Download MendeleyStructural basis for transthiolation intermediates in the ubiquitin pathway
Kochanczyk, T., Hann, Z.S., Lux, M.C., Reyes, A.M.V.D., Ji, C., Tan, D.S., Lima, C.D.To be published.
9B5A
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 6
- PDB DOI: https://doi.org/10.2210/pdb9B5A/pdb
- EM Map EMD-44205: EMDB EMDataResource
- Classification: LIGASE
- Organism(s): Schizosaccharomyces pombe 972h-
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2024-03-22 Released: 2024-06-05
- Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.65 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
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 |
| Ubiquitin-conjugating enzyme E2 4 | 153 | Schizosaccharomyces pombe 972h- | Mutation(s): 2 Gene Names: ubc4, SPBC119.02 EC: 2.3.2.23 |  | |
UniProt | |||||
Find proteins for P46595 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P46595 Go to UniProtKB: P46595 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P46595 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin | 79 | Schizosaccharomyces pombe 972h- | Mutation(s): 0 Gene Names: uep1, ubi2, SPAC1805.12c |  | |
UniProt | |||||
Find proteins for P0CH07 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P0CH07 Go to UniProtKB: P0CH07 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0CH07 | ||||
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 pub2 | 380 | Schizosaccharomyces pombe 972h- | Mutation(s): 0 Gene Names: pub2, SPAC1805.15c EC: 2.3.2.26 |  | |
UniProt | |||||
Find proteins for Q9UTG2 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9UTG2 Go to UniProtKB: Q9UTG2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UTG2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A1AIV (Subject of Investigation/LOI) Query on A1AIV | D [auth B] | 4-aminobutanenitrile C4 H8 N2 XGYKKVTZDQDYJQ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.65 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | 1.20.1_4487: |
| RECONSTRUCTION | cryoSPARC |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-06-05 Deposition Author(s): Kochanczyk, T., Lima, C.D.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Howard Hughes Medical Institute (HHMI) | United States | -- |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R35GM118080 |
Revision History (Full details and data files)
- Version 1.0: 2024-06-05
Type: Initial release
