8YI7 | pdb_00008yi7

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 1.4 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 32: 1640

  • 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

View Full Validation Report



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
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Data collection