6B0O: Wilms tumor protein

Zinc finger Domain of WT1(-KTS form) with 12+1mer Oligonucleotide with 3' Triplet TGT. Determined by X-ray diffraction at 1.55 Å resolution. Released 3 Jan 2018.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,395
Mol. weight: 45.79 kDa
Ligands: ZN
Released: 3 Jan 2018

Explore 6B0O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B0O contains 11 α-helices and 18 β-strands across 2 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	323-324	2	1
β-strand	333-334	2	1
α-helix	337-348	12
β-strand	353-354	2	2
β-strand	357	1	3
β-strand	363-364	2	2
α-helix	367-373	7
α-helix	375-378	4
β-strand	383-384	2	4
β-strand	391-392	2	4
α-helix	395-406	12
β-strand	411-412	2	5
β-strand	421-422	2	5
α-helix	425-432	8

Chain D: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	323-324	2	6
β-strand	333-334	2	6
α-helix	337-344	8
α-helix	345-347	3
α-helix	349-350	2
β-strand	353-354	2	7
β-strand	357	1	3
β-strand	363-364	2	7
α-helix	367-378	12
β-strand	383-384	2	8
β-strand	391-392	2	8
α-helix	395-406	12
β-strand	411-412	2	9
β-strand	421-422	2	9
α-helix	425-434	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Wilms tumor protein	A, D	protein	119	Homo sapiens	P19544 (AlphaFold model)
DNA (5'-d(apgpcpgptpgpgpgpapgptpgp*t)-3')	B, E	DNA	13	Homo sapiens
DNA (5'-d(tpapcpapcptpcpcpcpapcpgp*c)-3')	C, F	DNA	13	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>6B0O_1 Wilms tumor protein (chains A, D)
HMRPFMCAYPGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHT
GVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFARSDELVRHHNMHQR

Sequence of entity 2 (B, E), FASTA

>6B0O_2 DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*T)-3') (chains B, E)
AGCGTGGGAGTGT

Sequence of entity 3 (C, F), FASTA

>6B0O_3 DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3') (chains C, F)
TACACTCCCACGC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

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

Primary citation

Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites. Wang, D., Horton, J.R., Zheng, Y. et al. Nucleic Acids Res (2018) 46:3864-3877. DOI 10.1093/nar/gkx1274 · PubMed

Other PDB entries of the same protein (UniProt P19544 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KL3 1.45 Å, Wilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with DNA
4R2Q 1.54 Å, Wilms Tumor Protein (WT1) zinc fingers in complex with formylated DNA
5KL7 1.58 Å, Wilms Tumor Protein (WT1) ZnF2-4Q369R in complex with carboxylated DNA
5KL6 1.64 Å, Wilms Tumor Protein (WT1) Q369R ZnF2-4 in complex with DNA
5KL2 1.69 Å, Wilms Tumor Protein (WT1) ZnF2-4 in complex with DNA
5KL4 1.78 Å, Wilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with formylated DNA
4R2P 1.79 Å, Wilms Tumor Protein (WT1) zinc fingers in complex with hydroxymethylated DNA
6B0R 1.82 Å, Zinc finger Domain of WT1(-KTS form) with M342R Mutation and 14+1mer Oligonucleotide…
6BLW 1.83 Å, Zinc finger Domain of WT1(+KTS form) with M342R Mutation and 17+1mer Oligonucleotide…
4R2E 1.84 Å, Wilms Tumor Protein (WT1) zinc fingers in complex with methylated DNA
3MYJ 1.89 Å, Human Class I MHC HLA-A2 in complex with the WT-1 (126-134) (R1Y) peptide variant.
3HPJ 2.0 Å, Human Class I MHC HLA-A2 in complex with the WT-1 (126-134) peptide

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