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- EMDB-13427: Structure of a fully assembled T-cell receptor engaging a tumor-a... -

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Entry
Database: EMDB / ID: EMD-13427
TitleStructure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
Map data
Sample
  • Complex: Fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
    • Protein or peptide: T-cell receptor alpha chain
    • Protein or peptide: T-cell receptor beta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain, green fluorescent protein
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: HLA class I histocompatibility antigen, A alpha chain
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Tumor-associated antigentic peptide gp100
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / cis-Golgi network membrane / positive regulation of melanin biosynthetic process / Fc-gamma receptor signaling pathway / CD4-positive, alpha-beta T cell proliferation ...regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / cis-Golgi network membrane / positive regulation of melanin biosynthetic process / Fc-gamma receptor signaling pathway / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / melanin biosynthetic process / melanosome membrane / multivesicular body, internal vesicle / melanosome organization / positive regulation of CD4-positive, alpha-beta T cell proliferation / multivesicular body membrane / alpha-beta T cell receptor complex / positive regulation of protein localization to cell surface / positive thymic T cell selection / signal complex assembly / Nef and signal transduction / positive regulation of cell-matrix adhesion / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / TAP complex binding / smoothened signaling pathway / establishment or maintenance of cell polarity / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / CD8 receptor binding / dendrite development / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Generation of second messenger molecules / immunological synapse / TAP binding / FCGR activation / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / Role of phospholipids in phagocytosis / beta-2-microglobulin binding / positive regulation of calcium-mediated signaling / T cell receptor binding / negative regulation of smoothened signaling pathway / detection of bacterium / positive regulation of T cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / positive regulation of interleukin-2 production / T cell activation / bioluminescence / cerebellum development / FCGR3A-mediated IL10 synthesis / protein tyrosine kinase binding / 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 / DAP12 interactions / negative regulation of receptor binding / generation of precursor metabolites and energy / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / calcium-mediated signaling / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / apoptotic signaling pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCGR3A-mediated phagocytosis / cellular response to iron(III) ion / clathrin-coated endocytic vesicle membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / Regulation of actin dynamics for phagocytic cup formation / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / SH3 domain binding
Similarity search - Function
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain ...PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 CD3 delta chain / HLA class I histocompatibility antigen, A alpha chain / T-cell surface glycoprotein CD3 epsilon chain / T-cell surface glycoprotein CD3 gamma chain / T-cell surface glycoprotein CD3 zeta chain / Melanocyte protein PMEL / Green fluorescent protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsSusac L / Thomas C / Tampe R
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC 807/P16 No. 57566863 Germany
German Research Foundation (DFG)TA157/12-1 Germany
European Research Council (ERC)Advanced Grant No. 789121 Germany
Wellcome Trust207547/Z/17/Z Germany
CitationJournal: Cell / Year: 2022
Title: Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC.
Authors: Lukas Sušac / Mai T Vuong / Christoph Thomas / Sören von Bülow / Caitlin O'Brien-Ball / Ana Mafalda Santos / Ricardo A Fernandes / Gerhard Hummer / Robert Tampé / Simon J Davis /
Abstract: The T cell receptor (TCR) expressed by T lymphocytes initiates protective immune responses to pathogens and tumors. To explore the structural basis of how TCR signaling is initiated when the ...The T cell receptor (TCR) expressed by T lymphocytes initiates protective immune responses to pathogens and tumors. To explore the structural basis of how TCR signaling is initiated when the receptor binds to peptide-loaded major histocompatibility complex (pMHC) molecules, we used cryogenic electron microscopy to determine the structure of a tumor-reactive TCRαβ/CD3δγεζ complex bound to a melanoma-specific human class I pMHC at 3.08 Å resolution. The antigen-bound complex comprises 11 subunits stabilized by multivalent interactions across three structural layers, with clustered membrane-proximal cystines stabilizing the CD3-εδ and CD3-εγ heterodimers. Extra density sandwiched between transmembrane helices reveals the involvement of sterol lipids in TCR assembly. The geometry of the pMHC/TCR complex suggests that efficient TCR scanning of pMHC requires accurate pre-positioning of T cell and antigen-presenting cell membranes. Comparisons of the ligand-bound and unliganded receptors, along with molecular dynamics simulations, indicate that TCRs can be triggered in the absence of spontaneous structural rearrangements.
History
DepositionAug 18, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13427.png

Downloads & links

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Map

FileDownload / File: emd_13427.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.8961347 - 2.7815263
Average (Standard dev.)2.5879719e-05 (±0.034666993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Fully assembled T-cell receptor engaging a tumor-associated pepti...

EntireName: Fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
Components
  • Complex: Fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
    • Protein or peptide: T-cell receptor alpha chain
    • Protein or peptide: T-cell receptor beta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain, green fluorescent protein
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: HLA class I histocompatibility antigen, A alpha chain
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Tumor-associated antigentic peptide gp100
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Fully assembled T-cell receptor engaging a tumor-associated pepti...

SupramoleculeName: Fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: T-cell receptor alpha chain

MacromoleculeName: T-cell receptor alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.979268 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MSQQGEEDPQ ALSIQEGENA TMNCSYKTSI NNLQWYRQNS GRGLVHLILI RSNEREKHSG RLRVTLDTSK KSSSLLITAS RAADTASYF CATDGSTPMQ FGKGTRLSVI PNIQNPDPAV YQLRDSKSSD KSVCLFTDFD SQTNVSQSKD SDVYITDKTV L DMRSMDFK ...String:
MSQQGEEDPQ ALSIQEGENA TMNCSYKTSI NNLQWYRQNS GRGLVHLILI RSNEREKHSG RLRVTLDTSK KSSSLLITAS RAADTASYF CATDGSTPMQ FGKGTRLSVI PNIQNPDPAV YQLRDSKSSD KSVCLFTDFD SQTNVSQSKD SDVYITDKTV L DMRSMDFK SNSAVAWSNK SDFACANAFN NSIIPEDTFF PSPESSCDVK LVEKSFETDT NLNFQNLSVI GFRILLLKVA GF NLLMTLR LWSS

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Macromolecule #2: T-cell receptor beta chain

MacromoleculeName: T-cell receptor beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.750736 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDGGITQSPK YLFRKEGQNV TLSCEQNLNH DAMYWYRQDP GQGLRLIYYS WAQGDFQKGD IAEGYSVSRE KKESFPLTVT SAQKNPTAF YLCASSWGAP YEQYFGPGTR LTVTEDLNKV FPPEVAVFEP SEAEISHTQK ATLVCLATGF FPDHVELSWW V NGKEVHSG ...String:
MDGGITQSPK YLFRKEGQNV TLSCEQNLNH DAMYWYRQDP GQGLRLIYYS WAQGDFQKGD IAEGYSVSRE KKESFPLTVT SAQKNPTAF YLCASSWGAP YEQYFGPGTR LTVTEDLNKV FPPEVAVFEP SEAEISHTQK ATLVCLATGF FPDHVELSWW V NGKEVHSG VSTDPQPLKE QPALNDSRYC LSSRLRVSAT FWQNPRNHFR CQVQFYGLSE NDEWTQDRAK PVTQIVSAEA WG RADCGFT SVSYQQGVLS ATILYEILLG KATLYAVLVS ALVLMAMVKR KDF

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Macromolecule #3: T-cell surface glycoprotein CD3 gamma chain

MacromoleculeName: T-cell surface glycoprotein CD3 gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.713741 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSIKGNHLVK VYDYQEDGSV LLTCDAEAKN ITWFKDGKMI GFLTEDKKKW NLGSNAKDPR GMYQCKGSQN KSKPLQVYYR MCQNCIELN AATISGFLFA EIVSIFVLAV GVYFIAGQDG VRQ

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Macromolecule #4: T-cell surface glycoprotein CD3 delta chain, green fluorescent protein

MacromoleculeName: T-cell surface glycoprotein CD3 delta chain, green fluorescent protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 39.858188 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: FKIPIEELED RVFVNCNTSI TWVEGTVGTL LSDITRLDLG KRILDPRGIY RCNGTDIYKD KESTVQVHYR MCQSCVELDP ATVAGIIVT DVIATLLLAL GVFCFAGHET GRDPPVATMV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK L TLKFICTT ...String:
FKIPIEELED RVFVNCNTSI TWVEGTVGTL LSDITRLDLG KRILDPRGIY RCNGTDIYKD KESTVQVHYR MCQSCVELDP ATVAGIIVT DVIATLLLAL GVFCFAGHET GRDPPVATMV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK L TLKFICTT GKLPVPWPTL VTTLSYGVQC FSRYPDHMKQ HDFFKSAMPE GYVQERTIFF KDDGNYKTRA EVKFEGDTLV NR IELKGID FKEDGNILGH KLEYNYNSHN VYIMADKQKN GIKVNFKIRH NIEDGSVQLA DHYQQNTPIG DGPVLLPDNH YLS TQSALS KDPNEKRDHM VLLEFVTAAG ITLGMDELYK

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Macromolecule #5: T-cell surface glycoprotein CD3 epsilon chain

MacromoleculeName: T-cell surface glycoprotein CD3 epsilon chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.316222 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DGNEEMGGIT QTPYKVSISG TTVILTCPQY PGSEILWQHN DKNIGGDEDD KNIGSDEDHL SLKEFSELEQ SGYYVCYPRG SKPEDANFY LYLRARVCEN CMEMDVMSVA TIVIVDICIT GGLLLLVYYW SKNRKAK

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Macromolecule #6: HLA class I histocompatibility antigen, A alpha chain

MacromoleculeName: HLA class I histocompatibility antigen, A alpha chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.054613 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH GSGSHSMRYF FTSVSRPGRG EPRFIAVGYV DDTQFVRFDS DAASQRMEPR APWIEQEGPE YWDGETRKVK AHSQTHRVD LGTLRGYYNQ SEAGSHTVQR MYGCDVGSDW RFLRGYHQYA YDGKDYIALK EDLRSWTAAD MAAQTTKHKW E AAHVAEQL ...String:
MGSSHHHHHH GSGSHSMRYF FTSVSRPGRG EPRFIAVGYV DDTQFVRFDS DAASQRMEPR APWIEQEGPE YWDGETRKVK AHSQTHRVD LGTLRGYYNQ SEAGSHTVQR MYGCDVGSDW RFLRGYHQYA YDGKDYIALK EDLRSWTAAD MAAQTTKHKW E AAHVAEQL RAYLEGTCVE WLRRYLENGK ETLQRTDAPK THMTHHAVSD HEATLRCWAL SFYPAEITLT WQRDGEDQTQ DT ELVETRP AGDGTFQKWA AVVVPSGQEQ RYTCHVQHEG LPKPLTLRWE PSSQPEDQVD PRLIDGK

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Macromolecule #7: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.936408 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGIQRTPKIQ VYSRHPAENG KSNFLNCYVS GFHPSDIEVD LLKNGERIEK VEHSDLSFSK DWSFYLLYYT EFTPTEKDEY ACRVNHVTL SQPKIVKWDR DM

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Macromolecule #8: Tumor-associated antigentic peptide gp100

MacromoleculeName: Tumor-associated antigentic peptide gp100 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 974.107 Da
SequenceString:
YLEPGPVTV

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Macromolecule #9: T-cell surface glycoprotein CD3 zeta chain

MacromoleculeName: T-cell surface glycoprotein CD3 zeta chain / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.138015 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSFGLLDPKL CYLLDGILFI YGVILTALFL RVKFSR

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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: 6 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154408
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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