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- PDB-9hui: CryoEM structure of human peptidylarginine deiminase type 4 (PAD4... -

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Basic information

Entry
Database: PDB / ID: 9hui
TitleCryoEM structure of human peptidylarginine deiminase type 4 (PAD4) in complex with heparin oligomer (20 subunits).
ComponentsProtein-arginine deiminase type-4
KeywordsHYDROLASE / PAD4 / citrullination / calcium
Function / homology
Function and homology information


histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification ...histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification / protein modification process / nucleosome assembly / chromatin organization / chromatin remodeling / innate immune response / calcium ion binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / Cupredoxin
Similarity search - Domain/homology
Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsBereta, G. / Bielecka, E. / Biela, A. / Wilk, P. / Wator-Wilk, E. / Grudnik, P. / Kantyka, T.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2019/34/H/NZ1/00674 Poland
Polish National Science Centre2018/30/M/NZ1/00367 Poland
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Glycosaminoglycans activate peptidylarginine deiminase 4 by enhancing calcium affinity.
Authors: Grzegorz P Bereta / Ewa Bielecka / Karolina Marzec / Łukasz Pijanowski / Artur P Biela / Piotr Wilk / Marta Kamińska / Jakub Nowak / Elżbieta Wątor-Wilk / Przemysław Grudnik / Dominik ...Authors: Grzegorz P Bereta / Ewa Bielecka / Karolina Marzec / Łukasz Pijanowski / Artur P Biela / Piotr Wilk / Marta Kamińska / Jakub Nowak / Elżbieta Wątor-Wilk / Przemysław Grudnik / Dominik Kowalczyk / Joanna Kozieł / Piotr Mydel / Marcin Poręba / Tomasz Kantyka /
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 ...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.
History
DepositionDec 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-arginine deiminase type-4
B: Protein-arginine deiminase type-4


Theoretical massNumber of molelcules
Total (without water)151,7462
Polymers151,7462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein-arginine deiminase type-4 / HL-60 PAD / Peptidylarginine deiminase IV / Protein-arginine deiminase type IV


Mass: 75872.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PAD4, PADI5, PDI5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UM07, protein-arginine deiminase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human peptidylarginine deiminase type 4 (PAD4) in complex with heparin oligomer (20 subunits).
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 9.3
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMglycine1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 217170
Details: auto-picked particles using blob picker from 1000 micrographs
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209466 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 3.73 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0179100
ELECTRON MICROSCOPYf_angle_d1.30212353
ELECTRON MICROSCOPYf_dihedral_angle_d7.8371182
ELECTRON MICROSCOPYf_chiral_restr0.0531406
ELECTRON MICROSCOPYf_plane_restr0.011581

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