7YTA: NtAGDP3 AGD1-2
crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide. Determined by X-ray diffraction at 2.31 Å resolution. Released 12 Oct 2022.
- Method
- X-ray diffraction
- Resolution
- 2.31 Å
- Organisms
- Nicotiana tabacum, Arabidopsis thaliana
- Chains
- 6
- Atoms
- 3,677
- Mol. weight
- 56.79 kDa
- Released
- 12 Oct 2022
Explore 7YTA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7YTA contains 12 α-helices and 44 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 3 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-20 | 4 | 1 |
| β-strand | 30-31 | 2 | 2 |
| β-strand | 32-39 | 8 | 1 |
| β-strand | 48-57 | 10 | 1 |
| β-strand | 65-71 | 7 | 1 |
| α-helix | 72-74 | 3 | |
| β-strand | 75-77 | 3 | 1 |
| α-helix | 78-81 | 4 | |
| β-strand | 92-97 | 6 | 2 |
| β-strand | 100-110 | 11 | 2 |
| β-strand | 114-119 | 6 | 2 |
| β-strand | 124-129 | 6 | 2 |
| α-helix | 130-132 | 3 | |
| β-strand | 133-135 | 3 | 2 |
| β-strand | 138-140 | 3 | 3 |
| β-strand | 143-145 | 3 | 3 |
Chain B: 4 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-20 | 4 | 4 |
| β-strand | 22 | 1 | 5 |
| β-strand | 28 | 1 | 5 |
| β-strand | 31 | 1 | 6 |
| β-strand | 32-39 | 8 | 4 |
| β-strand | 48-57 | 10 | 4 |
| β-strand | 65-71 | 7 | 4 |
| α-helix | 72-74 | 3 | |
| β-strand | 75-77 | 3 | 4 |
| α-helix | 78-81 | 4 | |
| β-strand | 92-97 | 6 | 6 |
| β-strand | 100-109 | 10 | 6 |
| β-strand | 114-119 | 6 | 6 |
| β-strand | 124-129 | 6 | 6 |
| α-helix | 130-132 | 3 | |
| β-strand | 133-135 | 3 | 6 |
| β-strand | 138-140 | 3 | 7 |
| β-strand | 143-145 | 3 | 7 |
| α-helix | 146-149 | 4 | |
Chain C: 3 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-20 | 4 | 8 |
| β-strand | 30-31 | 2 | 9 |
| β-strand | 32-39 | 8 | 8 |
| β-strand | 48-57 | 10 | 8 |
| β-strand | 65-71 | 7 | 8 |
| α-helix | 72-74 | 3 | |
| β-strand | 75-77 | 3 | 8 |
| α-helix | 78-81 | 4 | |
| β-strand | 92-97 | 6 | 9 |
| β-strand | 100-109 | 10 | 9 |
| β-strand | 114-119 | 6 | 9 |
| β-strand | 124-129 | 6 | 9 |
| α-helix | 130-132 | 3 | |
| β-strand | 133-135 | 3 | 9 |
| β-strand | 138-140 | 3 | 10 |
| β-strand | 143-145 | 3 | 10 |
Chain P: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 1 |
Chain Q: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 4 |
| α-helix | 4-7 | 4 | |
Chain R: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-3 | 2 | 8 |
| α-helix | 5-7 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| AGDP3 AGD1-2 | A, B, C | protein | 151 | Nicotiana tabacum | A0A1S4CD29 (AlphaFold model) |
| H3(1-15)K9me2 peptide | P, Q, R | protein | 15 | Arabidopsis thaliana | P59226 (AlphaFold model) |
Sequence of entity 1 (A, B, C), FASTA
>7YTA_1 AGDP3 AGD1-2 (chains A, B, C)
SMRGGRHQKYSHIAKGSIVEVTSDEEGFKGVWFEATVLGASSPGSKSKEVWVEYKSIVAE
ENGSEPLKEVLHVSFIRPVPPVEKIERFELYDVVDAFHKDGWWTGVVTRVMEDSRYQVTF
DNPPDELEFGVSELRFHQKWVKGKWVRPGKQ
Sequence of entity 2 (P, Q, R), FASTA
>7YTA_2 H3(1-15)K9me2 peptide (chains P, Q, R)
ARTKQTARKSTGGKA
Primary citation
The H3K9me2-binding protein AGDP3 limits DNA methylation and transcriptional gene silencing in Arabidopsis. Zhou, X., Wei, M., Nie, W. et al. J Integr Plant Biol (2022) 64:2385-2395. DOI 10.1111/jipb.13369 · PubMed
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