Download MendeleyStructural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic Sinefungin
Nilson, D.J., Schwer, B., Shuman, S., Almo, S.C.(2025) Nucleic Acids Res
9MG4 | pdb_00009mg4
Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with SAH
- PDB DOI: https://doi.org/10.2210/pdb9MG4/pdb
- Classification: TRANSFERASE
- Organism(s): Saccharomyces cerevisiae YJM789
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-12-10 Released: 2025-07-09
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.186 (Depositor), 0.187 (DCC)
- R-Value Work: 0.164 (Depositor), 0.164 (DCC)
- R-Value Observed: 0.165 (Depositor)
Starting Model: experimental
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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 |
| mRNA cap guanine-N7 methyltransferase | 297 | Saccharomyces cerevisiae YJM789 | Mutation(s): 0 Gene Names: ABD1, SCY_0445 EC: 2.1.1.56 |  | |
UniProt | |||||
Find proteins for A6ZLH5 (Saccharomyces cerevisiae (strain YJM789)) Explore A6ZLH5 Go to UniProtKB: A6ZLH5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A6ZLH5 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAH Query on SAH | B [auth A] | S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N |  | ||
| EDO Query on EDO | C [auth A], D [auth A], E [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | F [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.186 (Depositor), 0.187 (DCC)
- R-Value Work: 0.164 (Depositor), 0.164 (DCC)
- R-Value Observed: 0.165 (Depositor)
Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 95.16 | α = 90 |
| b = 95.16 | β = 90 |
| c = 248.942 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Aimless | data scaling |
| iMOSFLM | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-07-09 Deposition Author(s): Nilson, D.J., Fedorov, E., Ghosh, A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | 5T32GM007491 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | S10 OD020068 |
Revision History (Full details and data files)
- Version 1.0: 2025-07-09
Type: Initial release
