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- EMDB-69608: Structure of the PADI6 dimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-69608
TitleStructure of the PADI6 dimer
Map data
Sample
  • Complex: PADI6
    • Protein or peptide: PADI6
Keywordsoocytes cytoplasmic lattices / STRUCTURAL PROTEIN
Function / homology
Function and homology information


regulation of translation by machinery localization / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / ooplasm / cytoplasm organization / cortical granule / embryonic cleavage / intermediate filament cytoskeleton ...regulation of translation by machinery localization / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / ooplasm / cytoplasm organization / cortical granule / embryonic cleavage / intermediate filament cytoskeleton / epigenetic programming in the zygotic pronuclei / cytoskeleton organization / tubulin binding / intracellular protein localization / in utero embryonic development / calcium ion binding / identical protein binding / nucleus / 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
Inactive protein-arginine deiminase type-6
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiu Q / Gui M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Vita / Year: 2026
Title: Hierarchical assembly of native cytoplasmic lattices revealed by cryo-EM
Authors: Zhang YL / Liu Y / Liu Q / Zhang Q / Jin J / Liu S / Yang S / Liu Y / Peng YJ / Lai M / Sun Y / Zhang YY / Mei Y / Tong X / Zhang S / Gui M
History
DepositionMar 9, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69608.png

Downloads & links

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Map

FileDownload / File: emd_69608.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 260 pix.
= 241.8 Å		0.93 Å/pix.
x 260 pix.
= 241.8 Å		0.93 Å/pix.
x 260 pix.
= 241.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.068326004 - 0.107648246
Average (Standard dev.)0.000060592833 (±0.0019439984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 241.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_69608_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69608_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_69608_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PADI6

EntireName: PADI6
Components
  • Complex: PADI6
    • Protein or peptide: PADI6

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Supramolecule #1: PADI6

SupramoleculeName: PADI6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: PADI6

MacromoleculeName: PADI6 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GGSGGGSLEV LFQGPMSFQN SLSLSLVNPT HALCMVGMEI TLDISKCAPD KCKSFTIRGS PRILIHISSS VIAGKEDTVV WRSMNHPTVA LVRMVAPSPT VDEDKVLVSY FCPDQEVPTA TAVLFLTGIE ISLEADIYRD ...String:
MWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GGSGGGSLEV LFQGPMSFQN SLSLSLVNPT HALCMVGMEI TLDISKCAPD KCKSFTIRGS PRILIHISSS VIAGKEDTVV WRSMNHPTVA LVRMVAPSPT VDEDKVLVSY FCPDQEVPTA TAVLFLTGIE ISLEADIYRD GQLDMPSDKQ AKKKWMWGMN GWGAILLVNC SPNAVGQPDE QSFQEGPREI QNLSQMNVTV EGPTSILQNY QLILHTSEEE AKKTRVYWSQ RGSSAYELVV GPNKPVYLLP TFENRRKEAF YVEATEFPSP SFSGLISLSL SLVEKAHDEC IPEIPLYKDT VMFRVAPYIF MPSTQMPLEV YLCRELQLQG FVDSVTKLSE KSKVQVVKVY EDPNRQSKWL QDEMAFCYTQ APHKTVSLIL DTPRVSKLED FPMKYTLTPG SGYLIRQTED HRVASLDSIG NLMVSPPVKA QGKDYPLGRV LIGGSFYPSS EGRDMNKGLR EFVYAQQVQA PVELFSDWLM TGHMDQFMCF VPTNDKNNDQ KDFRLLLASP SACFELFEQK QKEGYGNVTL FEDIGAEQLL SNGRESKTIS QILADKSFRE QNTYVEKCIS LNRTLLKTEL GLEDKDIILI PQLFCLEQLT NVPSNQQSTK LFARPYFPDM LQIIVLGKNL GIPKPFGPKI NGTCCLEEKV CGLLEPLGLK CTFIDDFDCY LANIGDVCAS AIINRVPFAF KWWKMTP

UniProtKB: Inactive protein-arginine deiminase type-6

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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

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9fmn

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 358348
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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