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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Vgamma5Vdelta1 EH TCR-CD3 complex | |||||||||
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Function / homology | ![]() regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Xin W / Huang B / Chi X / Xu M / Zhang Y / Li X / Su Q / Zhou Q | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 27.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.6 KB 20.6 KB | Display Display | ![]() |
Images | ![]() | 49.5 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 23.2 MB 23.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wxeMC ![]() 8jbvC ![]() 8jc0C ![]() 8jcbC ![]() 8wy0C ![]() 8wyiC ![]() 8yc0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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_37904_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37904_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : T cell receptor delta 1 gamma 5 EH mutant
Entire | Name: T cell receptor delta 1 gamma 5 EH mutant |
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Components |
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-Supramolecule #1: T cell receptor delta 1 gamma 5 EH mutant
Supramolecule | Name: T cell receptor delta 1 gamma 5 EH mutant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / Details: Y106E and R120H in TCR gamma 5 chain |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: T-cell surface glycoprotein CD3 zeta chain
Macromolecule | Name: T-cell surface glycoprotein CD3 zeta chain / type: protein_or_peptide / ID: 1 / Details: 165-167: linker 168-195: twin-Strep tag / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.809695 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKWKALFTAA ILQAQLPITE AQSFGLLDPK LCYLLDGILF IYGVILTALF LRVKFSRSAD APAYQQGQNQ LYNELNLGRR EEYDVLDKR RGRDPEMGGK PQRRKNPQEG LYNELQKDKM AEAYSEIGMK GERRRGKGHD GLYQGLSTAT KDTYDALHMQ A LPPRAAAW ...String: MKWKALFTAA ILQAQLPITE AQSFGLLDPK LCYLLDGILF IYGVILTALF LRVKFSRSAD APAYQQGQNQ LYNELNLGRR EEYDVLDKR RGRDPEMGGK PQRRKNPQEG LYNELQKDKM AEAYSEIGMK GERRRGKGHD GLYQGLSTAT KDTYDALHMQ A LPPRAAAW SHPQFEKGGG SGGGSGGSAW SHPQFEK UniProtKB: ![]() |
-Macromolecule #2: T-cell surface glycoprotein CD3 delta chain
Macromolecule | Name: T-cell surface glycoprotein CD3 delta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 18.949537 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEHSTFLSGL VLATLLSQVS PFKIPIEELE DRVFVNCNTS ITWVEGTVGT LLSDITRLDL GKRILDPRGI YRCNGTDIYK DKESTVQVH YRMCQSCVEL DPATVAGIIV TDVIATLLLA LGVFCFAGHE TGRLSGAADT QALLRNDQVY QPLRDRDDAQ Y SHLGGNWA RNK UniProtKB: T-cell surface glycoprotein CD3 delta chain |
-Macromolecule #3: T-cell surface glycoprotein CD3 epsilon chain
Macromolecule | Name: T-cell surface glycoprotein CD3 epsilon chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.174227 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MQSGTHWRVL GLCLLSVGVW GQDGNEEMGG ITQTPYKVSI SGTTVILTCP QYPGSEILWQ HNDKNIGGDE DDKNIGSDED HLSLKEFSE LEQSGYYVCY PRGSKPEDAN FYLYLRARVC ENCMEMDVMS VATIVIVDIC ITGGLLLLVY YWSKNRKAKA K PVTRGAGA ...String: MQSGTHWRVL GLCLLSVGVW GQDGNEEMGG ITQTPYKVSI SGTTVILTCP QYPGSEILWQ HNDKNIGGDE DDKNIGSDED HLSLKEFSE LEQSGYYVCY PRGSKPEDAN FYLYLRARVC ENCMEMDVMS VATIVIVDIC ITGGLLLLVY YWSKNRKAKA K PVTRGAGA GGRQRGQNKE RPPPVPNPDY EPIRKGQRDL YSGLNQRRI UniProtKB: T-cell surface glycoprotein CD3 epsilon chain |
-Macromolecule #4: T-cell surface glycoprotein CD3 gamma chain
Macromolecule | Name: T-cell surface glycoprotein CD3 gamma chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.493457 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEQGKGLAVL ILAIILLQGT LAQSIKGNHL VKVYDYQEDG SVLLTCDAEA KNITWFKDGK MIGFLTEDKK KWNLGSNAKD PRGMYQCKG SQNKSKPLQV YYRMCQNCIE LNAATISGFL FAEIVSIFVL AVGVYFIAGQ DGVRQSRASD KQTLLPNDQL Y QPLKDRED DQYSHLQGNQ LRRN UniProtKB: T-cell surface glycoprotein CD3 gamma chain |
-Macromolecule #5: Signal peptide,flag tag,T cell receptor delta variable 1,T cell r...
Macromolecule | Name: Signal peptide,flag tag,T cell receptor delta variable 1,T cell receptor delta constant type: protein_or_peptide / ID: 5 Details: 1-22: signal peptide, 23-31: Flag tag, 38-131: A0A1B0GX56, 155-307: B7Z8K6 Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34.320574 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 #6: Signal peptide,flag tag,T cell receptor gamma variable 5,T cell r...
Macromolecule | Name: Signal peptide,flag tag,T cell receptor gamma variable 5,T cell receptor gamma constant 1 type: protein_or_peptide / ID: 6 Details: 1-22: signal peptide, 23-31: Flag tag, 38-137: UniprotKB ID A0A0B4J1U4, 159-331: UniprotKB ID P0CF51 with Y106E and R120H Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 37.702062 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGSSN LEGGTKSVTR PTRSSAEITC DLTVINAFYI HWYLHQEGKA PQRLLYYDV SNSKDVLESG LSPGKYETHT PRRWSWILIL HNLIENDSGV YYCATWDRGN PKTHYYKKLF GSGTTLVVTD K QLDADVSP ...String: MDMRVPAQLL GLLLLWLSGA RCMDYKDDDD KGGSETGSSN LEGGTKSVTR PTRSSAEITC DLTVINAFYI HWYLHQEGKA PQRLLYYDV SNSKDVLESG LSPGKYETHT PRRWSWILIL HNLIENDSGV 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 |
-Macromolecule #7: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 1 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 342095 |