7Y3K: SALL4 ZFC4

Structure of SALL4 ZFC4 bound with 16 bp AT-rich dsDNA. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Oct 2022.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,500
Mol. weight: 27.47 kDa
Ligands: ZN
Released: 26 Oct 2022

Explore 7Y3K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y3K contains 6 α-helices and 6 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, 4 β-strands

Element	Residues	Length	Sheet
β-strand	870-871	2	1
β-strand	878-879	2	1
α-helix	882-893	12
β-strand	898-899	2	2
β-strand	906-907	2	2
α-helix	910-917	8
α-helix	918-920	3

Chain B: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	882-892	11
β-strand	898-899	2	3
β-strand	906-907	2	3
α-helix	910-916	7
α-helix	917-919	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sal-like protein 4	A, B	protein	79	Homo sapiens	Q9UJQ4 (AlphaFold model)
DNA (16-mer)	G	DNA	16	synthetic construct
DNA (16-mer)	H	DNA	16	synthetic construct

Sequence of entity 1 (A, B), FASTA

>7Y3K_1 Sal-like protein 4 (chains A, B)
GHMMTPLLAAQPRRQAKQHGCTRCGKNFSSASALQIHERTHTGEKPFVCNICGRAFTTKG
NLKVHYMTHGANNNSARRG

Sequence of entity 2 (G), FASTA

>7Y3K_2 DNA (16-mer) (chains G)
GGAAATATTATATTCC

Sequence of entity 3 (H), FASTA

>7Y3K_3 DNA (16-mer) (chains H)
GGAATATAATATTTCC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif. Ru, W., Koga, T., Wang, X. et al. J Biol Chem (2022) 298:102607-102607. DOI 10.1016/j.jbc.2022.102607 · PubMed

Other PDB entries of the same protein (UniProt Q9UJQ4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BQV 1.8 Å, Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide
7BQU 1.9 Å, Cereblon in complex with SALL4 and (S)-thalidomide
8CUC 2.09 Å, Crystal structure analysis of SALL4 zinc finger domain in complex with DNA
7Y3I 2.45 Å, Structure of DNA bound SALL4
5XWR 2.69 Å, Crystal Structure of RBBP4-peptide complex
9NWS 2.7 Å, Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449)
9NWT 2.7 Å, Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A)
7Y3M 2.72 Å, Structure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA
8U16 2.9 Å, The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide
8U15 2.95 Å, The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220
8U17 3.1 Å, The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide
9SQ4 3.49 Å, Cryo-EM structure of the DDB1deltaB-CRBN-Pomalidomide complex bound to…

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