3D87 | pdb_00003d87

Crystal structure of Interleukin-23

PDB DOI: https://doi.org/10.2210/pdb3D87/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2008-05-22 Released: 2008-09-02
Deposition Author(s): Beyer, B.M., Ingram, R., Ramanathan, L., Reichert, P., Le, H., Madison, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.323 (Depositor), 0.338 (DCC)
R-Value Work:
0.268 (Depositor), 0.269 (DCC)
R-Value Observed:
0.269 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody

Beyer, B.M., Ingram, R., Ramanathan, L., Reichert, P., Le, H.V., Madison, V., Orth, P.

(2008) J Mol Biology 382: 942-955

PubMed: 18708069 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2008.08.001
Primary Citation Related Structures:
3D85, 3D87

PubMed Abstract:
Interleukin (IL)-23 is a pro-inflammatory cytokine playing a key role in the pathogenesis of several autoimmune and inflammatory diseases. We have determined the crystal structures of the heterodimeric p19-p40 IL-23 and its complex with the Fab (antigen-binding fragment) of a neutralizing antibody at 2.9 and 1.9 A, respectively. The IL-23 structure closely resembles that of IL-12. They share the common p40 subunit, and IL-23 p19 overlaps well with IL-12 p35. Along the hydrophilic heterodimeric interface, fewer charged residues are involved for IL-23 compared with IL-12. The binding site of the Fab is located exclusively on the p19 subunit, and comparison with published cytokine-receptor structures suggests that it overlaps with the IL-23 receptor binding site.

Organizational Affiliation

Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.

Macromolecule Content

Total Structure Weight: 109.29 kDa
Atom Count: 7,104
Modeled Residue Count: 914
Deposited Residue Count: 968
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-23 subunit p19	A, C	178	Homo sapiens	Mutation(s): 0 Gene Names: IL23A, SGRF, UNQ2498/PRO5798
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF7 (Homo sapiens) Explore Q9NPF7 Go to UniProtKB: Q9NPF7
PHAROS: Q9NPF7 GTEx: ENSG00000110944
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NPF7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-12 subunit p40	B, D	306	Homo sapiens	Mutation(s): 1 Gene Names: IL12B, NKSF2
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29460
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain H [auth D] MOL2 format, chain E [auth B] MOL2 format, chain H [auth D] mmCIF format, chain E [auth B] mmCIF format, chain H [auth D]	E [auth B], H [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth B] Focus chain H [auth D] Interactions & Density Focus chain E [auth B] Focus chain H [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain F [auth B] MOL2 format, chain I [auth D] MOL2 format, chain F [auth B] mmCIF format, chain I [auth D] mmCIF format, chain F [auth B]	F [auth B], I [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.323 (Depositor), 0.338 (DCC)
R-Value Work: 0.268 (Depositor), 0.269 (DCC)
R-Value Observed: 0.269 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.098	α = 90
b = 240.587	β = 90
c = 141.781	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
BUSTER-TNT	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2021-10-20
Changes: Database references, Structure summary
Version 1.4: 2023-08-30
Changes: Data collection, Refinement description