UniProt) _(Homo sapiens)_Explore P0CG48 Go to UniProtKB: P0CG48 | |||||
| PHAROS: P0CG48GTEx: ENSG00000150991 | |||||
| Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0CG48 | ||||
| Sequence AnnotationsExpand | |||||
| Reference Sequence |
| Ligands 3 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| FLCQuery on FLCDownload Ideal Coordinates CCD File | Y [auth F],Z [auth F] | CITRATE ANIONC6 H5 O7KRKNYBCHXYNGOX-UHFFFAOYSA-K |  |
Interactions Interactions & Density |
| EDOQuery on EDODownload Ideal Coordinates CCD File | AA [auth F]BA [auth H]CA [auth I]EA [auth J]FA [auth K]AA [auth F],BA [auth H],CA [auth I],EA [auth J],FA [auth K],GA [auth L],HA [auth L],IA [auth L],M [auth A],N [auth A],O [auth A],Q [auth B],R [auth B],S [auth B],T [auth C],V [auth D],X [auth E] | 1,2-ETHANEDIOLC2 H6 O2LYCAIKOWRPUZTN-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| CLQuery on CLDownload Ideal Coordinates CCD File | DA [auth I]JA [auth L]KA [auth L]LA [auth L]P [auth A]DA [auth I],JA [auth L],KA [auth L],LA [auth L],P [auth A],U [auth C],W [auth D] | CHLORIDE IONClVEXZGXHMUGYJMC-UHFFFAOYSA-M |  |
Interactions Interactions & Density |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.252 (Depositor), 0.250 (DCC)
- R-Value Work: 0.205 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.207 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 79.23 | α = 90 |
| b = 79.96 | β = 90 |
| c = 221.23 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| iMOSFLM | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
Revision History (Full details and data files)
- Version 1.0: 2010-07-14
Type: Initial release - Version 1.1: 2011-05-08
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2019-07-31
Changes: Advisory, Data collection, Derived calculations - Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description