Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 199.00 kDa 
• Atom Count: 13131 
• Residue Count: 1587 
• Unique protein chains: 5

4GRW

Structure of a complex of human IL-23 with 3 Nanobodies (Llama vHHs)

• DOI: 10.2210/pdb4GRW/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-08-27 Released: 2014-02-19 
• Deposition Author(s): Desmyter, A., Spinelli, S., Button, C., Saunders, M., de Haard, H., Rommelaere, H., Union, A., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.218 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

Neutralization of Human Interleukin 23 by Multivalent Nanobodies Explained by the Structure of Cytokine-Nanobody Complex.

Desmyter, A., Spinelli, S., Boutton, C., Saunders, M., Blachetot, C., de Haard, H., Denecker, G., Van Roy, M., Cambillau, C., Rommelaere, H.

(2017) Front Immunol 8: 884-884

• PubMed: 28871249 
• DOI: 10.3389/fimmu.2017.00884
• Primary Citation of Related Structures:  
  4GRW


• PubMed Abstract: 
  

The heterodimeric cytokine interleukin (IL) 23 comprises the IL12-shared p40 subunit and an IL23-specific subunit, p19. Together with IL12 and IL27, IL23 sits at the apex of the regulatory mechanisms shaping adaptive immune responses. IL23, together with IL17, plays an important role in the development of chronic inflammation and autoimmune inflammatory diseases. In this context, we generated monovalent antihuman IL23 variable heavy chain domain of llama heavy chain antibody (V _HH ) domains (Nanobodies ^® ) with low nanomolar affinity for human interleukin (hIL) 23. The crystal structure of a quaternary complex assembling hIL23 and several nanobodies against p19 and p40 subunits allowed identification of distinct epitopes and enabled rational design of a multivalent IL23-specific blocking nanobody. Taking advantage of the ease of nanobody formatting, multivalent IL23 nanobodies were assembled with properly designed linkers flanking an antihuman serum albumin nanobody, with improved hIL23 neutralization capacity in vitro and in vivo , as compared to the monovalent nanobodies. These constructs with long exposure time are excellent candidates for further developments targeting Crohn's disease, rheumatoid arthritis, and psoriasis.

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Organizational Affiliation: 

Ablynx N.V., Ghent, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-23 subunit alpha	A, C	189	Homo sapiens	Mutation(s): 0  Gene Names: IL23 p19, IL23A, SGRF, UNQ2498/PRO5798
Find proteins for Q9NPF7 (Homo sapiens) Explore Q9NPF7  Go to UniProtKB:  Q9NPF7
NIH Common Fund Data Resources
PHAROS  Q9NPF7 GTEx  ENSG00000110944

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-12 subunit beta	B, D	328	Homo sapiens	Mutation(s): 0  Gene Names: IL12 p40, IL12B, NKSF2
Find proteins for P29460 (Homo sapiens) Explore P29460  Go to UniProtKB:  P29460
NIH Common Fund Data Resources
PHAROS  P29460 GTEx  ENSG00000113302

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 124C4	E, G	125	Lama glama	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 37D5	F, J	126	Lama glama	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 22E11	H, I	123	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L	5		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.218 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.27	α = 90
b = 135.14	β = 90
c = 139.01	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-27 
• Released Date: 2014-02-19 
Deposition Author(s): Desmyter, A., Spinelli, S., Button, C., Saunders, M., de Haard, H., Rommelaere, H., Union, A., Cambillau, C.

Revision History 

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary