[English] 日本語
Yorodumi
- EMDB-60321: 3D structure of Y-50 TCR-TMM-CD1b ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60321
Title3D structure of Y-50 TCR-TMM-CD1b ternary complex
Map data
Sample
  • Complex: Ternary complex of Y-50TCR,TMM and CD1b
    • Protein or peptide: T-cell surface glycoprotein CD1b
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Y-50 TCR alpha
    • Protein or peptide: Y-50 TCR beta
  • Ligand: TETRACOSYL PALMITATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-glucopyranose
  • Ligand: [(2R,3S,4S,5R,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl (2R,3R)-3-oxidanyl-2-tetradecyl-octadecanoate
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / MHC class II protein complex / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...MHC-I family domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD1b / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsAsa M / Hirose M / Nagae M / Yamasaki S / Kato T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J Clin Invest / Year: 2024
Title: A conserved human CD4+ T cell subset recognizing the mycobacterial adjuvant, trehalose monomycolate.
Authors: Yuki Sakai / Minori Asa / Mika Hirose / Wakana Kusuhara / Nagatoshi Fujiwara / Hiroto Tamashima / Takahiro Ikazaki / Shiori Oka / Kota Kuraba / Kentaro Tanaka / Takashi Yoshiyama / Masamichi ...Authors: Yuki Sakai / Minori Asa / Mika Hirose / Wakana Kusuhara / Nagatoshi Fujiwara / Hiroto Tamashima / Takahiro Ikazaki / Shiori Oka / Kota Kuraba / Kentaro Tanaka / Takashi Yoshiyama / Masamichi Nagae / Yoshihiko Hoshino / Daisuke Motooka / Ildiko Van Rhijn / Xiuyuan Lu / Eri Ishikawa / D Branch Moody / Takayuki Kato / Shinsuke Inuki / Go Hirai / Sho Yamasaki /
Abstract: Mycobacterium tuberculosis causes human tuberculosis. As mycobacteria are protected by thick lipid cell wall, humans have developed immune responses against diverse mycobacterial lipids. Most of ...Mycobacterium tuberculosis causes human tuberculosis. As mycobacteria are protected by thick lipid cell wall, humans have developed immune responses against diverse mycobacterial lipids. Most of these immunostimulatory lipids are known as adjuvants acting through innate immune receptors, such as C-type lectin receptors. Although a few mycobacterial lipid antigens activate unconventional T cells, antigenicity of most adjuvantic lipids are unknown. Here, we identified that trehalose monomycolate (TMM), an abundant mycobacterial adjuvant, activates human T cells bearing a unique ɑβTCR. This recognition was restricted by CD1b, a monomorphic antigen-presenting molecule conserved in primates but not mice. Single-cell TCR-RNA sequencing using newly established CD1b-TMM tetramers revealed that TMM-specific T cells are present as CD4+ effector memory T cells in the periphery of uninfected donors, but express IFNγ, TNF and anti-mycobacterial effectors upon TMM stimulation. TMM-specific T cells are detected in cord blood and PBMCs of non-BCG-vaccinated donors, but are expanded in active tuberculosis patients. A cryo-electron microscopy study of CD1b-TMM-TCR complexes revealed unique antigen recognition by conserved features of TCRs, positively-charged CDR3ɑ and long CDR3β regions. These results indicate that humans have a commonly-shared and pre-formed CD4+ T cell subset recognizing a typical mycobacterial adjuvant as an antigen. Furthermore, the dual role of TMM justifies reconsideration of the mechanism of action of adjuvants.
History
DepositionMay 29, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60321.png

Downloads & links

-
Map

FileDownload / File: emd_60321.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 416 pix.
= 280.8 Å		0.68 Å/pix.
x 416 pix.
= 280.8 Å		0.68 Å/pix.
x 416 pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0271
Minimum - Maximum-0.0382163 - 0.10486379
Average (Standard dev.)0.000102282545 (±0.0022700957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 280.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_60321_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60321_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of Y-50TCR,TMM and CD1b

EntireName: Ternary complex of Y-50TCR,TMM and CD1b
Components
  • Complex: Ternary complex of Y-50TCR,TMM and CD1b
    • Protein or peptide: T-cell surface glycoprotein CD1b
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Y-50 TCR alpha
    • Protein or peptide: Y-50 TCR beta
  • Ligand: TETRACOSYL PALMITATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-glucopyranose
  • Ligand: [(2R,3S,4S,5R,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl (2R,3R)-3-oxidanyl-2-tetradecyl-octadecanoate

-
Supramolecule #1: Ternary complex of Y-50TCR,TMM and CD1b

SupramoleculeName: Ternary complex of Y-50TCR,TMM and CD1b / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: T-cell surface glycoprotein CD1b

MacromoleculeName: T-cell surface glycoprotein CD1b / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.00599 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASEHAFQGP TSFHVIQTSS FTNSTWAQTQ GSGWLDDLQI HGWDSDSGTA IFLKPWSKGN FSDKEVAELE EIFRVYIFGF AREVQDFAG DFQMKYPFEI QGIAGCELHS GGAIVSFLRG ALGGLDFLSV KNASCVPSPE GGSRAQKFCA LIIQYQGIME T VRILLYET ...String:
MASEHAFQGP TSFHVIQTSS FTNSTWAQTQ GSGWLDDLQI HGWDSDSGTA IFLKPWSKGN FSDKEVAELE EIFRVYIFGF AREVQDFAG DFQMKYPFEI QGIAGCELHS GGAIVSFLRG ALGGLDFLSV KNASCVPSPE GGSRAQKFCA LIIQYQGIME T VRILLYET CPRYLLGVLN AGKADLQRQV KPEAWLSSGP SPGPGRLQLV CHVSGFYPKP VWVMWMRGEQ EQQGTQLGDI LP NANWTWY LRATLDVADG EAAGLSCRVK HSSLEGQDII LYW

UniProtKB: T-cell surface glycoprotein CD1b

-
Macromolecule #2: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.879356 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLS QPKIVKWDRD M

UniProtKB: Beta-2-microglobulin

-
Macromolecule #3: Y-50 TCR alpha

MacromoleculeName: Y-50 TCR alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.14266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AQKITQTQPG MFVQEKEAVT LDCTYDTSDQ SYGLFWYKQP SSGEMIFLIY QGSYDEQNAT EGRYSLNFQK ARKSANLVIS ASQLGDSAM YFCAMRRNTG RRALTFGSGT RLQVQPNIQN PDPAVYQLRD SKSSDKFVCL FTDFDSQINV SQSKDSDVYI T DKCVLDMR ...String:
AQKITQTQPG MFVQEKEAVT LDCTYDTSDQ SYGLFWYKQP SSGEMIFLIY QGSYDEQNAT EGRYSLNFQK ARKSANLVIS ASQLGDSAM YFCAMRRNTG RRALTFGSGT RLQVQPNIQN PDPAVYQLRD SKSSDKFVCL FTDFDSQINV SQSKDSDVYI T DKCVLDMR SMDFKSNSAV AWSNKSDFTC ANAFNNSIIP EDTFFPS

-
Macromolecule #4: Y-50 TCR beta

MacromoleculeName: Y-50 TCR beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.191834 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DTEVTQTPKH LVMGMTNKKS LKCEQHMGHR AMYWYKQKAK KPPELMFVYS YEKLSINESV PSRFSPECPN SSLLNLHLHA LQPEDSALY LCASSHLGLA GGIDGTDTQY FGPGTRLTVL EDLKNVFPPE VAVFEPSKAE ISRTQKATLV CLATGFYPPH V ELSWWVNG ...String:
DTEVTQTPKH LVMGMTNKKS LKCEQHMGHR AMYWYKQKAK KPPELMFVYS YEKLSINESV PSRFSPECPN SSLLNLHLHA LQPEDSALY LCASSHLGLA GGIDGTDTQY FGPGTRLTVL EDLKNVFPPE VAVFEPSKAE ISRTQKATLV CLATGFYPPH V ELSWWVNG KEVHDGVCTD PQPLKEQPAL NDSRYALSSR LRVSATFWQD PRNHFRCQVQ FYGLSENDEW TQDRAKPVTQ IV SAEAWGR AD

-
Macromolecule #5: TETRACOSYL PALMITATE

MacromoleculeName: TETRACOSYL PALMITATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: 6UL
Molecular weightTheoretical: 593.062 Da
Chemical component information

ChemComp-6UL:
TETRACOSYL PALMITATE

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #7: alpha-D-glucopyranose

MacromoleculeName: alpha-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: GLC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GLC:
alpha-D-glucopyranose

-
Macromolecule #8: [(2R,3S,4S,5R,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl (2R,...

MacromoleculeName: [(2R,3S,4S,5R,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl (2R,3R)-3-oxidanyl-2-tetradecyl-octadecanoate
type: ligand / ID: 8 / Number of copies: 1 / Formula: A1L2B
Molecular weightTheoretical: 658.989 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.2 K / Max: 78.2 K
Specialist opticsSpherical aberration corrector: CEOS corrector was used. / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 8533 / Average exposure time: 3.169 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.036 µm / Calibrated defocus min: 0.521 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.06 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4075153
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.41) / Number images used: 114111
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.41)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.41)

-
Atomic model buiding 1

Initial modelPDB ID:

8xub


Chain - Chain ID: D / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8zox:
3D structure of Y-50 TCR-TMM-CD1b ternary complex

+
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