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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.USA / Year: 2025
Title: CryoEM structures of human peptidylarginine deiminase type 4 (PAD4)
Authors: Bereta, G.P. / Bielecka, E. / Biela, A.P. / Wilk, P. / Wator-Wilk, E. / Grudnik, P. / Kantyka, T.
History
DepositionDec 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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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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