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- EMDB-70555: cryo-EM structure of human innate immune receptor conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-70555
Titlecryo-EM structure of human innate immune receptor conformation 1
Map data
Sample
  • Complex: Apo structure of a human innate immune receptor conformation 1
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 6
KeywordsMonomer / receptor / cell death / enzyme / IMMUNE SYSTEM
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
NACHT, LRR and PYD domains-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsCui Z / Shen C
Funding support United States, 1 items
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 3.8 Angstroms resolution.
Authors: Cui Z / Shen C
History
DepositionMay 9, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70555.png

Downloads & links

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Map

FileDownload / File: emd_70555.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 300 pix.
= 219. Å		0.73 Å/pix.
x 300 pix.
= 219. Å		0.73 Å/pix.
x 300 pix.
= 219. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-1.0398133 - 1.807088
Average (Standard dev.)-0.0008638385 (±0.032159276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 219.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70555_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_70555_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 : Apo structure of a human innate immune receptor conformation 1

EntireName: Apo structure of a human innate immune receptor conformation 1
Components
  • Complex: Apo structure of a human innate immune receptor conformation 1
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 6

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Supramolecule #1: Apo structure of a human innate immune receptor conformation 1

SupramoleculeName: Apo structure of a human innate immune receptor conformation 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NACHT, LRR and PYD domains-containing protein 6

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.897938 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDQPEAPCSS TGPRLAVARE LLLAALEELS QEQLKRFRHK LRDVGPDGRS IPWGRLERAD AVDLAEQLAQ FYGPEPALEV ARKTLKRAD ARDVAAQLQE RRLQRLGLGS GTLLSVSEYK KKYREHVLQL HARVKERNAR SVKITKRFTK LLIAPESAAP E EAMGPAEE ...String:
MDQPEAPCSS TGPRLAVARE LLLAALEELS QEQLKRFRHK LRDVGPDGRS IPWGRLERAD AVDLAEQLAQ FYGPEPALEV ARKTLKRAD ARDVAAQLQE RRLQRLGLGS GTLLSVSEYK KKYREHVLQL HARVKERNAR SVKITKRFTK LLIAPESAAP E EAMGPAEE PEPGRARRSD THTFNRLFRR DEEGRRPLTV VLQGPAGIGK TMAAKKILYD WAAGKLYQGQ VDFAFFMPCG EL LERPGTR SLADLILDQC PDRGAPVPQM LAQPQRLLFI LDGADELPAL GGPEAAPCTD PFEAASGARV LGGLLSKALL PTA LLLVTT RAAAPGRLQG RLCSPQCAEV RGFSDKDKKK YFYKYFRDER RAERAYRFVK ENETLFALCF VPFVCWIVCT VLRQ QLELG RDLSRTSKTT TSVYLLFITS VLSSAPVADG PRLQGDLRNL CRLAREGVLG RRAQFAEKEL EQLELRGSKV QTLFL SKKE LPGVLETEVT YQFIDQSFQE FLAALSYLLE DGGVPRTAAG GVGTLLRGDA QPHSHLVLTT RFLFGLLSAE RMRDIE RHF GCMVSERVKQ EALRWVQGQG QGCPGVAPEV TEGAKGLEDT EEPEEEEEGE EPNYPLELLY CLYETQEDAF VRQALCR FP ELALQRVRFC RMDVAVLSYC VRCCPAGQAL RLISCRLVAA QEKKKKSLGK RLQASLGGGS SSQGTTKQLP ASLLHPLF Q AMTDPLCHLS SLTLSHCKLP DAVCRDLSEA LRAAPALTEL GLLHNRLSEA GLRMLSEGLA WPQCRVQTVR VQLPDPQRG LQYLVGMLRQ SPALTTLDLS GCQLPAPMVT YLCAVLQHQG CGLQTLSLAS VELSEQSLQE LQAVKRAKPD LVITHPALDG HPQPPKELI STF

UniProtKB: NACHT, LRR and PYD domains-containing protein 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: 7.4
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: 48.44 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76219
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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