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- PDB-9ok8: cryo-EM structure of a human innate immune receptor conformation 2 -

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Basic information

Entry
Database: PDB / ID: 9ok8
Titlecryo-EM structure of a human innate immune receptor conformation 2
ComponentsNACHT, LRR and PYD domains-containing protein 6
KeywordsIMMUNE SYSTEM / Monomer / receptor / cell death / enzyme
Function / homology
Function and homology information


membraneless organelle / NLRP6 inflammasome complex assembly / canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / lipoteichoic acid binding / host-mediated modulation of intestinal microbiota composition / NLRP6 inflammasome complex / vasopressin receptor activity / acute inflammatory response / pattern recognition receptor activity ...membraneless organelle / NLRP6 inflammasome complex assembly / canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / lipoteichoic acid binding / host-mediated modulation of intestinal microbiota composition / NLRP6 inflammasome complex / vasopressin receptor activity / acute inflammatory response / pattern recognition receptor activity / pyroptotic inflammatory response / peptide binding / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / antiviral innate immune response / negative regulation of inflammatory response to antigenic stimulus / molecular condensate scaffold activity / lipopolysaccharide binding / negative regulation of ERK1 and ERK2 cascade / protein homooligomerization / positive regulation of inflammatory response / double-stranded RNA binding / nuclear membrane / regulation of inflammatory response / defense response to virus / defense response to Gram-positive bacterium / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain profile. / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / DAPIN domain ...: / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain profile. / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Death-like domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / NACHT, LRR and PYD domains-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsCui, Z. / Shen, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI173896 United States
CitationJournal: To Be Published
Title: cryo-EM structure of a human innate immune receptor at 3.7 Angstroms resolution
Authors: Cui, Z. / Shen, C.
History
DepositionMay 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4052
Polymers98,8981
Non-polymers5071
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 NACHT, LRR and PYD domains-containing protein 6 / Angiotensin II/vasopressin receptor / PYRIN-containing APAF1-like protein 5


Mass: 98897.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP6, NALP6, PYPAF5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59044
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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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: Structure of a human innate immune receptor / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 48.44 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153064 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044713
ELECTRON MICROSCOPYf_angle_d0.8866358
ELECTRON MICROSCOPYf_dihedral_angle_d21.236650
ELECTRON MICROSCOPYf_chiral_restr0.049723
ELECTRON MICROSCOPYf_plane_restr0.007809

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