7M5W | pdb_00007m5w

Crystal structure of the HMG-C1 domain of human capicua bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb7M5W/pdb
• NAKB: 7M5W

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-03-25 Released: 2022-04-06 
• Deposition Author(s): Webb, J.P., Liew, J.J.M., Gnann, A.D., Dowling, D.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Molecular basis of DNA recognition by the HMG-box-C1 module of capicua.

Webb, J., Liew, J.J.M., Gnann, A.D., Ilkhani, K., Patterson, M., Paul, S., Fores, M., Jimenez, G., Veraksa, A., Dowling, D.P.

(2025) Structure 

• PubMed: 40967212 
• DOI: https://doi.org/10.1016/j.str.2025.08.018
• Primary Citation of Related Structures:  
  7M5W


• PubMed Abstract: 
  

  The HMG-box protein capicua (CIC) is a conserved transcriptional repressor with key functions in development and disease. CIC binding of DNA requires both its HMG-box and a separate domain called C1. How these domains cooperate to recognize specific DNA sequences is not known. Here, we report the crystal structure of the human CIC HMG-box and C1 domains complexed with a DNA oligomer containing a consensus octameric binding site. We find that both domains adopt tri-helical structures that pack against opposite sides of the DNA helix. The C1 domain folds into a helix-turn-helix (HTH) structure, inserting into the DNA major groove to enhance affinity. We investigate the system using molecular dynamics simulations and binding assays that interrogate the observed HMG-box and C1 domain interface and prominent cancer variants. Our results reveal a unique bipartite DNA-binding module and provide insights into the effects of cancer and domain interface mutations.

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Organizational Affiliation: 
• Chemistry Department, University of Massachusetts Boston, Boston, MA 02125, USA.
Biology Department, University of Massachusetts Boston, Boston, MA 02125, USA.
Instituto de Biología Molecular de Barcelona-Consejo Superior de Investigaciones Científicas (CSIC), Parc Cientific de Barcelona, 08028 Barcelona, Spain.
Instituto de Biología Molecular de Barcelona-Consejo Superior de Investigaciones Científicas (CSIC), Parc Cientific de Barcelona, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
Chemistry Department, University of Massachusetts Boston, Boston, MA 02125, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.03 kDa 
• Atom Count: 1,912 
• Modeled Residue Count: 174 
• Deposited Residue Count: 222 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein capicua homolog	A	186	Homo sapiens	Mutation(s): 0  Gene Names: CIC, KIAA0306
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RK0 (Homo sapiens) Explore Q96RK0  Go to UniProtKB:  Q96RK0
PHAROS:  Q96RK0 GTEx:  ENSG00000079432

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*AP*AP*GP*C)-3')	B	18	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*TP*AP*AP*CP*C)-3')	C	18	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.89	α = 90
b = 79.92	β = 90
c = 106.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Webb, J.P., Liew, J.J.M., Gnann, A.D., Dowling, D.P.

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-11-05
  Changes: Database references, Structure summary