4GRW

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

• PDB DOI: https://doi.org/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 

Biological Assembly 1  

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  

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 kDa 
• Atom Count: 13,131 
• Modelled Residue Count: 1,587 
• Deposited Residue Count: 1,782 
• Unique protein chains: 5

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
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF7 (Homo sapiens) Explore Q9NPF7  Go to UniProtKB:  Q9NPF7
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
UniProt & NIH Common Fund Data Resources
Find proteins for P29460 (Homo sapiens) Explore P29460  Go to UniProtKB:  P29460
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	Length	2D Diagram	Glycosylation	3D Interactions
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
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

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

• 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
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2023-12-27
  Changes: Advisory, Derived calculations