8SML

hPAD4 bound to inhibitory Fab hI365

  • Classification: HYDROLASE/IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2023-04-26 Released: 2024-03-06 
  • Deposition Author(s): Maker, A., Verba, K.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB), National Institutes of Health/National Cancer Institute (NIH/NCI), Damon Runyon Cancer Research Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antibody discovery identifies regulatory mechanisms of protein arginine deiminase 4.

Zhou, X.Kong, S.Maker, A.Remesh, S.G.Leung, K.K.Verba, K.A.Wells, J.A.

(2024) Nat Chem Biol 20: 742-750

  • DOI: https://doi.org/10.1038/s41589-023-01535-8
  • Primary Citation of Related Structures:  
    8SMK, 8SML

  • PubMed Abstract: 

    Unlocking the potential of protein arginine deiminase 4 (PAD4) as a drug target for rheumatoid arthritis requires a deeper understanding of its regulation. In this study, we use unbiased antibody selections to identify functional antibodies capable of either activating or inhibiting PAD4 activity. Through cryogenic-electron microscopy, we characterized the structures of these antibodies in complex with PAD4 and revealed insights into their mechanisms of action. Rather than steric occlusion of the substrate-binding catalytic pocket, the antibodies modulate PAD4 activity through interactions with allosteric binding sites adjacent to the catalytic pocket. These binding events lead to either alteration of the active site conformation or the enzyme oligomeric state, resulting in modulation of PAD4 activity. Our study uses antibody engineering to reveal new mechanisms for enzyme regulation and highlights the potential of using PAD4 agonist and antagonist antibodies for studying PAD4-dependency in disease models and future therapeutic development.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-arginine deiminase type-4
A, D
695Homo sapiensMutation(s): 1 
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab hI365 light chain
B, E
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab hI365 heavy chain
C, F
231Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
MODEL REFINEMENTISOLDE
RECONSTRUCTIONcisTEM1.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesK99EB030587
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United StatesR00EB030587
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1P41CA1962 76
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA191018
Damon Runyon Cancer Research FoundationUnited StatesDRG-2297-17
Damon Runyon Cancer Research FoundationUnited StatesDFS-52-22

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Database references