7OX3

Fab 6D3: hIL-9 complex

• PDB DOI: https://doi.org/10.2210/pdb7OX3/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-22 Released: 2022-12-28 
• Deposition Author(s): De Vos, T., Savvides, S.N.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Models: experimental

Literature

Structural basis for the mechanism and antagonism of receptor signaling mediated by Interleukin-9 (IL-9)

De Vos, T., Godar, M., Bick, F., Papageorgiou, A.C., Evangelidis, T., Markovic, I., Mortier, E., Dumoutier, L., Tripsianes, K., Blanchetot, C., Savvides, S.N.

(2022) bioRxiv 

• DOI: https://doi.org/10.1101/2022.12.30.522308

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 61.44 kDa 
• Atom Count: 4,566 
• Modelled Residue Count: 543 
• Deposited Residue Count: 567 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain (Fab 6D3)	A [auth B]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain (Fab 6D3)	B [auth A]	223	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-9	C	130	Homo sapiens	Mutation(s): 0  Gene Names: IL9
UniProt & NIH Common Fund Data Resources
Find proteins for P15248 (Homo sapiens) Explore P15248  Go to UniProtKB:  P15248
PHAROS:  P15248 GTEx:  ENSG00000145839

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth B], E [auth C], F [auth C], G [auth C], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.48	α = 90
b = 81.86	β = 90
c = 116.54	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): De Vos, T., Savvides, S.N.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1S56318N

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2023-01-11
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary