8Z8L | pdb_00008z8l

structure of IL-4Ra in complex with an nanobody 4E9

• PDB DOI: https://doi.org/10.2210/pdb8Z8L/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens, Vicugna pacos
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-04-22 Released: 2025-04-30 
• Deposition Author(s): Song, G., Qiu, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.96 Å
• R-Value Free: 
  0.334 (Depositor), 0.335 (DCC) 
• R-Value Work: 
  0.301 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.303 (Depositor) 

Starting Model: experimental

Literature

structure of IL-4Ra in complex with an nanobody 4E9

Song, G., Qiu, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.79 kDa 
• Atom Count: 2,380 
• Modeled Residue Count: 303 
• Deposited Residue Count: 338 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-4 receptor subunit alpha	A [auth B]	214	Homo sapiens	Mutation(s): 1  Gene Names: IL4R, IL4RA, 582J2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P24394 (Homo sapiens) Explore P24394  Go to UniProtKB:  P24394
PHAROS:  P24394 GTEx:  ENSG00000077238
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P24394-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody dAb1	B [auth A]	124	Vicugna pacos	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.96 Å
• R-Value Free:  0.334 (Depositor), 0.335 (DCC) 
• R-Value Work:  0.301 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.303 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.936	α = 90
b = 142.936	β = 90
c = 149.087	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Song, G., Qiu, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release