9E6R: BCL11A ZF4-6

BCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGACCA. Determined by X-ray diffraction at 2.09 Å resolution. Released 9 Apr 2025.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Homo sapiens
Chains: 5
Atoms: 2,503
Mol. weight: 50.2 kDa
Ligands: MG, ZN
Released: 9 Apr 2025

Explore 9E6R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E6R contains 8 α-helices and 14 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	743	1	1
β-strand	750	1	1
α-helix	754-765	12
β-strand	770-771	2	2
β-strand	778-779	2	2
α-helix	782-789	8
α-helix	790-792	3
β-strand	800-801	2	3
β-strand	808-809	2	3
α-helix	812-822	11

Chain D: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	770-771	2	4
β-strand	778-779	2	4
α-helix	782-789	8
β-strand	800-801	2	5
β-strand	808-809	2	5
α-helix	812-822	11

Chain Y: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	743	1	6
β-strand	750	1	6
α-helix	754-765	12
β-strand	770-771	2	7
β-strand	778-779	2	7
α-helix	782-789	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B-cell lymphoma/leukemia 11A	A, D, Y	protein	108	Homo sapiens	Q9H165 (AlphaFold model)
DNA Strand I	B	DNA	20	Homo sapiens
DNA Strand II	C	DNA	19	Homo sapiens

Sequence of entity 1 (A, D, Y), FASTA

>9E6R_1 B-cell lymphoma/leukemia 11A (chains A, D, Y)
GSPGRPSSKEGRRSDTCEYCGKVFKNCSNLTVHRRSHTGERPYKCELCNYACAQSSKLTR
HMKTHGQVGKDVYKCEICKMPFSVYSTLEKHMKKWHSDRVLNNDIKTE

Sequence of entity 2 (B), FASTA

>9E6R_2 DNA Strand I (chains B)
AATGAATCTATTGGTCAAGG

Sequence of entity 3 (C), FASTA

>9E6R_3 DNA Strand II (chains C)
CCTTGACCAATAGATTCAT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	8

Water and common crystallization additives (EDO) are not listed.

Primary citation

Multimeric transcription factor BCL11A utilizes two zinc-finger tandem arrays to bind clustered short sequence motifs. Horton, J.R., Yu, M., Zhou, J. et al. Nat Commun (2025) 16:3672-3672. DOI 10.1038/s41467-025-58998-7 · 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…
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
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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