3VD6: Both Zn Fingers of GATA1

Both Zn Fingers of GATA1 Bound to Palindromic DNA Recognition Site, P21 Crystal Form. Determined by X-ray diffraction at 1.98 Å resolution. Released 16 Jan 2013.

Method: X-ray diffraction
Resolution: 1.98 Å
Organisms: synthetic construct, Mus musculus
Chains: 3
Atoms: 1,675
Mol. weight: 26.03 kDa
Ligands: ZN
Released: 16 Jan 2013

Explore 3VD6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VD6 contains 6 α-helices and 4 β-strands across 1 chain. 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 C: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	216-217	2	1
β-strand	223-224	2	1
α-helix	226-235	10
α-helix	238-240	3
β-strand	270-271	2	2
β-strand	277-278	2	2
α-helix	280-289	10
α-helix	292-294	3
α-helix	295-297	3
α-helix	307-309	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(tptpgptpcptptpaptpcpapgpaptpgpgpapcptpc)-3')	A	DNA	20	synthetic construct
DNA (5'-d(apapgpapgptpcpcpaptpcptpgpaptpapapgpapc)-3')	B	DNA	20	synthetic construct
Erythroid transcription factor	C	protein	119	Mus musculus	P17679 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VD6_1 DNA (5'-D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3') (chains A)
TTGTCTTATCAGATGGACTC

Sequence of entity 2 (B), FASTA

>3VD6_2 DNA (5'-D(*AP*AP*GP*AP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*C)-3') (chains B)
AAGAGTCCATCTGATAAGAC

Sequence of entity 3 (C), FASTA

>3VD6_3 Erythroid transcription factor (chains C)
EARECVNCGATATPLWRRDRTGHYLCNACGLYHKMNGQNRPLIRPKKRMIVSKRAGTQCT
NCQTTTTTLWRRNASGDPVCNACGLYFKLHQVNRPLTMRKDGIQTRNRKASGKGKKKRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

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

Primary citation

GATA1 directly mediates interactions with closely spaced pseudopalindromic but not distantly spaced double GATA sites on DNA. Wilkinson-White, L., Lester, K.L., Ripin, N. et al. Protein Sci (2015) 24:1649-1659. DOI 10.1002/pro.2760 · PubMed

Other PDB entries of the same protein (UniProt P17679 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VEK 2.63 Å, Both Zn Fingers of GATA1 Bound to Palindromic DNA Recognition Site, P1 Crystal Form
1GNF Solution structure of the N-terminal zinc finger of murine gata-1, NMR, 25 structures
1Y0J Zinc fingers as protein recognition motifs: structural basis for the GATA-1/Friend of…
2L5E Complex between BD1 of Brd3 and GATA-1 C-tail
2L6Y haddock model of GATA1NF:Lmo2LIM2-Ldb1LID
2L6Z haddock model of GATA1NF:Lmo2LIM2-Ldb1LID with FOG

Browse structure collections

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