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- EMDB-76948: CryoEM structure of IL36RA-Fab complex -

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Basic information

Entry
Database: EMDB / ID: EMD-76948
TitleCryoEM structure of IL36RA-Fab complex
Map datastructure of IL36RA-Fab complex
Sample
  • Complex: IL36RA-Fab complex
    • Protein or peptide: Interleukin-36 receptor antagonist protein
    • Protein or peptide: Fab heavy chain
    • Protein or peptide: Fab light chain
KeywordsAntigen antibody interaction / cytokine receptor / immune regulation / inflammation / IMMUNE SYSTEM
Function / homology
Function and homology information


interleukin-1 receptor antagonist activity / Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / negative regulation of type II interferon production / cytokine activity / cellular response to lipopolysaccharide / immune response ...interleukin-1 receptor antagonist activity / Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / negative regulation of type II interferon production / cytokine activity / cellular response to lipopolysaccharide / immune response / inflammatory response / innate immune response / : / extracellular region / cytoplasm
Similarity search - Function
Interleukin-1 receptor antagonist/Interleukin-36 / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF
Similarity search - Domain/homology
Interleukin-36 receptor antagonist protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMedina E / Joseph JS / Gowda M / Shanehsazzadeh A / Panwar P
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: CryoEM structure of IL36RA-Fab complex
Authors: Levine S / Shanehsazzadeh A
History
DepositionApr 28, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76948.png

Downloads & links

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Map

FileDownload / File: emd_76948.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of IL36RA-Fab complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 298.24 Å		0.93 Å/pix.
x 320 pix.
= 298.24 Å		0.93 Å/pix.
x 320 pix.
= 298.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.053134434 - 0.08311198
Average (Standard dev.)0.000014934949 (±0.0015609582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 298.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_76948_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_76948_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IL36RA-Fab complex

EntireName: IL36RA-Fab complex
Components
  • Complex: IL36RA-Fab complex
    • Protein or peptide: Interleukin-36 receptor antagonist protein
    • Protein or peptide: Fab heavy chain
    • Protein or peptide: Fab light chain

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Supramolecule #1: IL36RA-Fab complex

SupramoleculeName: IL36RA-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Interleukin-36 receptor antagonist protein

MacromoleculeName: Interleukin-36 receptor antagonist protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.832156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SLSGALCFRM KDSALKVLYL HNNQLLAGGL HAGKVIKGEE ISVVPNRWLD ASLSPVILGV QGGSQCLSCG VGQEPTLTLE PVNIMELYL GAKESKSFTF YRRDMGLTSS FESAAYPGWF LCTVPEADQP VRLTQLPENG GWNAPITDFY FQQCD

UniProtKB: Interleukin-36 receptor antagonist protein

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Macromolecule #2: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.08692 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFT SYGISWVRQA PGQGLEWMGW ISAYSGNTNY AQKFQGRVTM TTDTSTTTGY MELRRLRSD DTAVYYCARD TLSGAFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT SYGISWVRQA PGQGLEWMGW ISAYSGNTNY AQKFQGRVTM TTDTSTTTGY MELRRLRSD DTAVYYCARD TLSGAFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHT

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Macromolecule #3: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.090621 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSVG SFLAWYQQKP GQAPRLLIYG ASNRATGIPD RFSGSGSGTD FTLTISRLEP EDFAVYYCQ QGSGSPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSVG SFLAWYQQKP GQAPRLLIYG ASNRATGIPD RFSGSGSGTD FTLTISRLEP EDFAVYYCQ QGSGSPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: TFS FALCON 4i (4k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 566000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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