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- EMDB-53784: HD6 defensin filament with IP6 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53784
TitleHD6 defensin filament with IP6
Map dataHD6 with IP5 full map
Sample
  • Complex: HD6
    • Protein or peptide: Defensin-6
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: water
Keywordsfilament / intestinal / IP5 / phytic acid / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


disruption of plasma membrane integrity in another organism / Defensins / pore-forming activity / Alpha-defensins / defense response to fungus / transport vesicle / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / killing of cells of another organism ...disruption of plasma membrane integrity in another organism / Defensins / pore-forming activity / Alpha-defensins / defense response to fungus / transport vesicle / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / innate immune response / protein homodimerization activity / : / extracellular region
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKamyshinsky R / Fass D / Elad N
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101097867European Union
CitationJournal: To Be Published
Title: Common Diet Components Drive Self-Assembly of Intestinal Defensin Nanonets
Authors: Kamyshinsky R / Khmelnitsky L / Kalepu R / Haim N / Fishilevich S / Korobko I / Falkovitch A / Motiei L / Cohen SR / Elad N / Avraham R / Gokhman D / Tayar AM / Fass D
History
DepositionMay 14, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53784.png

Downloads & links

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Map

FileDownload / File: emd_53784.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHD6 with IP5 full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 421.99 Å		0.82 Å/pix.
x 512 pix.
= 421.99 Å		0.82 Å/pix.
x 512 pix.
= 421.99 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8242 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.31389347 - 0.455231
Average (Standard dev.)0.000049069407 (±0.01191271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 421.9904 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HD6 with IP5 half map A

Fileemd_53784_half_map_1.map
AnnotationHD6 with IP5 half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HD6 with IP5 half map A

Fileemd_53784_half_map_2.map
AnnotationHD6 with IP5 half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HD6

EntireName: HD6
Components
  • Complex: HD6
    • Protein or peptide: Defensin-6
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: water

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Supramolecule #1: HD6

SupramoleculeName: HD6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Defensin-6

MacromoleculeName: Defensin-6 / type: protein_or_peptide / ID: 1 / Number of copies: 48 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.719304 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
AFTCHCRRSC YSTEYSYGTC TVMGINHRFC CL

UniProtKB: Defensin-6

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Macromolecule #2: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 10 / 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 statefilament

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Sample preparation

Concentration0.037 mg/mL
BufferpH: 7
Component:
ConcentrationName
10.0 mMinositol pentaphosphate
200.0 mMsodium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 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: INSILICO MODEL / In silico model: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87585
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: non-uniform refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1zmq


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9r7m:
HD6 defensin filament with IP6

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