BMRB Entry 19939
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19939
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Title: Solution structure of MBD4 methyl-cytosine binding domain bound to methylated DNA PubMed: 25183517
Deposition date: 2014-04-24 Original release date: 2014-09-05
Authors: Williams, David; Walavalkar, Ninad
Citation: Walavalkar, Ninad; Cramer, Jason; Buchwald, William; Scarsdale, Neel; Williams, David. "Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches" Nucleic Acids Res. ., .-. (2014).
Assembly members:
MBD4mbd, polymer, 71 residues, 8088.318 Da.
DNAfor, polymer, 10 residues, Formula weight is not available
DNArev, polymer, 10 residues, Formula weight is not available
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
MBD4mbd: GSTECRKSVPCGWERVVKQR
LFGKTAGRFDVYFISPQGLK
FRSKSSLANYLHKNGETSLK
PEDFDFTVLSK
DNAfor: GGATXGGCTC
DNArev: GAGCXGATCC
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 291 |
| 1H chemical shifts | 526 |
| 15N chemical shifts | 75 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | MBD4mbd | 1 |
| 2 | methylated DNA, 1 | 2 |
| 3 | methylated DNA, 2 | 3 |
Entities:
Entity 1, MBD4mbd 71 residues - 8088.318 Da.
| 1 | GLY | SER | THR | GLU | CYS | ARG | LYS | SER | VAL | PRO | ||||
| 2 | CYS | GLY | TRP | GLU | ARG | VAL | VAL | LYS | GLN | ARG | ||||
| 3 | LEU | PHE | GLY | LYS | THR | ALA | GLY | ARG | PHE | ASP | ||||
| 4 | VAL | TYR | PHE | ILE | SER | PRO | GLN | GLY | LEU | LYS | ||||
| 5 | PHE | ARG | SER | LYS | SER | SER | LEU | ALA | ASN | TYR | ||||
| 6 | LEU | HIS | LYS | ASN | GLY | GLU | THR | SER | LEU | LYS | ||||
| 7 | PRO | GLU | ASP | PHE | ASP | PHE | THR | VAL | LEU | SER | ||||
| 8 | LYS |
Entity 2, methylated DNA, 1 10 residues - Formula weight is not available
| 1 | DG | DG | DA | DT | 5CM | DG | DG | DC | DT | DC |
Entity 3, methylated DNA, 2 10 residues - Formula weight is not available
| 1 | DG | DA | DG | DC | 5CM | DG | DA | DT | DC | DC |
Samples:
sample_1: MBD4mbd, [U-99% 13C; U-99% 15N], 0.2 – 1.0 mM; DNAfor0.2 – 1.0 mM; DNArev0.2 – 1.0 mM; Na2PO4 10 mM
sample_2: MBD4mbd, [U-13C; U-15N; U-2H], 0.2 – 1.0 mM; DNAfor0.2 – 1.0 mM; DNArev0.2 – 1.0 mM; Pf1 phage 12 mg/mL; Na2PO4 10 mM
sample_conditions_1: temperature: 298 K; pH: 6.5; pressure: 1 atm; ionic strength: 30 mM
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | anisotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
CcpNmr v2.3, CCPN - data analysis, peak picking
X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMR spectrometers:
- Bruker Avance 700 MHz
Related Database Links:
| PDB | |
| DBJ | BAE02211 BAG64144 BAK62846 |
| EMBL | CAG29301 CAH89518 |
| GB | AAC68879 AAD22195 AAD50374 AAH11752 AAM00008 |
| REF | NP_001127160 NP_001263199 NP_001263200 NP_001263201 NP_001267403 |
| SP | O95243 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts