4DEP

Structure of the IL-1b signaling complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Structure of the activating IL-1 receptor signaling complex.

Thomas, C., Bazan, J.F., Garcia, K.C.

(2012) Nat Struct Mol Biol 19: 455-457

  • DOI: https://doi.org/10.1038/nsmb.2260
  • Primary Citation of Related Structures:  
    4DEP

  • PubMed Abstract: 

    Interleukin-1 (IL-1)-family cytokines are mediators of innate and adaptive immunity. They exert proinflammatory effects by binding a primary receptor that recruits a receptor accessory protein to form a signaling-competent heterotrimeric complex. Here we present the crystal structure of IL-1β bound to its primary receptor IL-1RI and its receptor accessory protein IL-1RAcP, providing insight into how IL-1-type cytokines initiate signaling and revealing an evolutionary relationship with the fibroblast growth factor receptor family.

    • Organizational Affiliation: 

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 beta
A, D
158Homo sapiensMutation(s): 0 
Gene Names: IL-1b, IL1B, IL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens)
Explore P01584 
Go to UniProtKB:  P01584
PHAROS:  P01584
GTEx:  ENSG00000125538 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01584
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 receptor type 1
B, E
321Homo sapiensMutation(s): 0 
Gene Names: IL-1RI, IL1R, IL1R1, IL1RA, IL1RT1
EC: 3.2.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for P14778 (Homo sapiens)
Explore P14778 
Go to UniProtKB:  P14778
PHAROS:  P14778
GTEx:  ENSG00000115594 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14778
Glycosylation
Glycosylation Sites: 3
Go to GlyGen: P14778-1
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 receptor accessory protein
C, F
349Homo sapiensMutation(s): 0 
Gene Names: C3orf13, IL-1RAcP, IL1R3, IL1RAP
EC: 3.2.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPH3 (Homo sapiens)
Explore Q9NPH3 
Go to UniProtKB:  Q9NPH3
PHAROS:  Q9NPH3
GTEx:  ENSG00000196083 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPH3
Glycosylation
Glycosylation Sites: 4
Go to GlyGen: Q9NPH3-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
I [auth B]
J [auth C]
K [auth C]
G [auth B],
H [auth B],
I [auth B],
J [auth C],
K [auth C],
L [auth C],
M [auth C],
N [auth E],
O [auth E],
P [auth E],
Q [auth E],
R [auth F],
S [auth F],
T [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.99α = 90
b = 65.9β = 90.35
c = 163.4γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Structure summary