7Y3M: SALL4 ZFC1

Structure of SALL4 ZFC1 bound with 16 bp AT-rich dsDNA. Determined by X-ray diffraction at 2.72 Å resolution. Released 26 Oct 2022.

Method: X-ray diffraction
Resolution: 2.72 Å
Organisms: synthetic construct, Homo sapiens
Chains: 12
Atoms: 4,703
Mol. weight: 84.07 kDa
Ligands: ZN
Released: 26 Oct 2022

Explore 7Y3M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y3M contains 18 α-helices and 22 β-strands across 6 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: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	382-383	2	5
β-strand	390-391	2	5
α-helix	394-405	12
β-strand	410-411	2	6
β-strand	418-419	2	6
α-helix	422-429	8

Chain B: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	383	1	1
β-strand	390	1	1
α-helix	394-405	12
β-strand	410-411	2	2
β-strand	418-419	2	2
α-helix	422-429	8
α-helix	433-434	2

Chain C: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	382-383	2	3
β-strand	390-391	2	3
α-helix	394-405	12
β-strand	410-411	2	4
β-strand	418-419	2	4
α-helix	422-429	8
α-helix	433-437	5
α-helix	439-442	4
α-helix	446-448	3

Chain F: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	383	1	7
β-strand	390	1	7
α-helix	394-405	12
β-strand	410-411	2	8
β-strand	418-419	2	8
α-helix	422-429	8
α-helix	433-436	4
α-helix	441-444	4

Chain I: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	383	1	10
β-strand	390	1	10
α-helix	398-405	8
β-strand	410-411	2	11
β-strand	418-419	2	11
α-helix	423-429	7

Chain J: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	395-405	11
β-strand	410-411	2	9
β-strand	418-419	2	9
α-helix	422-428	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (16-mer)	D, G, K	DNA	16	synthetic construct
DNA (16-mer)	E, H, L	DNA	16	synthetic construct
Sal-like protein 4	A, B, C, F, I, J	protein	79	Homo sapiens	Q9UJQ4 (AlphaFold model)

Sequence of entity 1 (D, G, K), FASTA

>7Y3M_1 DNA (16-mer) (chains D, G, K)
GGAAATATTATATTCC

Sequence of entity 2 (E, H, L), FASTA

>7Y3M_2 DNA (16-mer) (chains E, H, L)
GGAATATAATATTTCC

Sequence of entity 3 (A, B, C, F, I, J), FASTA

>7Y3M_3 Sal-like protein 4 (chains A, B, C, F, I, J)
GHMALYKHKCKYCSKVFGTDSSLQIHLRSHTGERPFVCSVCGHRFTTKGNLKVHFHRHPQ
VKANPQLFAEFQDKVAAGN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	12

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
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)
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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