RCSB PDB - 3ZNI: Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex (original) (raw)
3ZNI | pdb_00003zni
Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex
This is version 1.8 of the entry. See complete history.
Essentiality of a Non-Ring Element in Priming Donor Ubiquitin for Catalysis by a Monomeric E3.
[Dou, H.](/search?q=citation.rcsb%5Fauthors:Dou, H.), [Buetow, L.](/search?q=citation.rcsb%5Fauthors:Buetow, L.), [Sibbet, G.J.](/search?q=citation.rcsb%5Fauthors:Sibbet, G.J.), [Cameron, K.](/search?q=citation.rcsb%5Fauthors:Cameron, K.), [Huang, D.T.](/search?q=citation.rcsb%5Fauthors:Huang, D.T.)
(2013) Nat Struct Mol Biol 20: 982
PubMed Abstract:
RING E3 ligases catalyze the transfer of ubiquitin (Ub) from E2 ubiquitin-conjugating enzyme thioesterified with Ub (E2~Ub) to substrate. For RING E3 dimers, the RING domain of one subunit and tail of the second cooperate to prime Ub, but how this is accomplished by monomeric RING E3s in the absence of a tail-like component is currently unknown. Here, we present a crystal structure of a monomeric RING E3, Tyr363-phosphorylated human CBL-B, bound to a stabilized Ub-linked E2, revealing a similar mechanism in activating E2~Ub. Both pTyr363 and the pTyr363-induced element interact directly with Ub's Ile36 surface, improving the catalytic efficiency of Ub transfer by ~200-fold. Hence, interactions outside the canonical RING domain are crucial for optimizing Ub transfer in both monomeric and dimeric RING E3s. We propose that an additional non-RING Ub-priming element may be a common RING E3 feature.
Organizational Affiliation:
The Beatson Institute for Cancer Research, Glasgow, United Kingdom.
Macromolecule Content
- Total Structure Weight: 291.87 kDa
- Atom Count: 20,546
- Modelled Residue Count: 2,482
- Deposited Residue Count: 2,532
- Unique protein chains: 4
Find similar proteins by:
(by identity cutoff) | 3D Structure
Find similar proteins by: Sequence | 3D Structure
Find similar proteins by:
(by identity cutoff) | 3D Structure
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Ligands 3 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| ZNQuery on ZNDownload Ideal Coordinates CCD File | CA [auth M]DA [auth M]Q [auth A]R [auth A]U [auth E]CA [auth M],DA [auth M],Q [auth A],R [auth A],U [auth E],V [auth E],Y [auth I],Z [auth I] | ZINC IONZnPTFCDOFLOPIGGS-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| EDOQuery on EDODownload Ideal Coordinates CCD File | BA [auth I],FA [auth M],T [auth A],X [auth E] | 1,2-ETHANEDIOLC2 H6 O2LYCAIKOWRPUZTN-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| CAQuery on CADownload Ideal Coordinates CCD File | AA [auth I],EA [auth M],S [auth A],W [auth E] | CALCIUM IONCaBHPQYMZQTOCNFJ-UHFFFAOYSA-N |  |
Interactions Interactions & Density |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PTRQuery on PTR | A, E, I, M | L-PEPTIDE LINKING | C9 H12 N O6 P |  |
TYR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.21 Å
- R-Value Free: 0.211 (Depositor), 0.210 (DCC)
- R-Value Work: 0.175 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.177 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 94.97 | α = 90 |
| b = 131.8 | β = 91.92 |
| c = 122 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PHASER | phasing |
Revision History (Full details and data files)
- Version 1.0: 2013-07-10
Type: Initial release - Version 1.1: 2013-07-17
Changes: Database references - Version 1.2: 2013-07-24
Changes: Database references, Other, Source and taxonomy - Version 1.3: 2013-08-21
Changes: Database references - Version 1.4: 2015-09-23
Changes: Data collection - Version 1.5: 2017-09-13
Changes: Data collection - Version 1.6: 2019-07-31
Changes: Advisory, Data collection, Derived calculations - Version 1.7: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description - Version 1.8: 2024-11-06
Changes: Structure summary