PDBsum entry 3o4o

Immune system

PDB id

3o4o

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Contents

			Protein chains

					152 a.a. *


					316 a.a. *


					323 a.a. *

			Ligands

					NAG-NAG ×2


					NAG ×4

* Residue conservation analysis

PDB id:

3o4o

Links

Name:

Immune system

Title:

Crystal structure of an interleukin-1 receptor complex

Structure:

Interleukin-1 beta. Chain: a. Synonym: il-1beta, il-1 beta, catabolin. Engineered: yes. Interleukin-1 receptor type 2. Chain: c. Fragment: il-1rii ectodomain, residues 14-343. Synonym: il-1rii, il-1rt-2, il-1rt2, il-1r-2, interleukin-1 receptor type ii, interleukin-1 receptor beta, il-1r-beta, cd121 antigen-like

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.

Resolution:

3.30Å

R-factor:

0.253

R-free:

0.289

Authors:

X.Q.Wang,D.L.Wang,S.Y.Zhang,L.Li,X.Liu,K.R.Mei

Key ref:

D.Wang et al. (2010). Structural insights into the assembly and activation of IL-1β with its receptors. Nat Immunol, 11, 905-911. PubMed id: 20802483

Date:

27-Jul-10

Release date:

01-Sep-10

PROCHECK

	Headers

	References

Protein chain

P01584 (IL1B_HUMAN) - Interleukin-1 beta from Homo sapiens

Seq: Struc:					269 a.a. 152 a.a.

Protein chain

P27930 (IL1R2_HUMAN) - Interleukin-1 receptor type 2 from Homo sapiens

Seq: Struc:					398 a.a. 316 a.a.

Protein chain

Q9NPH3 (IL1AP_HUMAN) - Interleukin-1 receptor accessory protein from Homo sapiens

Seq: Struc:

Seq: Struc:					570 a.a. 323 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

Chain B: E.C.3.2.2.6 - ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

NAD⁺ + H2O = ADP-D-ribose + nicotinamide + H⁺

NAD(+)	+	H2O	=	ADP-D-ribose	+	nicotinamide	+	H(+) Bound ligand (Het Group name = NAG) matches with 43.75% similarity

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

	Nat Immunol 11:905-911 (2010)
PubMed id: 20802483

Structural insights into the assembly and activation of IL-1β with its receptors.
D.Wang, S.Zhang, L.Li, X.Liu, K.Mei, X.Wang.

ABSTRACT

Interleukin 1β (IL-1β) is a key orchestrator of inflammation and host defense that exerts its effects through IL-1 receptor type I (IL-1RI) and IL-1 receptor accessory protein (IL-1RAcP). How IL-1RAcP is recruited by IL-1β-IL-1RI to form the signaling-competent complex remains elusive. Here we present the crystal structure of IL-1β bound to IL-1 receptor type II (IL-1RII) and IL-1RAcP. IL-1β-IL-1RII generated a composite binding surface to recruit IL-1RAcP. Biochemical analysis demonstrated that IL-1β-IL-1RI and IL-1β-IL-1RII interacted similarly with IL-1RAcP. It also showed the importance of two loops of IL-1 receptor antagonist (IL-1Ra) in determining its antagonism. Our results provide a structural basis for assembly and activation of the IL-1 receptor and offer a general cytokine-receptor architecture that governs the IL-1 family of cytokines.

Literature references that cite this PDB file's key reference

PubMed id

Reference

22426547

C.Thomas, J.F.Bazan, and K.C.Garcia (2012).
Structure of the activating IL-1 receptor signaling complex.

Nat Struct Mol Biol, 19, 455-457.

PDB code:

4dep

21127706

X.Y.Zheng, H.L.Zhang, Q.Luo, and J.Zhu (2011).
Kainic acid-induced neurodegenerative model: potentials and limitations.

J Biomed Biotechnol, 2011, 457079.

20856217

J.E.Sims (2010).
Accessory to inflammation.

Nat Immunol, 11, 883-885.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.