4DEP | pdb_00004dep

Structure of the IL-1b signaling complex

PDB DOI: https://doi.org/10.2210/pdb4DEP/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2012-01-21 Released: 2012-03-21
Deposition Author(s): Thomas, C., Garcia, K.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.277 (Depositor), 0.266 (DCC)
R-Value Work:
0.210 (Depositor), 0.204 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

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

PubMed: 22426547 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 192.86 kDa
Atom Count: 11,679
Modelled Residue Count: 1,482
Deposited Residue Count: 1,656
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta	A, D	158	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01584
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor type 1	B, E	321	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14778
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B Focus chain E	Go to GlyGen: P14778-1
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor accessory protein	C, F	349	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NPH3
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C Focus chain F	Go to GlyGen: Q9NPH3-1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain T [auth F] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth F] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth F]	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		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.277 (Depositor), 0.266 (DCC)
R-Value Work: 0.210 (Depositor), 0.204 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.99	α = 90
b = 65.9	β = 90.35
c = 163.4	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

Thomas, C.

Garcia, K.C.

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