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

Structural insight into interleukin-4R alpha and interleukin-5 inhibition by nanobodies from a bispecific antibody.

Qiu, W., Meng, J., Su, Z., Xie, W., Song, G.

(2024) MedComm (2020) 5: e700-e700

• PubMed: 39252822 
• DOI: https://doi.org/10.1002/mco2.700
• Primary Citation Related Structures: 
  8Z8L

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Organizational Affiliation: 
• Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences East China Normal University Shanghai China.
The Thoth Institutes for Health Research, RegeneCore Biotech Co., Ltd Nanjing China.
The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education and The School of Life Science and Technology Southeast University Nanjing China.

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	D 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
  
• Version 1.1: 2026-05-13
  Changes: Database references