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- EMDB-62427: Cryo-EM structure of the heterotrimeric interleukin-2 receptor in... -

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Entry
Database: EMDB / ID: EMD-62427
TitleCryo-EM structure of the heterotrimeric interleukin-2 receptor in complex with interleukin-2 and anti-CD25 Fab S417
Map data
Sample
  • Complex: Heterotrimeric interleukin-2 receptor in complex with interleukin-2 and Fab S417
    • Complex: Interleukin-2 receptor subunit alpha
      • Protein or peptide: Interleukin-2 receptor subunit alpha
    • Complex: Interleukin-2 receptor subunit beta
      • Protein or peptide: Interleukin-2 receptor subunit beta
    • Complex: Cytokine receptor common subunit gamma
      • Protein or peptide: Cytokine receptor common subunit gamma
    • Complex: Interleukin-2
      • Protein or peptide: Interleukin-2
    • Complex: Fab S417
      • Protein or peptide: Fab S417 heavy chain
      • Protein or peptide: Fab S417 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCYTOKINE / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of T cell tolerance induction / mature B cell differentiation / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / response to tacrolimus / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation ...regulation of T cell tolerance induction / mature B cell differentiation / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / response to tacrolimus / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of lymphocyte proliferation / activation-induced cell death of T cells / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / positive regulation of T cell differentiation in thymus / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / lymphocyte differentiation / Interleukin-9 signaling / Interleukin-21 signaling / leukocyte activation involved in immune response / interleukin-7-mediated signaling pathway / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / positive regulation of isotype switching to IgG isotypes / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15-mediated signaling pathway / inflammatory response to antigenic stimulus / activated T cell proliferation / cellular homeostasis / Interleukin-15 signaling / STAT3 nuclear events downstream of ALK signaling / cytokine receptor activity / cell surface receptor signaling pathway via STAT / Interleukin-2 signaling / natural killer cell activation / kinase activator activity / positive regulation of activated T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of B cell differentiation / positive regulation of T cell differentiation / positive regulation of immunoglobulin production / interleukin-2-mediated signaling pathway / cytokine binding / positive regulation of dendritic spine development / positive regulation of interleukin-17 production / immunoglobulin mediated immune response / T cell differentiation / Interleukin receptor SHC signaling / coreceptor activity / negative regulation of T cell proliferation / positive regulation of B cell proliferation / Notch signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / Interleukin-7 signaling / positive regulation of phagocytosis / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / cytokine-mediated signaling pathway / positive regulation of inflammatory response / T cell differentiation in thymus / cell-cell signaling / carbohydrate binding / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / gene expression / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription by RNA polymerase II / response to ethanol / adaptive immune response / cell surface receptor signaling pathway / signaling receptor complex / cell adhesion / endosome / immune response / inflammatory response / external side of plasma membrane / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / : / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Interleukin-2 receptor alpha / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 ...Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Interleukin-2 receptor alpha / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Four-helical cytokine-like, core / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-2 receptor subunit alpha / Interleukin-2 receptor subunit beta / Cytokine receptor common subunit gamma / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human) / sythetic construct (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsKatsura K / Matsumoto T / Shirouzu M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: CXCR4 induces memory formation over exhaustion in CAR-T cells to achieve durable leukemia targeting.
Authors: Ari Itoh-Nakadai / Minggao Liang / Michiho Shindo / Chen Bibi / Mariko Tomizawa-Murasawa / Saera Fujiki / Akiko Kaneko / Emi Kanamaru / Mari Hashimoto / Hiroshi Kajita / Yoshinari Ando / ...Authors: Ari Itoh-Nakadai / Minggao Liang / Michiho Shindo / Chen Bibi / Mariko Tomizawa-Murasawa / Saera Fujiki / Akiko Kaneko / Emi Kanamaru / Mari Hashimoto / Hiroshi Kajita / Yoshinari Ando / Miki Kojima / Jonathan Moody / Makoto Iwasaki / Shinsuke Takagi / Ryo Nakagawa / Saumya Agrawal / Hanae Amitani-Iijima / Kaori Sato / Yuriko Sorimachi / Nahoko Suzuki / Takehiro Fukami / Kazuharu Hanada / Satoshi Morita / Kazushige Katsura / Takehisa Matsumoto / Maiko Kobayashi / Masahiko Kato / Yasuyuki Negishi / Mikako Shirouzu / Yuho Najima / Keiyo Takubo / Chung Chau Hon / Naoyuki Uchida / Shuichi Taniguchi / Yukihide Momozawa / Piero Carninci / Leonard D Shultz / Yoriko Saito / Michiel de Hoon / Jay W Shin / Fumihiko Ishikawa /
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 ...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.
History
DepositionNov 15, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62427.png

Downloads & links

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Map

FileDownload / File: emd_62427.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 380 pix.
= 314.83 Å		0.83 Å/pix.
x 380 pix.
= 314.83 Å		0.83 Å/pix.
x 380 pix.
= 314.83 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-3.6250217 - 4.878181
Average (Standard dev.)0.000000000000098 (±0.05864429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 314.83 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62427_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_62427_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62427_half_map_2.map
Projections & Slices
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Sample components

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Entire : Heterotrimeric interleukin-2 receptor in complex with interleukin...

EntireName: Heterotrimeric interleukin-2 receptor in complex with interleukin-2 and Fab S417
Components
  • Complex: Heterotrimeric interleukin-2 receptor in complex with interleukin-2 and Fab S417
    • Complex: Interleukin-2 receptor subunit alpha
      • Protein or peptide: Interleukin-2 receptor subunit alpha
    • Complex: Interleukin-2 receptor subunit beta
      • Protein or peptide: Interleukin-2 receptor subunit beta
    • Complex: Cytokine receptor common subunit gamma
      • Protein or peptide: Cytokine receptor common subunit gamma
    • Complex: Interleukin-2
      • Protein or peptide: Interleukin-2
    • Complex: Fab S417
      • Protein or peptide: Fab S417 heavy chain
      • Protein or peptide: Fab S417 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Heterotrimeric interleukin-2 receptor in complex with interleukin...

SupramoleculeName: Heterotrimeric interleukin-2 receptor in complex with interleukin-2 and Fab S417
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Interleukin-2 receptor subunit alpha

SupramoleculeName: Interleukin-2 receptor subunit alpha / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Interleukin-2 receptor subunit beta

SupramoleculeName: Interleukin-2 receptor subunit beta / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Cytokine receptor common subunit gamma

SupramoleculeName: Cytokine receptor common subunit gamma / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Interleukin-2

SupramoleculeName: Interleukin-2 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Fab S417

SupramoleculeName: Fab S417 / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: sythetic construct (others)

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Macromolecule #1: Interleukin-2 receptor subunit alpha

MacromoleculeName: Interleukin-2 receptor subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.625502 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELCDDDPPEI PHATFKAMAY KEGTMLNCEC KRGFRRIKSG SLYMLCTGNS SHSSWDNQCQ CTSSATRNTT KQVTPQPEEQ KERKTTEMQ SPMQPVDQAS LPGHCREPPP WENEATERIY HFVVGQMVYY QCVQGYRALH RGPAESVCKM THGKTRWTQP Q LICTGEME ...String:
ELCDDDPPEI PHATFKAMAY KEGTMLNCEC KRGFRRIKSG SLYMLCTGNS SHSSWDNQCQ CTSSATRNTT KQVTPQPEEQ KERKTTEMQ SPMQPVDQAS LPGHCREPPP WENEATERIY HFVVGQMVYY QCVQGYRALH RGPAESVCKM THGKTRWTQP Q LICTGEME TSQFPGEEKP QASPEGRPES ETSCLVTTTD FQIQTEMAAT METSIFTTEY QGGGGSGGGG SGGGGSHHHH HH

UniProtKB: Interleukin-2 receptor subunit alpha

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Macromolecule #2: Interleukin-2 receptor subunit beta

MacromoleculeName: Interleukin-2 receptor subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.824219 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: AVNGTSQFTC FYNSRANISC VWSQDGALQD TSCQVHAWPD RRRWNQTCEL LPVSQASWAC NLILGAPDSQ KLTTVDIVTL RVLCREGVR WRVMAIQDFK PFENLRLMAP ISLQVVHVET HRCNISWEIS QASHYFERHL EFEARTLSPG HTWEEAPLLT L KQKQEWIC ...String:
AVNGTSQFTC FYNSRANISC VWSQDGALQD TSCQVHAWPD RRRWNQTCEL LPVSQASWAC NLILGAPDSQ KLTTVDIVTL RVLCREGVR WRVMAIQDFK PFENLRLMAP ISLQVVHVET HRCNISWEIS QASHYFERHL EFEARTLSPG HTWEEAPLLT L KQKQEWIC LETLTPDTQY EFQVRVKPLQ GEFTTWSPWS QPLAFRTKPA ALGKDTHHHH HHHH

UniProtKB: Interleukin-2 receptor subunit beta

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Macromolecule #3: Cytokine receptor common subunit gamma

MacromoleculeName: Cytokine receptor common subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.628816 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: LNTTILTPNG NEDTTADFFL TTMPTDSLSV STLPLPEVQC FVFNVEYMNC TWQSSSEPQP TNLTLHYWYK NSDNDKVQKC SHYLFSEEI TSGCQLQKKE IHLYQTFVVQ LQDPREPRRQ ATQMLKLQNL VIPWAPENLT LHKLSESQLE LNWNNRFLNH C LEHLVQYR ...String:
LNTTILTPNG NEDTTADFFL TTMPTDSLSV STLPLPEVQC FVFNVEYMNC TWQSSSEPQP TNLTLHYWYK NSDNDKVQKC SHYLFSEEI TSGCQLQKKE IHLYQTFVVQ LQDPREPRRQ ATQMLKLQNL VIPWAPENLT LHKLSESQLE LNWNNRFLNH C LEHLVQYR TDWDHSWTEQ SVDYRHKFSL PSVDGQKRYT FRVRSRFNPL CGSAQHWSEW SHPIHWGSNT SKENPHHHHH HH H

UniProtKB: Cytokine receptor common subunit gamma

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Macromolecule #4: Interleukin-2

MacromoleculeName: Interleukin-2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.435979 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
APTSSSTKKT QLQLEHLLLD LQMILNGINN YKNPKLTRML TFKFYMPKKA TELKHLQCLE EELKPLEEVL NLAQSKNFHL RPRDLISNI NVIVLELKGS ETTFMCEYAD ETATIVEFLN RWITFCQSII STLT

UniProtKB: Interleukin-2

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Macromolecule #5: Fab S417 heavy chain

MacromoleculeName: Fab S417 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.459379 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLHQSGDD LVKPGASVKL SCRASGYTFT SYWINWVKQR PGQGLEWIGR ILPGTNSIYY SEIFKGKASL TVDTSSNTAY IQLSSLSSE DSAVYFCARL LWNKGAMDYW GQGTSVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
QVQLHQSGDD LVKPGASVKL SCRASGYTFT SYWINWVKQR PGQGLEWIGR ILPGTNSIYY SEIFKGKASL TVDTSSNTAY IQLSSLSSE DSAVYFCARL LWNKGAMDYW GQGTSVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKAE PKSCENLYFQ

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Macromolecule #6: Fab S417 light chain

MacromoleculeName: Fab S417 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.004434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIVLSQSPVI LSASPGEKVT MTCRASSGVS SIHWYQQQPG SSPKPWIYDT SSLASGVPAR FSGSGSGTSY SLTISRVEAE DAATYYCQQ WSSNPPTFGA GTKLELKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
QIVLSQSPVI LSASPGEKVT MTCRASSGVS SIHWYQQQPG SSPKPWIYDT SSLASGVPAR FSGSGSGTSY SLTISRVEAE DAATYYCQQ WSSNPPTFGA GTKLELKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 353002
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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