Download MendeleyAssembly of the Xrn2/Rat1-Rai1-Rtt103 termination complexes in mesophilic and thermophilic organisms
Dikunova, A., Noskova, N., Overbeck, J.H., Polak, M., Stelzig, D., Zapletal, D., Kubicek, K., Novacek, J., Sprangers, R., Stefl, R.(2024) Structure
9FMS
Cryo-EM structure of S. cerevisiae Rai1-Rat1-Rtt103(252-273) complex.
- PDB DOI: https://doi.org/10.2210/pdb9FMS/pdb
- EM Map EMD-50566: EMDB EMDataResource
- Classification: RNA BINDING PROTEIN
- Organism(s): Saccharomyces cerevisiae
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-06-07 Released: 2024-12-18
- Funding Organization(s): Czech Science Foundation
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.65 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Model: in silico
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 5'-3' exoribonuclease 2 | A [auth B] | 1,006 | Saccharomyces cerevisiae | Mutation(s): 0 Gene Names: RAT1 EC: 3.1.13 |  |
UniProt | |||||
Find proteins for Q02792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02792 Go to UniProtKB: Q02792 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q02792 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Regulator of Ty1 transposition protein 103 | B [auth D] | 22 | Saccharomyces cerevisiae | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for Q05543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05543 Go to UniProtKB: Q05543 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q05543 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Decapping nuclease RAI1 | C [auth A] | 387 | Saccharomyces cerevisiae | Mutation(s): 0 Gene Names: RAI1, YGL246C, NRE387 EC: 3.6.1 |  |
UniProt | |||||
Find proteins for P53063 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53063 Go to UniProtKB: P53063 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P53063 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG (Subject of Investigation/LOI) Query on MG | D [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.65 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC | 4.4.1 |
| MODEL REFINEMENT | Coot | 0.9.8.7 |
| MODEL REFINEMENT | ISOLDE |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-12-18 Deposition Author(s): Noskova, N., Dikunova, A., Stefl, R.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Czech Science Foundation | Czech Republic | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-12-18
Type: Initial release
