5KL4: Wilms Tumor Protein (WT1) ZnF2-4 Q369H

Wilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with formylated DNA. Determined by X-ray diffraction at 1.78 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 1.78 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 2,622
Mol. weight: 36.71 kDa
Ligands: CA, ZN
Released: 14 Sept 2016

Explore 5KL4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KL4 contains 6 α-helices and 12 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: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	353-354	2	1
β-strand	363-364	2	1
α-helix	367-378	12
β-strand	383-384	2	2
β-strand	391-392	2	2
α-helix	395-406	12
β-strand	411-412	2	3
β-strand	421-422	2	3
α-helix	425-436	12

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	353-354	2	4
β-strand	363-364	2	4
α-helix	367-378	12
β-strand	383-384	2	5
β-strand	391-392	2	5
α-helix	395-406	12
β-strand	411-412	2	6
β-strand	421-422	2	6
α-helix	425-435	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Wilms tumor protein	A, D	protein	93	Homo sapiens	P19544 (AlphaFold model)
DNA (5'-D(APGPCPGPTPGPGPGP(5FC)PGP*T)-3')	B, E	DNA	11	synthetic construct
DNA (5'-D(TPAP(5CM)PGPCPCPCPAPCPGP*C)-3')	C, F	DNA	11	synthetic construct

Sequence of entity 1 (A, D), FASTA

>5KL4_1 Wilms tumor protein (chains A, D)
GPLGSEKPYQCDFKDCERRFSRSDHLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRT
HTGEKPFSCRWPSCQKKFARSDELVRHHNMHQR

Sequence of entity 2 (B, E), FASTA

>5KL4_2 DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3') (chains B, E)
AGCGTGGGCGT

Sequence of entity 3 (C, F), FASTA

>5KL4_3 DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3') (chains C, F)
TACGCCCACGC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	6

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

Primary citation

Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications. Hashimoto, H., Zhang, X., Zheng, Y. et al. Nucleic Acids Res (2016) 44:10165-10176. DOI 10.1093/nar/gkw766 · 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
6B0O 1.55 Å, Zinc finger Domain of WT1(-KTS form) with 12+1mer Oligonucleotide with 3' Triplet TGT
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
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

Browse structure collections

About this viewer

MolViewer shows 5KL4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.