Download MendeleyLinkage and substrate specificity conferred by NZF ubiquitin binding domains
Michel, M.A., Scutts, S., Komander, D.To be published.
9B12
Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1
- PDB DOI: https://doi.org/10.2210/pdb9B12/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-03-12 Released: 2024-07-31
- Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Research Council (ERC), National Health and Medical Research Council (NHMRC, Australia)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.81 Å
- R-Value Free: 0.269
- R-Value Work: 0.231
- R-Value Observed: 0.233
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Optineurin | A [auth C], B [auth D], C [auth E], D [auth F] | 96 | Homo sapiens | Mutation(s): 0 Gene Names: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q96CV9 (Homo sapiens) Explore Q96CV9 Go to UniProtKB: Q96CV9 | |||||
PHAROS: Q96CV9 GTEx: ENSG00000123240 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96CV9 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin | E [auth A], F [auth B] | 152 | Homo sapiens | Mutation(s): 0 Gene Names: UBB |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47 | |||||
PHAROS: P0CG47 GTEx: ENSG00000170315 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0CG47 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| E3 ubiquitin-protein ligase RNF31 | 30 | Homo sapiens | Mutation(s): 0 Gene Names: RNF31, ZIBRA EC: 2.3.2.31 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q96EP0 (Homo sapiens) Explore Q96EP0 Go to UniProtKB: Q96EP0 | |||||
PHAROS: Q96EP0 GTEx: ENSG00000092098 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96EP0 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | N [auth F], O [auth A], S [auth H], X [auth J] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| PG4 Query on PG4 | K [auth C], V [auth J] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PGE Query on PGE | L [auth C] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | Q [auth G], R [auth H], T [auth I], U [auth J] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | M [auth F], P [auth B], W [auth J] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.81 Å
- R-Value Free: 0.269
- R-Value Work: 0.231
- R-Value Observed: 0.233
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 110.413 | α = 90 |
| b = 70.191 | β = 102.25 |
| c = 193.944 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| STARANISO | data scaling |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-07-31 Deposition Author(s): Michel, M.A., Scutts, S., Komander, D.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Medical Research Council (MRC, United Kingdom) | United Kingdom | U105192732 |
| European Research Council (ERC) | European Union | 724804 |
| National Health and Medical Research Council (NHMRC, Australia) | Australia | GNT1178122 |
Revision History (Full details and data files)
- Version 1.0: 2024-07-31
Type: Initial release
