8DTU: The complex of nanobody 5344N74D with BCL11A ZF6

The complex of nanobody 5344N74D with BCL11A ZF6. Determined by X-ray diffraction at 2.45 Å resolution. Released 1 Feb 2023.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Lama glama, Homo sapiens
Chains: 3
Atoms: 1,154
Mol. weight: 16.42 kDa
Ligands: ZN
Released: 1 Feb 2023

Explore 8DTU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DTU contains 7 α-helices and 13 β-strands across 3 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: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	2
β-strand	18-23	6	1
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	3
α-helix	99-101	3
α-helix	106-108	3
β-strand	113-115	3	3
β-strand	116-117	2	2

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-5	3	1

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	800-801	2	4
α-helix	802	1
β-strand	808-809	2	4
α-helix	815-823	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody 5344N74D	B	protein	6	Lama glama
Nanobody 5344N74D	A	protein	113	Lama glama
B-cell lymphoma/leukemia 11A	C	protein	28	Homo sapiens	Q9H165 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8DTU_1 Nanobody 5344N74D (chains B)
QVQLVK

Sequence of entity 2 (A), FASTA

>8DTU_2 Nanobody 5344N74D (chains A)
SGGGLVQAGDSLRLSCAASGSTFSGYAMGWYRQAPGKERELVAAITSSGASTYYADSVRG
RFTISRDDAKNTVYLQMNSLKPEDTAVYYCAALDEGYLDYDSWGQGTQVTVSS

Sequence of entity 3 (C), FASTA

>8DTU_3 B-cell lymphoma/leukemia 11A (chains C)
VYKCEICKMPFSVYSTLEKHMKKWHSDR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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…
8DTN 2.2 Å, The complex of nanobody 6101 with BCL11A ZF6
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
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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