4DEP

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
R-Value Work: 0.210
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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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
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
Sequence Annotations Expand
Reference Sequence

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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
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
Sequence Annotations Expand
Reference Sequence

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 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 Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [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 Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain I [auth B]	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
R-Value Work: 0.210
R-Value Observed: 0.213
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

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Deposit Data

Help and Resources

4DEP

Structure of the IL-1b signaling complex

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)