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- EMDB-52413: CryoEM structure of human peptidylarginine deiminase type 4 (PAD4... -

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Basic information

Entry
Database: EMDB / ID: EMD-52413
TitleCryoEM structure of human peptidylarginine deiminase type 4 (PAD4) in 10 mM calcium
Map datamain map
Sample
  • Complex: Human peptidylarginine deiminase type 4 (PAD4) in 10 mM calcium
    • Protein or peptide: Protein-arginine deiminase type-4
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsPAD4 / citrullination / calcium / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsBereta GP / Bielecka E / Biela AP / Wilk P / Wator-Wilk E / Grudnik P / Kantyka T
Funding support Poland, 2 items
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 GP / Bielecka E / Biela AP / Wilk P / Wator-Wilk E / Grudnik P / Kantyka T
History
DepositionDec 23, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52413.png

Downloads & links

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Map

FileDownload / File: emd_52413.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 338.24 Å		0.85 Å/pix.
x 400 pix.
= 338.24 Å		0.85 Å/pix.
x 400 pix.
= 338.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8456 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0686
Minimum - Maximum-0.0017140503 - 1.9539152
Average (Standard dev.)0.00052425946 (±0.017140292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 338.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_52413_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_52413_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human peptidylarginine deiminase type 4 (PAD4) in 10 mM calcium

EntireName: Human peptidylarginine deiminase type 4 (PAD4) in 10 mM calcium
Components
  • Complex: Human peptidylarginine deiminase type 4 (PAD4) in 10 mM calcium
    • Protein or peptide: Protein-arginine deiminase type-4
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Human peptidylarginine deiminase type 4 (PAD4) in 10 mM calcium

SupramoleculeName: Human peptidylarginine deiminase type 4 (PAD4) in 10 mM calcium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Protein-arginine deiminase type-4

MacromoleculeName: Protein-arginine deiminase type-4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein-arginine deiminase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.872906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHHMAQGTLI RVTPEQPTHA VCVLGTLTQL DICSSAPEDC TSFSINASPG VVVDIAHGPP AKKKSTGSST WPLDPGVEV TLTMKVASGS TGDQKVQISY YGPKTPPVKA LLYLTGVEIS LCADITRTGK VKPTRAVKDQ RTWTWGPCGQ G AILLVNCD ...String:
MGHHHHHHHH HHHMAQGTLI RVTPEQPTHA VCVLGTLTQL DICSSAPEDC TSFSINASPG VVVDIAHGPP AKKKSTGSST WPLDPGVEV TLTMKVASGS TGDQKVQISY YGPKTPPVKA LLYLTGVEIS LCADITRTGK VKPTRAVKDQ RTWTWGPCGQ G AILLVNCD RDNLESSAMD CEDDEVLDSE DLQDMSLMTL STKTPKDFFT NHTLVLHVAR SEMDKVRVFQ ATRGKLSSKC SV VLGPKWP SHYLMVPGGK HNMDFYVEAL AFPDTDFPGL ITLTISLLDT SNLELPEAVV FQDSVVFRVA PWIMTPNTQP PQE VYACSI FENEDFLKSV TTLAMKAKCK LTICPEEENM DDQWMQDEME IGYIQAPHKT LPVVFDSPRN RGLKEFPIKR VMGP DFGYV TRGPQTGGIS GLDSFGNLEV SPPVTVRGKE YPLGRILFGD SCYPSNDSRQ MHQALQDFLS AQQVQAPVKL YSDWL SVGH VDEFLSFVPA PDRKGFRLLL ASPRSCYKLF QEQQNEGHGE ALLFEGIKKK KQQKIKNILS NKTLREHNSF VERCID WNR ELLKRELGLA ESDIIDIPQL FKLKEFSKAE AFFPNMVNML VLGKHLGIPK PFGPVINGRC CLEEKVCSLL EPLGLQC TF INDFFTYHIR HGEVHCGTNV RRKPFSFKWW NMVP

UniProtKB: Protein-arginine deiminase type-4

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.35 mg/mL
BufferpH: 9.3
Component:
ConcentrationNameFormula
200.0 mMglycine
150.0 mMsodium chlorideNaCl
10.0 mMcalcium chlorideCaCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 169855 / Details: autopicked from 500 micrographs
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93239
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 64000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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