9KMC | pdb_00009kmc

Cryo-EM structure of the heterotrimeric interleukin-2 receptor in complex with interleukin-2 and anti-CD25 Fab S417

• PDB DOI: https://doi.org/10.2210/pdb9KMC/pdb
• EM Map EMD-62427: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens, Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-15 Released: 2025-11-19 
• Deposition Author(s): Katsura, K., Matsumoto, T., Shirouzu, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CXCR4 induces memory formation over exhaustion in CAR-T cells to achieve durable leukemia targeting

Itoh-Nakadai, A., Liang, M., Ishikawa, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 146.78 kDa 
• Atom Count: 8,935 
• Modeled Residue Count: 1,102 
• Deposited Residue Count: 1,277 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2 receptor subunit alpha	A	240	Homo sapiens	Mutation(s): 0  Gene Names: IL2RA
UniProt & NIH Common Fund Data Resources
Find proteins for P01589 (Homo sapiens) Explore P01589  Go to UniProtKB:  P01589
PHAROS:  P01589 GTEx:  ENSG00000134460

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2 receptor subunit beta	B	222	Homo sapiens	Mutation(s): 0  Gene Names: IL2RB, IL15RB
UniProt & NIH Common Fund Data Resources
Find proteins for P14784 (Homo sapiens) Explore P14784  Go to UniProtKB:  P14784
PHAROS:  P14784 GTEx:  ENSG00000100385
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P14784-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokine receptor common subunit gamma	C	241	Homo sapiens	Mutation(s): 0  Gene Names: IL2RG
UniProt & NIH Common Fund Data Resources
Find proteins for P31785 (Homo sapiens) Explore P31785  Go to UniProtKB:  P31785
PHAROS:  P31785 GTEx:  ENSG00000147168
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P31785-1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2	D	133	Homo sapiens	Mutation(s): 0  Gene Names: IL2
UniProt & NIH Common Fund Data Resources
Find proteins for P60568 (Homo sapiens) Explore P60568  Go to UniProtKB:  P60568
PHAROS:  P60568 GTEx:  ENSG00000109471

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab S417 heavy chain	E	228	synthetic construct	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab S417 light chain	F	213	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K	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	L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.97 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Katsura, K., Matsumoto, T., Shirouzu, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release