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

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

PubMed: 41587986 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-67745-x
Primary Citation 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.

Department of Hygiene and Public Health, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.

Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan.

Department of Comprehensive Pathology, Institute of Science Tokyo, Tokyo, Japan.

Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan.

Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan.

Department of Hematology, Toranomon Hospital, Tokyo, Japan.

Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan.

Department of Stem Cell Biology, National Institute of Global Health and Medicine, Japan Institute for Health Security (JIHS), Tokyo, Japan.

Drug Discovery Structural Biology Platform Unit, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan.

Department of Obstetrics and Gynecology, Nippon Medical School, Tokyo, Japan.

Department of Microbiology and Immunology, Nippon Medical School, Tokyo, Japan.

Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan.

Department of Cell Fate Biology and Stem Cell Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.

Hamanomachi Hospital, Fukuoka, Japan.

Functional Genomics, Genomics Research Center, Human Technopole, Milan, Italy.

The Jackson Laboratory, Bar Harbor, ME, USA.

Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan.

Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, Republic of Singapore.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Dr, Singapore, Republic of Singapore.

Laboratory for Human Disease Models, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan. fumihiko.ishikawa@riken.jp.

Department of Comprehensive Pathology, Institute of Science Tokyo, Tokyo, Japan. fumihiko.ishikawa@riken.jp.

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01589
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14784
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B	Go to GlyGen: P14784-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31785
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C	Go to GlyGen: P31785-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60568
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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

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| 3D Structure

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

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, K	2		N-Glycosylation	Interactions Focus chain J Focus chain K Interactions & Density Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]