9VFG | pdb_00009vfg

Solution structure of silver bound XPC binding domain of hHR23B (holo form)

• PDB DOI: https://doi.org/10.2210/pdb9VFG/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-11 Released: 2025-10-01 
• Deposition Author(s): Xiao, T., He, D., Kelly, M.J.S., Chang, C.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

RAD23B acquires a copper metalloadaptor function in amphibian-to-reptile evolution to increase metabolism and regulate genomic integrity.

Xiao, T., He, D., Liu, D., Jia, S., Chen, Q., Silverman, D., Maitra, N., Huang, A.Y., Pezacki, A., Nguyen, T.T., Rao, G., Tillage, R., Deng, K., Weinshenker, D., Britt, R.D., Kelly, M.J.S., Dan, Y., Chang, C.J.

(2025) Mol Cell 85: 3443-3459.e11

• PubMed: 40972527 
• DOI: https://doi.org/10.1016/j.molcel.2025.08.024
• Primary Citation of Related Structures:  
  9VFE, 9VFF, 9VFG


• PubMed Abstract: 
  

  Increasing brain complexity is a major step in the evolution of species. Here, we show that, in the transition from amphibians to reptiles, the DNA repair protein RAD23B acquires a metalloadaptor function that allows it to serve as a central hub for both metabolism and protection of genomic integrity. More specifically, RAD23B gains an allosteric H274/H323 copper-binding site to enable the transfer of copper from the universal copper transporter 1 (CTR1) uptake protein to all known copper metallochaperone pathways, while simultaneously making its canonical functions in DNA repair copper dependent. This layer of nutrient regulation allows organisms to withstand elevated levels of potentially toxic copper while augmenting metabolism in cells with high energetic needs across both physiology and disease, including neurons in the locus coeruleus, a key brain structure that regulates sleep, and cancer cells.

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Organizational Affiliation: 
• Department of Chemistry, Princeton University, Princeton, NJ, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
Department of Chemistry, University of California, Davis, Davis, CA, USA.
Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA.
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
Department of Chemistry, Princeton University, Princeton, NJ, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, 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 (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 8.18 kDa 
• Atom Count: 568 
• Modeled Residue Count: 72 
• Deposited Residue Count: 72 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UV excision repair protein RAD23 homolog B	A	72	Homo sapiens	Mutation(s): 0  Gene Names: RAD23B EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for P54727 (Homo sapiens) Explore P54727  Go to UniProtKB:  P54727
PHAROS:  P54727 GTEx:  ENSG00000119318

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG (Subject of Investigation/LOI)	B [auth A]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Xiao, T., He, D., Kelly, M.J.S., Chang, C.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release