7M5W: HMG-C1 domain of human capicua

Crystal structure of the HMG-C1 domain of human capicua bound to DNA. Determined by X-ray diffraction at 2.95 Å resolution. Released 6 Apr 2022.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 1,912
Mol. weight: 33.03 kDa
Ligands: CA
Released: 6 Apr 2022

Explore 7M5W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M5W contains 7 α-helices and 0 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	36-38	3
α-helix	40-55	16
α-helix	61-74	14
α-helix	77-97	21
α-helix	120-140	21
α-helix	146-155	10
α-helix	163-179	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein capicua homolog	A	protein	186	Homo sapiens	Q96RK0 (AlphaFold model)
DNA (5'-d(gpgptptpaptpgpapaptpgpapapapapapgpc)-3')	B	DNA	18	synthetic construct
DNA (5'-d(gpcptptptptptpcpaptptpcpaptpapapcpc)-3')	C	DNA	18	synthetic construct

Sequence of entity 1 (A), FASTA

>7M5W_1 Protein capicua homolog (chains A)
MGSSHHHHHHSSGLVPRGSHMDGRSPNKREKDHIRRPMNAFMIFSKRHRALVHQRHPNQD
NRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKKSSSEFKVPYS
SLRRTLDQRRALVMQLFQDHGFFPSAQATAAFQARYADIFPSKVCLQLKIREVRQKIMQA
ATPTEQ

Sequence of entity 2 (B), FASTA

>7M5W_2 DNA (5'-D(*GP*GP*TP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*AP*AP*GP*C)-3') (chains B)
GGTTATGAATGAAAAAGC

Sequence of entity 3 (C), FASTA

>7M5W_3 DNA (5'-D(*GP*CP*TP*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*TP*AP*AP*CP*C)-3') (chains C)
GCTTTTTCATTCATAACC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Molecular basis of DNA recognition by the HMG-box-C1 module of capicua. Webb, J., Liew, J.J.M., Gnann, A.D. et al. Structure (2025). DOI 10.1016/j.str.2025.08.018 · PubMed

Other PDB entries of the same protein (UniProt Q96RK0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KZG 2.0 Å, 14-3-3 protein in Complex with CIC S301 phosphorylated peptide
4J2J 2.5 Å, Crystal structure of AXH domain complex with Capicua
6KZH 2.65 Å, 14-3-3 protein in Complex with CIC S173 phosphorylated peptide
6JRP 3.0 Å, Crystal structure of CIC-HMG-ETV5-DNA complex
4J2L 3.15 Å, Crystal Structure of AXH domain complexed with Capicua
2M41 Solution Structure of the AXH domain of Ataxin-1 in complex with ligand peptide from…

Browse structure collections

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