4R2R: Wilms Tumor Protein (WT1) zinc fingers

Wilms Tumor Protein (WT1) zinc fingers in complex with carboxylated DNA. Determined by X-ray diffraction at 2.09 Å resolution. Released 8 Oct 2014.

Method: X-ray diffraction
Resolution: 2.09 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 1,357
Mol. weight: 18.31 kDa
Ligands: ZN
Released: 8 Oct 2014

Explore 4R2R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R2R contains 3 α-helices and 6 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 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	425-434	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Wilms tumor protein, isoform 4/CRA_a	A	protein	93	Homo sapiens	P19544 (AlphaFold model)
DNA (5'-D(APGPCPGPTPGPGPGP(1CC)PGP*T)-3')	B	DNA	11	synthetic construct
DNA (5'-D(TPAP(5CM)PGPCPCPCPAPCPGP*C)-3')	C	DNA	11	synthetic construct

Sequence of entity 1 (A), FASTA

>4R2R_1 Wilms tumor protein, isoform 4/CRA_a (chains A)
GPLGSEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRT
HTGEKPFSCRWPSCQKKFARSDELVRHHNMHQR

Sequence of entity 2 (B), FASTA

>4R2R_2 DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(1CC)P*GP*T)-3') (chains B)
AGCGTGGGXGT

Sequence of entity 3 (C), FASTA

>4R2R_3 DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3') (chains C)
TACGCCCACGC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

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

Primary citation

Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Hashimoto, H., Olanrewaju, Y.O., Zheng, Y. et al. Genes Dev (2014) 28:2304-2313. DOI 10.1101/gad.250746.114 · 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
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.

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