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- EMDB-45615: T cell receptor complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45615
TitleT cell receptor complex
Map dataMain B-factor sharpened map
Sample
  • Complex: T cell receptor complex
    • Protein or peptide: UCHT1 Fab 2
    • Protein or peptide: UCHT1 Fab chain
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: T cell receptor delta constant
    • Protein or peptide: T cell receptor gamma constant 1
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
  • Ligand: CHOLESTEROL
KeywordsT cell receptor T cell immunity / IMMUNE SYSTEM
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 / CD4-positive, alpha-beta T cell proliferation / positive regulation of cell-cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / negative thymic T cell selection ...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 / CD4-positive, alpha-beta T cell proliferation / positive regulation of cell-cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / positive thymic T cell selection / signal complex assembly / positive regulation of protein localization to cell surface / Nef and signal transduction / alpha-beta T cell receptor complex / positive regulation of cell-matrix adhesion / T cell receptor complex / smoothened signaling pathway / Translocation of ZAP-70 to Immunological synapse / small molecule binding / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / dendrite development / establishment or maintenance of cell polarity / protein complex oligomerization / alpha-beta T cell activation / Generation of second messenger molecules / FCGR activation / immunological synapse / Co-inhibition by PD-1 / Role of phospholipids in phagocytosis / positive regulation of interleukin-2 production / T cell costimulation / T cell receptor binding / positive regulation of T cell proliferation / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / cerebellum development / protein tyrosine kinase binding / T cell activation / FCGR3A-mediated phagocytosis / negative regulation of smoothened signaling pathway / apoptotic signaling pathway / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / SH3 domain binding / Regulation of actin dynamics for phagocytic cup formation / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / T cell receptor signaling pathway / protein transport / Clathrin-mediated endocytosis / signaling receptor complex adaptor activity / cell body / protein-containing complex assembly / regulation of apoptotic process / dendritic spine / adaptive immune response / protein-macromolecule adaptor activity / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / protein heterodimerization activity / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / T-cell surface glycoprotein CD3 zeta subunit / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif ...: / : / T-cell surface glycoprotein CD3 zeta subunit / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 receptor delta constant / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 epsilon chain / T-cell surface glycoprotein CD3 gamma chain / T cell receptor gamma constant 1 / T-cell surface glycoprotein CD3 zeta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsGully BS / Rossjohn J
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230102073 Australia
CitationJournal: Nature / Year: 2024
Title: Structure of a fully assembled γδ T cell antigen receptor.
Authors: Benjamin S Gully / João Ferreira Fernandes / Sachith D Gunasinghe / Mai T Vuong / Yuan Lui / Michael T Rice / Liam Rashleigh / Chan-Sien Lay / Dene R Littler / Sumana Sharma / Ana Mafalda ...Authors: Benjamin S Gully / João Ferreira Fernandes / Sachith D Gunasinghe / Mai T Vuong / Yuan Lui / Michael T Rice / Liam Rashleigh / Chan-Sien Lay / Dene R Littler / Sumana Sharma / Ana Mafalda Santos / Hariprasad Venugopal / Jamie Rossjohn / Simon J Davis /
Abstract: T cells in jawed vertebrates comprise two lineages, αβ T cells and γδ T cells, defined by the antigen receptors they express-that is, αβ and γδ T cell receptors (TCRs), respectively. ...T cells in jawed vertebrates comprise two lineages, αβ T cells and γδ T cells, defined by the antigen receptors they express-that is, αβ and γδ T cell receptors (TCRs), respectively. The two lineages have different immunological roles, requiring that γδ TCRs recognize more structurally diverse ligands. Nevertheless, the receptors use shared CD3 subunits to initiate signalling. Whereas the structural organization of αβ TCRs is understood, the architecture of γδ TCRs is unknown. Here, we used cryogenic electron microscopy to determine the structure of a fully assembled, MR1-reactive, human Vγ8Vδ3 TCR-CD3δγεζ complex bound by anti-CD3ε antibody Fab fragments. The arrangement of CD3 subunits in γδ and αβ TCRs is conserved and, although the transmembrane α-helices of the TCR-γδ and -αβ subunits differ markedly in sequence, packing of the eight transmembrane-helix bundles is similar. However, in contrast to the apparently rigid αβ TCR, the γδ TCR exhibits considerable conformational heterogeneity owing to the ligand-binding TCR-γδ subunits being tethered to the CD3 subunits by their transmembrane regions only. Reducing this conformational heterogeneity by transfer of the Vγ8Vδ3 TCR variable domains to an αβ TCR enhanced receptor signalling, suggesting that γδ TCR organization reflects a compromise between efficient signalling and the ability to engage structurally diverse ligands. Our findings reveal the marked structural plasticity of the TCR on evolutionary timescales, and recast it as a highly versatile receptor capable of initiating signalling as either a rigid or flexible structure.
History
DepositionJul 3, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45615.png

Downloads & links

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Map

FileDownload / File: emd_45615.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain B-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.7002704 - 1.1624367
Average (Standard dev.)0.0007168783 (±0.023062745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45615_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: non-sharpened map

Fileemd_45615_additional_1.map
Annotationnon-sharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_45615_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_45615_half_map_2.map
AnnotationHalf map B
Projections & Slices
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Sample components

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Entire : T cell receptor complex

EntireName: T cell receptor complex
Components
  • Complex: T cell receptor complex
    • Protein or peptide: UCHT1 Fab 2
    • Protein or peptide: UCHT1 Fab chain
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: T cell receptor delta constant
    • Protein or peptide: T cell receptor gamma constant 1
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
  • Ligand: CHOLESTEROL

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Supramolecule #1: T cell receptor complex

SupramoleculeName: T cell receptor complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: UCHT1 Fab 2

MacromoleculeName: UCHT1 Fab 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.865157 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
MDIQMTQTTS SLSASLGDRV TISCRASQDI RNYLNWYQQK PDGTVKLLIY YTSRLHSGVP SKFSGSGSGT DYSLTISNLE QEDIATYFC QQGNTLPWTF AGGTKLEI

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Macromolecule #2: UCHT1 Fab chain

MacromoleculeName: UCHT1 Fab chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.415969 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLQQSGPE LVKPGASMKI SCKASGYSFT GYTMNWVKQS HGKNLEWMGL INPYKGVSTY NQKFKDKATL TVDKSSSTAY MELLSLTSE DSAVYYCARS GYYGDSDWYF DVWGQGTTLT V

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

MacromoleculeName: T-cell surface glycoprotein CD3 zeta chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.361154 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
LDPKLCYLLD GILFIYGVIL TALFLRVKF

UniProtKB: T-cell surface glycoprotein CD3 zeta chain

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Macromolecule #4: T-cell surface glycoprotein CD3 epsilon chain

MacromoleculeName: T-cell surface glycoprotein CD3 epsilon chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.982752 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QTPYKVSISG TTVILTCPQY PGSEILWQHN DKNIGGDEDD KNIGSDEDHL SLKEFSELEQ SGYYVCYPRG SKPEDANFYL YLRARVCEN CMEMDVMSVA TIVIVDICIT GGLLLLVYYW SKNR

UniProtKB: T-cell surface glycoprotein CD3 epsilon chain

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Macromolecule #5: T cell receptor delta constant

MacromoleculeName: T cell receptor delta constant / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.990903 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
HTEKVNMMSL TVLGLRMLFA KTVAVNFLLT AKLFF

UniProtKB: T cell receptor delta constant

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Macromolecule #6: T cell receptor gamma constant 1

MacromoleculeName: T cell receptor gamma constant 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.231204 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
TLLLQLTNTS AYYMYLLLLL KSVVYFAIIT CCLLRR

UniProtKB: T cell receptor gamma constant 1

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Macromolecule #7: T-cell surface glycoprotein CD3 delta chain

MacromoleculeName: T-cell surface glycoprotein CD3 delta chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.750582 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
FKIPIEELED RVFVNCNTSI TWVEGTVGTL LSDITRLDLG KRILDPRGIY RCNGTDIYKD KESTVQVHYR MCQSCVELDP ATVAGIIVT DVIATLLLAL GVFCFAG

UniProtKB: T-cell surface glycoprotein CD3 delta chain

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Macromolecule #8: T-cell surface glycoprotein CD3 gamma chain

MacromoleculeName: T-cell surface glycoprotein CD3 gamma chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.813813 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
IKGNHLVKVY DYQEDGSVLL TCDAEAKNIT WFKDGKMIGF LTEDKKKWNL GSNAKDPRGM YQCKGSQNKS KPLQVYYRMC QNCIELNAA TISGFLFAEI VSIFVLAVGV YFIAG

UniProtKB: T-cell surface glycoprotein CD3 gamma chain

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Macromolecule #9: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 9 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

Concentration5 mg/mL
BufferpH: 7.4 / Details: HEPES buffer saline
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum ER / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2663326
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7phr

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.0) / Number images used: 77000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7phr


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9cia:
T cell receptor complex

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