Download MendeleyDNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context
Adam, S., Anteneh, H., Hornisch, M., Wagner, V., Lu, J., Radde, N.E., Bashtrykov, P., Song, J., Jeltsch, A.(2020) Nat Commun
6W8W
Crystal structure of mouse DNMT1 in complex with CCG DNA
- PDB DOI: https://doi.org/10.2210/pdb6W8W/pdb
- NAKB: 6W8W
- Classification: TRANSFERASE/DNA
- Organism(s): Mus musculus, synthetic construct
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2020-03-21 Released: 2020-07-08
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.280
- R-Value Work: 0.238
- R-Value Observed: 0.240
Starting Model: experimental
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This is version 1.1 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 |
| DNA (cytosine-5)-methyltransferase 1 | 873 | Mus musculus | Mutation(s): 0 Gene Names: Dnmt1, Dnmt, Met1, Uim EC: 2.1.1.37 |  | |
UniProt | |||||
Find proteins for P13864 (Mus musculus) Explore P13864 Go to UniProtKB: P13864 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13864 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| CCG DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3') | C, D [auth E] | 12 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| CCG DNA (5'-D(*CP*CP*TP*TP*CP*(C49)P*GP*TP*AP*AP*GP*T)-3') | E [auth D], F | 12 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAH (Subject of Investigation/LOI) Query on SAH | G [auth A], J [auth B] | S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N |  | ||
| ZN (Subject of Investigation/LOI) Query on ZN | H [auth A], I [auth A], K [auth B], L [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.00 Å
- R-Value Free: 0.280
- R-Value Work: 0.238
- R-Value Observed: 0.240
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 89.794 | α = 90 |
| b = 152.593 | β = 94.74 |
| c = 95.631 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-07-08 Deposition Author(s): Anteneh, H., Song, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | 1R35GM119721 |
Revision History (Full details and data files)
- Version 1.0: 2020-07-08
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Database references, Derived calculations, Refinement description
