7Y3I: DNA bound SALL4

Structure of DNA bound SALL4. Determined by X-ray diffraction at 2.45 Å resolution. Released 26 Oct 2022.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: synthetic construct, Homo sapiens
Chains: 8
Atoms: 2,357
Mol. weight: 49.35 kDa
Ligands: ZN
Released: 26 Oct 2022

Explore 7Y3I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y3I contains 7 α-helices and 12 β-strands across 4 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.

Chains A and B: 2 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

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	898-899	2	5
β-strand	906-907	2	5
α-helix	910-918	9

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	898-899	2	6
β-strand	906-907	2	6
α-helix	910-917	8
α-helix	918-920	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (12-mer)	G, L	DNA	12	synthetic construct
DNA (12-mer)	H, K	DNA	12	synthetic construct
Sal-like protein 4	A, B, C, D	protein	78	Homo sapiens	Q9UJQ4 (AlphaFold model)

Sequence of entity 1 (G, L), FASTA

>7Y3I_1 DNA (12-mer) (chains G, L)
GGAAATATTACC

Sequence of entity 2 (H, K), FASTA

>7Y3I_2 DNA (12-mer) (chains H, K)
GGTAATATTTCC

Sequence of entity 3 (A, B, C, D), FASTA

>7Y3I_3 Sal-like protein 4 (chains A, B, C, D)
GHMTPLLAAQPRRQAKQHGCTRCGKNFSSASALQIHERTHTGEKPFVCNICGRAFTTKGN
LKVHYMTHGANNNSARRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

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
7Y3K 2.5 Å, Structure of SALL4 ZFC4 bound with 16 bp AT-rich dsDNA
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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