8DTN: The complex of nanobody 6101 with BCL11A ZF6
The complex of nanobody 6101 with BCL11A ZF6. Determined by X-ray diffraction at 2.2 Å resolution. Released 1 Feb 2023.
- Method
- X-ray diffraction
- Resolution
- 2.2 Å
- Organisms
- Lama glama, Homo sapiens
- Chains
- 8
- Atoms
- 4,920
- Mol. weight
- 66.55 kDa
- Ligands
- MG, ZN
- Released
- 1 Feb 2023
Explore 8DTN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8DTN contains 25 α-helices and 50 β-strands across 8 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, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 1 |
| β-strand | 10-13 | 4 | 2 |
| β-strand | 18-25 | 8 | 1 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 2 |
| β-strand | 46-51 | 6 | 2 |
| β-strand | 58-60 | 3 | 2 |
| β-strand | 68-73 | 6 | 1 |
| β-strand | 78-83 | 6 | 1 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-98 | 7 | 2 |
| α-helix | 99-104 | 6 | |
| β-strand | 111-116 | 6 | 2 |
Chains B, D and H: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 801 | 1 | 3 |
| α-helix | 807 | 1 | |
| β-strand | 808 | 1 | 3 |
| α-helix | 809 | 1 | |
| α-helix | 815-822 | 8 | |
Chain C: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 4 |
| β-strand | 11-13 | 3 | 5 |
| β-strand | 18-25 | 8 | 4 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 6 |
| β-strand | 46-51 | 6 | 6 |
| β-strand | 58-60 | 3 | 6 |
| β-strand | 65 | 1 | 4 |
| β-strand | 68-73 | 6 | 4 |
| β-strand | 78-83 | 6 | 4 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-98 | 7 | 6 |
| α-helix | 99-104 | 6 | |
| β-strand | 111-113 | 3 | 6 |
| β-strand | 114-116 | 3 | 5 |
Chain E: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 8 |
| β-strand | 10-13 | 4 | 9 |
| β-strand | 18-25 | 8 | 8 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 9 |
| β-strand | 46-51 | 6 | 9 |
| β-strand | 58-60 | 3 | 9 |
| α-helix | 62-64 | 3 | |
| β-strand | 68-73 | 6 | 8 |
| α-helix | 74-76 | 3 | |
| β-strand | 78-83 | 6 | 8 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-98 | 7 | 9 |
| α-helix | 99-104 | 6 | |
| β-strand | 111-116 | 6 | 9 |
Chain F: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 801 | 1 | 10 |
| β-strand | 808 | 1 | 10 |
| α-helix | 815-822 | 8 | |
Chain G: 4 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 11 |
| β-strand | 10-13 | 4 | 12 |
| β-strand | 18-25 | 8 | 11 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 12 |
| β-strand | 46-51 | 6 | 12 |
| β-strand | 58-60 | 3 | 12 |
| α-helix | 62-64 | 3 | |
| β-strand | 68-73 | 6 | 11 |
| β-strand | 78-83 | 6 | 11 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-98 | 7 | 12 |
| α-helix | 99-104 | 6 | |
| β-strand | 111-116 | 6 | 12 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Nanobody 6101 | A, C, E, G | protein | 117 | Lama glama | |
| B-cell lymphoma/leukemia 11A | B, D, F, H | protein | 30 | Homo sapiens | Q9H165 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G), FASTA
>8DTN_1 Nanobody 6101 (chains A, C, E, G)
RVQLVESGGGLVQAGGSLRLSCAASGFIFDSYAMGWYRQAPGKEMELVAAITSSGSSTYY
ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAALDYVIDGYWGQGTQVTVSS
Sequence of entity 2 (B, D, F, H), FASTA
>8DTN_2 B-cell lymphoma/leukemia 11A (chains B, D, F, H)
KDVYKCEICKMPFSVYSTLEKHMKKWHSDR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 4 |
| ZN | Zinc ion | Zn | 4 |
Primary citation
Evolution of nanobodies specific for BCL11A. Yin, M., Izadi, M., Tenglin, K. et al. Proc Natl Acad Sci U S A (2023) 120:e2218959120-e2218959120. DOI 10.1073/pnas.2218959120 · PubMed
Other PDB entries of the same protein (UniProt Q9H165 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6U9Q 1.83 Å, Crystal Structure Analysis of DNA-BCL11A Znf domain complex
- 9YLM 1.91 Å, BCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human Globin Locus…
- 9YLO 1.97 Å, BCL11A ZF2-3 in Complex with a DNA Sequence Observed in the Human Globin Locus…
- 9YLP 2.04 Å, BCL11A ZF2-3 in Complex with a DNA Sequence Observed in the Human Globin Locus…
- 9E6R 2.09 Å, BCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human Globin Locus…
- 9YLN 2.15 Å, BCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human Globin Locus…
- 9E6S 2.2 Å, BCL11A ZF4-6 with K784T Mutation in Complex with a DNA Sequence Observed in the Human…
- 9YLL 2.38 Å, BCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human Globin Locus…
- 5VTB 2.4 Å, Crystal structure of RBBP4 bound to BCL11a peptide
- 8DTU 2.45 Å, The complex of nanobody 5344N74D with BCL11A ZF6.
- 6KI6 2.5 Å, Crystal structure of BCL11A in complex with gamma-globin -115 HPFH region
- 9B4P 2.56 Å, Tetramer Formation of the BCL11A ZF0 Domain
Browse structure collections
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