8CUC: Sal-like protein 4

Crystal structure analysis of SALL4 zinc finger domain in complex with DNA. Determined by X-ray diffraction at 2.09 Å resolution. Released 24 May 2023.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Homo sapiens
Chains: 8
Atoms: 2,456
Mol. weight: 45.22 kDa
Ligands: ZN
Released: 24 May 2023

Explore 8CUC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CUC contains 6 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.

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	898-899	2	1
β-strand	906-907	2	1
α-helix	910-917	8

Chains F and G: 2 helices, 4 β-strands

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

Chain H: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	898-899	2	6
β-strand	906-907	2	6
α-helix	910-918	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(pcpgpapapaptpaptptpapgpc)-3')	A, C	DNA	12	Homo sapiens
DNA (5'-d(pgpcptpapaptpaptptptpcpg)-3')	B, D	DNA	12	Homo sapiens
Sal-like protein 4	E, F, G, H	protein	68	Homo sapiens	Q9UJQ4 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8CUC_1 DNA (5'-D(P*CP*GP*AP*AP*AP*TP*AP*TP*TP*AP*GP*C)-3') (chains A, C)
CGAAATATTAGC

Sequence of entity 2 (B, D), FASTA

>8CUC_2 DNA (5'-D(P*GP*CP*TP*AP*AP*TP*AP*TP*TP*TP*CP*G)-3') (chains B, D)
GCTAATATTTCG

Sequence of entity 3 (E, F, G, H), FASTA

>8CUC_3 Sal-like protein 4 (chains E, F, G, H)
GSRRQAKQHGCTRCGKNFSSASALQIHERTHTGEKPFVCNICGRAFTTKGNLKVHYMTHG
ANNNSARR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Crystal Structure Analysis of SALL4 Zinc Finger domain in complex with DNA. Seo, H.S., Dhe-Paganon, S. To be published.

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
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)
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…

Browse structure collections

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