[English] 日本語
Yorodumi
- EMDB-62427: Cryo-EM structure of the heterotrimeric interleukin-2 receptor in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / interleukin-2 receptor complex / interleukin-2 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation ...regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / activation-induced cell death of T cells / negative regulation of T-helper 17 cell differentiation / positive regulation of T cell differentiation in thymus / lymphocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / leukocyte activation involved in immune response / 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-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / activated T cell proliferation / inflammatory response to antigenic stimulus / cellular homeostasis / STAT3 nuclear events downstream of ALK signaling / Interleukin-15 signaling / cytokine receptor activity / cell surface receptor signaling pathway via STAT / Interleukin-2 signaling / kinase activator activity / natural killer cell activation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / positive regulation of T cell differentiation / cytokine binding / positive regulation of dendritic spine development / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / immunoglobulin mediated immune response / T cell differentiation / Interleukin receptor SHC signaling / coreceptor activity / negative regulation of T cell proliferation / Notch signaling pathway / positive regulation of B cell proliferation / 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 / cell-cell signaling / T cell differentiation in thymus / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / RAF/MAP kinase cascade / positive regulation of cell growth / protein-containing complex assembly / response to ethanol / Interleukin-4 and Interleukin-13 signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / adaptive immune response / transcription by RNA polymerase II / cell surface receptor signaling pathway / receptor complex / cell adhesion / endosome / immune response / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / apoptotic process / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / 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: To Be Published
Title: CXCR4 induces memory formation over exhaustion in CAR-T cells to achieve durable leukemia targeting
Authors: Itoh-Nakadai A / Liang M / Ishikawa F
History
DepositionNov 15, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62427.png

Downloads & links

-
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
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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 °

-
Supplemental data

-
Mask #1

Fileemd_62427_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62427_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62427_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
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

+
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

+
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)

+
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)

+
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)

+
Supramolecule #5: Interleukin-2

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

+
Supramolecule #6: Fab S417

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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more