RCSB PDB - 3LDZ: Crystal structure of human STAM1 VHS domain in complex with ubiquitin (original) (raw)
3LDZ | pdb_00003ldz
Crystal structure of human STAM1 VHS domain in complex with ubiquitin
This is version 1.4 of the entry. See complete history.
VHS domains of ESCRT-0 cooperate in high-avidity binding to polyubiquitinated cargo.
[Ren, X.](/search?q=citation.rcsb%5Fauthors:Ren, X.), [Hurley, J.H.](/search?q=citation.rcsb%5Fauthors:Hurley, J.H.)
(2010) EMBO J 29: 1045-1054
PubMed Abstract:
VHS (Vps27, Hrs, and STAM) domains occur in ESCRT-0 subunits Hrs and STAM, GGA adapters, and other trafficking proteins. The structure of the STAM VHS domain-ubiquitin complex was solved at 2.6 A resolution, revealing that determinants for ubiquitin recognition are conserved in nearly all VHS domains. VHS domains from all classes of VHS-domain containing proteins in yeast and humans, including both subunits of ESCRT-0, bound ubiquitin in vitro. ESCRTs have been implicated in the sorting of Lys63-linked polyubiquitinated cargo. Intact human ESCRT-0 binds Lys63-linked tetraubiquitin 50-fold more tightly than monoubiquitin, though only 2-fold more tightly than Lys48-linked tetraubiquitin. The gain in affinity is attributed to the cooperation of flexibly connected VHS and UIM motifs of ESCRT-0 in avid binding to the polyubiquitin chain. Mutational analysis of all the five ubiquitin-binding sites in yeast ESCRT-0 shows that cooperation between them is required for the sorting of the Lys63-linked polyubiquitinated cargo Cps1 to the vacuole.
Organizational Affiliation:
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA.
Macromolecule Content
- Total Structure Weight: 87.54 kDa
- Atom Count: 6,112
- Modelled Residue Count: 779
- Deposited Residue Count: 779
- Unique protein chains: 2
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: 2.60 Å
- R-Value Free: 0.234 (Depositor), 0.250 (DCC)
- R-Value Work: 0.225 (Depositor), 0.240 (DCC)
- R-Value Observed: 0.226 (Depositor)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.61 | α = 90 |
| b = 112.13 | β = 99.43 |
| c = 68.66 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| TNT | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| BUSTER | refinement |
Revision History (Full details and data files)
- Version 1.0: 2010-03-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2018-02-28
Changes: Data collection - Version 1.4: 2024-02-21
Changes: Data collection, Database references