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- PDB-13bs: CryoEM structure of IL36RA-Fab complex -

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Basic information

Entry
Database: PDB / ID: 13bs
TitleCryoEM structure of IL36RA-Fab complex
Components
  • Fab heavy chain
  • Fab light chain
  • Interleukin-36 receptor antagonist protein
KeywordsIMMUNE SYSTEM / Antigen antibody interaction / cytokine receptor / immune regulation / inflammation
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMedina, E. / Joseph, J.S. / Gowda, M. / Shanehsazzadeh, A. / Panwar, P.
Funding support United States, 1items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 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: Interleukin-36 receptor antagonist protein
H: Fab heavy chain
L: Fab light chain


Theoretical massNumber of molelcules
Total (without water)64,0103
Polymers64,0103
Non-polymers00
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 Interleukin-36 receptor antagonist protein / IL-36Ra / FIL1 delta / IL-1-related protein 3 / IL-1RP3 / Interleukin-1 HY1 / IL-1HY1 / Interleukin- ...IL-36Ra / FIL1 delta / IL-1-related protein 3 / IL-1RP3 / Interleukin-1 HY1 / IL-1HY1 / Interleukin-1 delta / IL-1 delta / Interleukin-1 family member 5 / IL-1F5 / Interleukin-1 receptor antagonist homolog 1 / IL-1ra homolog 1 / Interleukin-1-like protein 1 / IL-1L1


Mass: 16832.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: IL36RN, FIL1D, IL1F5, IL1HY1, IL1L1, IL1RP3, UNQ1896/PRO4342
Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBH0
#2: Antibody Fab heavy chain


Mass: 24086.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab light chain


Mass: 23090.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
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: IL36RA-Fab complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2PHENIX1.21rc1_5084model refinement
13RELION43D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 566000 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034520
ELECTRON MICROSCOPYf_angle_d0.5796139
ELECTRON MICROSCOPYf_dihedral_angle_d4.532626
ELECTRON MICROSCOPYf_chiral_restr0.042689
ELECTRON MICROSCOPYf_plane_restr0.006789

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