9HUH | pdb_00009huh

CryoEM structure of human peptidylarginine deiminase type 4 (PAD4) in 10 mM calcium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Glycosaminoglycans activate peptidylarginine deiminase 4 by enhancing calcium affinity.

Bereta, G.P.Bielecka, E.Marzec, K.Pijanowski, L.Biela, A.P.Wilk, P.Kaminska, M.Nowak, J.Wator-Wilk, E.Grudnik, P.Kowalczyk, D.Koziel, J.Mydel, P.Poreba, M.Kantyka, T.

(2025) Proc Natl Acad Sci U S A 122: e2508369122-e2508369122

  • DOI: https://doi.org/10.1073/pnas.2508369122
  • Primary Citation of Related Structures:  
    9HUH, 9HUI, 9HUJ

  • PubMed Abstract: 

    Rheumatoid arthritis is a chronic inflammatory disease driven by abnormal protein modifications. These include citrullination of arginine residues by the calcium-activated enzyme peptidylarginine deiminase 4 (PAD4). However, calcium in body fluids may not fully activate PAD4, suggesting the potential involvement of other activators. In this study, we investigated the ability of glycosaminoglycans (a class of negatively charged polysaccharides) to modulate PAD4 activity. We found that model glycosaminoglycans bind to the enzyme with a nanomolar affinity, increase its calcium sensitivity, and require enzyme dimerization for activation. These effects depend on the size and negative charge of the glycosaminoglycan, and its various natural forms activate PAD4. Thus, our findings elucidate a mechanism by which common physiological compounds modulate PAD4 activity, potentially contributing to disease etiology.


  • Organizational Affiliation
    • Malopolska Centre of Biotechnology, Jagiellonian University, Krakow 30-387, Poland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-arginine deiminase type-4
A, B
676Homo sapiensMutation(s): 0 
Gene Names: PADI4PAD4PADI5PDI5
EC: 3.5.3.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM07 (Homo sapiens)
Explore Q9UM07 
Go to UniProtKB:  Q9UM07
PHAROS:  Q9UM07
GTEx:  ENSG00000159339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM07
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2019/34/H/NZ1/00674
Polish National Science CentrePoland2018/30/M/NZ1/00367

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references