9KMC | pdb_00009kmc

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

Itoh-Nakadai, A.Liang, M.Shindo, M.Bibi, C.Tomizawa-Murasawa, M.Fujiki, S.Kaneko, A.Kanamaru, E.Hashimoto, M.Kajita, H.Ando, Y.Kojima, M.Moody, J.Iwasaki, M.Takagi, S.Nakagawa, R.Agrawal, S.Amitani-Iijima, H.Sato, K.Sorimachi, Y.Suzuki, N.Fukami, T.Hanada, K.Morita, S.Katsura, K.Matsumoto, T.Kobayashi, M.Kato, M.Negishi, Y.Shirouzu, M.Najima, Y.Takubo, K.Hon, C.C.Uchida, N.Taniguchi, S.Momozawa, Y.Carninci, P.Shultz, L.D.Saito, Y.de Hoon, M.Shin, J.W.Ishikawa, F.

(2026) Nat Commun 17: 101-101

  • DOI: https://doi.org/10.1038/s41467-025-67745-x
  • Primary Citation of Related Structures:  
    9KMC

  • PubMed Abstract: 

    Chimeric antigen receptor (CAR)-T cell therapy has transformed the treatment of B-cell malignancies, but its success in acute myeloid leukemia (AML) remains limited. Durable responses depend on the formation of long-lived memory T cells, whereas T cell exhaustion contributes to non-response and relapse. In patients with AML who achieved remission after cord blood transplantation, we here first observe enrichment of memory T cells with high expression of the chemokine receptor CXCR4. Next, we show that engineering CAR-T cells to co-express CXCR4 enhances their persistence and anti-leukemic activity in patient-derived xenograft models. Using single-cell profiling and metabolic analysis, we find that CXCR4 promotes memory-associated transcriptional programs, reduces exhaustion, and supports oxidative metabolism. These effects are observed with CAR-T cells targeting CD25 or CD96 as AML-associated targets. Our results indicate that CXCR4 strengthens CAR-T cell memory and durability, offering a strategy to improve immunotherapy outcomes in AML and beyond.


  • Organizational Affiliation
    • Laboratory for Human Disease Models, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-2 receptor subunit alpha240Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01589
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-2 receptor subunit beta222Homo sapiensMutation(s): 0 
Gene Names: IL2RBIL15RB
UniProt & NIH Common Fund Data Resources
Find proteins for P14784 (Homo sapiens)
Explore P14784 
Go to UniProtKB:  P14784
PHAROS:  P14784
GTEx:  ENSG00000100385 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14784
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P14784-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytokine receptor common subunit gamma241Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31785
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P31785-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-2133Homo sapiensMutation(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 
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UniProt GroupP60568
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fab S417 heavy chain228synthetic constructMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Fab S417 light chain213synthetic constructMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, K
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
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:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2026-02-04
    Changes: Data collection, Database references
  • Version 1.2: 2026-02-18
    Changes: Data collection, Database references