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- PDB-9r7l: HD6 defensin filament with IP6 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9r7l
TitleHD6 defensin filament with IP6
ComponentsDefensin-6
KeywordsANTIMICROBIAL PROTEIN / filament / intestinal / IP6 / phytic acid
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
INOSITOL HEXAKISPHOSPHATE / Defensin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsKamyshinsky, R. / Fass, D. / Elad, N.
Funding supportEuropean Union, 1items
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, S.R. / Elad, N. / Avraham, R. / Gokhman, D. / Tayar, A.M. / Fass, D.
History
DepositionMay 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defensin-6
B: Defensin-6
C: Defensin-6
D: Defensin-6
E: Defensin-6
F: Defensin-6
G: Defensin-6
H: Defensin-6
I: Defensin-6
J: Defensin-6
K: Defensin-6
L: Defensin-6
M: Defensin-6
N: Defensin-6
O: Defensin-6
P: Defensin-6
Q: Defensin-6
R: Defensin-6
S: Defensin-6
T: Defensin-6
U: Defensin-6
V: Defensin-6
W: Defensin-6
X: Defensin-6
Y: Defensin-6
Z: Defensin-6
a: Defensin-6
b: Defensin-6
c: Defensin-6
d: Defensin-6
e: Defensin-6
f: Defensin-6
g: Defensin-6
h: Defensin-6
i: Defensin-6
j: Defensin-6
k: Defensin-6
l: Defensin-6
m: Defensin-6
n: Defensin-6
o: Defensin-6
p: Defensin-6
q: Defensin-6
r: Defensin-6
s: Defensin-6
t: Defensin-6
u: Defensin-6
v: Defensin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,82753
Polymers178,52748
Non-polymers3,3005
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/peptide ...
Defensin-6 / Defensin / alpha 6


Mass: 3719.304 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEFA6, DEF6 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01524
#2: Chemical
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: HD6 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pET28
Buffer solutionpH: 7
Buffer component
IDConc.NameBuffer-ID
110 mMinositol hexaphosphate1
2200 mMsodium chloride1
SpecimenConc.: 0.037 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1800 nm / Nominal defocus min: 600 nm
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_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72649 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1ZMQ

1zmq


Accession code: 1ZMQ / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512717
ELECTRON MICROSCOPYf_angle_d0.59317161
ELECTRON MICROSCOPYf_dihedral_angle_d8.1051857
ELECTRON MICROSCOPYf_chiral_restr0.0411807
ELECTRON MICROSCOPYf_plane_restr0.0042114

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