8YI7

The Cryo-EM structure of IL-12, receptor subunit beta-1 and receptor subunit beta-2 complex, local refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and assembly of the human IL-12 signaling complex.

Chen, H.Ge, X.Li, C.Zeng, J.Wang, X.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.07.010
  • Primary Citation of Related Structures:  
    8XRP, 8YI7

  • PubMed Abstract: 

    Interleukin (IL)-12 is a heterodimeric pro-inflammatory cytokine. Our cryoelectron microscopy structure determination of human IL-12 in complex with IL-12Rβ1 and IL-12Rβ2 at a resolution of 3.75 Å reveals that IL-12Rβ2 primarily interacts with the IL-12p35 subunit via its N-terminal Ig-like domain, while IL-12Rβ1 binds to the p40 subunit with its N-terminal fibronectin III domain. This binding mode of IL-12 with its receptors is similar to that of IL-23 but shows notable differences with other cytokines. Through structural information and biochemical assays, we identified Y62, Y189, and K192 as key residues in IL-12p35, which bind to IL-12Rβ2 with high affinity and mediate IL-12 signal transduction. Furthermore, structural comparisons reveal two distinctive conformational states and structural plasticity of the heterodimeric interface in IL-12. As a result, our study advances our understanding of IL-12 signal initiation and opens up new opportunities for the engineering and therapeutic targeting of IL-12.


  • Organizational Affiliation

    The Ministry of Education Key Laboratory of Protein Science, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-12 subunit alpha207Homo sapiensMutation(s): 0 
Gene Names: IL12ANKSF1
UniProt & NIH Common Fund Data Resources
Find proteins for P29459 (Homo sapiens)
Explore P29459 
Go to UniProtKB:  P29459
PHAROS:  P29459
GTEx:  ENSG00000168811 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29459
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-12 subunit beta307Homo sapiensMutation(s): 0 
Gene Names: IL12BNKSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P29460 (Homo sapiens)
Explore P29460 
Go to UniProtKB:  P29460
PHAROS:  P29460
GTEx:  ENSG00000113302 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29460
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P29460-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-12 receptor subunit beta-2302Homo sapiensMutation(s): 0 
Gene Names: IL12RB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99665 (Homo sapiens)
Explore Q99665 
Go to UniProtKB:  Q99665
PHAROS:  Q99665
GTEx:  ENSG00000081985 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99665
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q99665-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-12 receptor subunit beta-1219Homo sapiensMutation(s): 0 
Gene Names: IL12RB1IL12RIL12RB
UniProt & NIH Common Fund Data Resources
Find proteins for P42701 (Homo sapiens)
Explore P42701 
Go to UniProtKB:  P42701
PHAROS:  P42701
GTEx:  ENSG00000096996 
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UniProt GroupP42701
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
F [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2024-08-21
    Changes: Data collection, Database references