+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36147 | |||||||||
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Title | Extracellular domain of gamma delta TCR | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Receptor / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information gamma-delta T cell receptor complex / gamma-delta T cell activation / T cell receptor complex / small molecule binding / T cell receptor signaling pathway / adaptive immune response / immune response / external side of plasma membrane / innate immune response / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / Resolution: 3.02 Å | |||||||||
Authors | Xin W / Chi X / Huang B / Su Q / Zhou Q | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2024 Title: Structures of human γδ T cell receptor-CD3 complex. Authors: Weizhi Xin / Bangdong Huang / Ximin Chi / Yuehua Liu / Mengjiao Xu / Yuanyuan Zhang / Xu Li / Qiang Su / Qiang Zhou / Abstract: Gamma delta (γδ) T cells, a unique T cell subgroup, are crucial in various immune responses and immunopathology. The γδ T cell receptor (TCR), which is generated by γδ T cells, recognizes a ...Gamma delta (γδ) T cells, a unique T cell subgroup, are crucial in various immune responses and immunopathology. The γδ T cell receptor (TCR), which is generated by γδ T cells, recognizes a diverse range of antigens independently of the major histocompatibility complex. The γδ TCR associates with CD3 subunits, initiating T cell activation and holding great potential in immunotherapy. Here we report the structures of two prototypical human Vγ9Vδ2 and Vγ5Vδ1 TCR-CD3 complexes, revealing two distinct assembly mechanisms that depend on Vγ usage. The Vγ9Vδ2 TCR-CD3 complex is monomeric, with considerable conformational flexibility in the TCRγ-TCRδ extracellular domain and connecting peptides. The length of the connecting peptides regulates the ligand association and T cell activation. A cholesterol-like molecule wedges into the transmembrane region, exerting an inhibitory role in TCR signalling. The Vγ5Vδ1 TCR-CD3 complex displays a dimeric architecture, whereby two protomers nestle back to back through the Vγ5 domains of the TCR extracellular domains. Our biochemical and biophysical assays further corroborate the dimeric structure. Importantly, the dimeric form of the Vγ5Vδ1 TCR is essential for T cell activation. These findings reveal organizing principles of the γδ TCR-CD3 complex, providing insights into the unique properties of γδ TCR and facilitating immunotherapeutic interventions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36147.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-36147-v30.xml emd-36147.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36147_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_36147.png | 42.5 KB | ||
Filedesc metadata | emd-36147.cif.gz | 5.4 KB | ||
Others | emd_36147_half_map_1.map.gz emd_36147_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36147 | HTTPS FTP |
-Validation report
Summary document | emd_36147_validation.pdf.gz | 787.1 KB | Display | EMDB validaton report |
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Full document | emd_36147_full_validation.pdf.gz | 786.7 KB | Display | |
Data in XML | emd_36147_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_36147_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36147 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36147 | HTTPS FTP |
-Related structure data
Related structure data | 8jbvMC 8jc0C 8jcbC 8wxeC 8wy0C 8wyiC 8yc0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36147.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36147_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36147_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Extracellular domain of gamma delta TCR
Entire | Name: Extracellular domain of gamma delta TCR |
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Components |
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-Supramolecule #1: Extracellular domain of gamma delta TCR
Supramolecule | Name: Extracellular domain of gamma delta TCR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: T cell receptor delta variable 1,T cell receptor delta constant
Macromolecule | Name: T cell receptor delta variable 1,T cell receptor delta constant type: protein_or_peptide / ID: 1 Details: Author stated: 1-22:Signal peptide, 23-31:Flag tag. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.320574 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGAQK VTQAQSSVSM PVRKAVTLNC LYETSWWSYY IFWYKQLPSK EMIFLIRQG SDEQNAKSGR YSVNFKKAAK SVALTISALQ LEDSAKYFCA LGDPGGLNTD KLIFGKGTRV TVEPRSQPHT K PSVFVMKN ...String: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGAQK VTQAQSSVSM PVRKAVTLNC LYETSWWSYY IFWYKQLPSK EMIFLIRQG SDEQNAKSGR YSVNFKKAAK SVALTISALQ LEDSAKYFCA LGDPGGLNTD KLIFGKGTRV TVEPRSQPHT K PSVFVMKN GTNVACLVKE FYPKDIRINL VSSKKITEFD PAIVISPSGK YNAVKLGKYE DSNSVTCSVQ HDNKTVHSTD FE VKTDSTD HVKPKETENT KQPSKSCHKP KAIVHTEKVN MMSLTVLGLR MLFAKTVAVN FLLTAKLFFL UniProtKB: T cell receptor delta variable 1, T cell receptor delta constant |
-Macromolecule #2: T cell receptor gamma variable 5,T cell receptor gamma constant 1
Macromolecule | Name: T cell receptor gamma variable 5,T cell receptor gamma constant 1 type: protein_or_peptide / ID: 2 Details: Author stated: 1-22:Signal peptide, 23-31:Flag tag. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.755172 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGSSN LEGGTKSVTR PTRSSAEITC DLTVINAFYI HWYLHQEGKA PQRLLYYDV SNSKDVLESG LSPGKYYTHT PRRWSWILIL RNLIENDSGV YYCATWDRGN PKTHYYKKLF GSGTTLVVTD K QLDADVSP ...String: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGSSN LEGGTKSVTR PTRSSAEITC DLTVINAFYI HWYLHQEGKA PQRLLYYDV SNSKDVLESG LSPGKYYTHT PRRWSWILIL RNLIENDSGV YYCATWDRGN PKTHYYKKLF GSGTTLVVTD K QLDADVSP KPTIFLPSIA ETKLQKAGTY LCLLEKFFPD VIKIHWQEKK SNTILGSQEG NTMKTNDTYM KFSWLTVPEK SL DKEHRCI VRHENNKNGV DQEIIFPPIK TDVITMDPKD NCSKDANDTL LLQLTNTSAY YMYLLLLLKS VVYFAIITCC LLR RTAFCC NGEKS UniProtKB: T cell receptor gamma variable 5, T cell receptor gamma constant 1 |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |