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- EMDB-45810: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-45810
TitleG115 gamma delta TCR/CD3 complex bound by OKT3 Fab
Map data
Sample
  • Complex: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
    • Protein or peptide: G115 TCR delta chain
    • Protein or peptide: G115 TCR gamma chain
    • Protein or peptide: anti TCR variable delta 2 Fab heavy chain
    • Protein or peptide: anti TCR variable delta 2 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTCR / CD3 / gamma delta / Fab / OKT3 / immune receptor / T cell / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsHoque M / Saotome K / Franklin MC
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterization of two γδ TCR/CD3 complexes.
Authors: Mohammed Hoque / John Benji Grigg / Trudy Ramlall / Jennifer Jones / Luke L McGoldrick / John C Lin / William C Olson / Eric Smith / Matthew C Franklin / Tong Zhang / Kei Saotome /
Abstract: The T-cell receptor (TCR)/CD3 complex plays an essential role in the immune response and is a key player in cancer immunotherapies. There are two classes of TCR/CD3 complexes, defined by their TCR ...The T-cell receptor (TCR)/CD3 complex plays an essential role in the immune response and is a key player in cancer immunotherapies. There are two classes of TCR/CD3 complexes, defined by their TCR chain usage (αβ or γδ). Recently reported structures have revealed the organization of the αβ TCR/CD3 complex, but similar studies regarding the γδ TCR/CD3 complex have lagged behind. Here, we report cryoelectron microscopy (cryoEM) structural analysis of two γδ TCRs, G115 (Vγ9 Vδ2) and 9C2 (Vγ5 Vδ1), in complex with CD3 subunits. Our results show that the overall subunit organization of the γδ TCR/CD3 complexes is similar to αβ TCRs. However, both γδ TCRs display highly mobile extracellular domains (ECDs), unlike αβ TCRs, which have TCR ECDs that are rigidly coupled to its transmembrane (TM) domains. We corroborate this finding in cells by demonstrating that a γδ T-cell specific antibody can bind a site that would be inaccessible in the more rigid αβ TCR/CD3 complex. Furthermore, we observed that the Vγ5 Vδ1 complex forms a TCR γ5 chain-mediated dimeric species whereby two TCR/CD3 complexes are assembled. Collectively, these data shed light on γδ TCR/CD3 complex formation and may aid the design of γδ TCR-based therapies.
History
DepositionJul 19, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45810.png

Downloads & links

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Map

FileDownload / File: emd_45810.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 420 pix.
= 352.38 Å		0.84 Å/pix.
x 420 pix.
= 352.38 Å		0.84 Å/pix.
x 420 pix.
= 352.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.235
Minimum - Maximum-1.1466886 - 1.6439728
Average (Standard dev.)-0.0004783228 (±0.019684881)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 352.38 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45810_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45810_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : G115 gamma delta TCR/CD3 complex bound by OKT3 Fab

EntireName: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
Components
  • Complex: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
    • Protein or peptide: G115 TCR delta chain
    • Protein or peptide: G115 TCR gamma chain
    • Protein or peptide: anti TCR variable delta 2 Fab heavy chain
    • Protein or peptide: anti TCR variable delta 2 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab

SupramoleculeName: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: G115 TCR delta chain

MacromoleculeName: G115 TCR delta chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.519264 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AIELVPEHQT VPVSIGVPAT LRCSMKGEAI GNYYINWYRK TQGNTMTFIY REKDIYGPGF KDNFQGDIDI AKNLAVLKIL APSERDEGS YYCACDTLGM GGEYTDKLIF GKGTRVTVEP RSQPHTKPSV FVMKNGTNVA CLVKEFYPKD IRINLVSSKK I TEFDPAIV ...String:
AIELVPEHQT VPVSIGVPAT LRCSMKGEAI GNYYINWYRK TQGNTMTFIY REKDIYGPGF KDNFQGDIDI AKNLAVLKIL APSERDEGS YYCACDTLGM GGEYTDKLIF GKGTRVTVEP RSQPHTKPSV FVMKNGTNVA CLVKEFYPKD IRINLVSSKK I TEFDPAIV ISPSGKYNAV KLGKYEDSNS VTCSVQHDNK TVHSTDFEVK TDSTDHVKPK ETENTKQPSK SCHKPKAIVH TE KVNMMSL TVLGLRMLFA KTVAVNFLLT AKLFFLSRGR AKRGSG

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Macromolecule #2: G115 TCR gamma chain

MacromoleculeName: G115 TCR gamma chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.349344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AGHLEQPQIS STKTLSKTAR LECVVSGITI SATSVYWYRE RPGEVIQFLV SISYDGTVRK ESGIPSGKFE VDRIPETSTS TLTIHNVEK QDIATYYCAL WEAQQELGKK IKVFGPGTKL IITDKQLDAD VSPKPTIFLP SIAETKLQKA GTYLCLLEKF F PDVIKIHW ...String:
AGHLEQPQIS STKTLSKTAR LECVVSGITI SATSVYWYRE RPGEVIQFLV SISYDGTVRK ESGIPSGKFE VDRIPETSTS TLTIHNVEK QDIATYYCAL WEAQQELGKK IKVFGPGTKL IITDKQLDAD VSPKPTIFLP SIAETKLQKA GTYLCLLEKF F PDVIKIHW QEKKSNTILG SQEGNTMKTN DTYMKFSWLT VPEKSLDKEH RCIVRHENNK NGVDQEIIFP PIKTDVITMD PK DNCSKDA NDTLLLQLTN TSAYYMYLLL LLKSVVYFAI ITCCLLRRTA FCCNGEKS

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Macromolecule #3: anti TCR variable delta 2 Fab heavy chain

MacromoleculeName: anti TCR variable delta 2 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.048842 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLQQPGAE LVKPGASVKL SCKASGYTFT NHWISWVKQR PGQGLEWIGN IFPGSSSPNY NEKFKSKATL TVDTSSSTAY MQLSSLTSD ASAVYYCTRW GNYGYYYAMD YWGQGTSVTV SSAKTTPPSV YPLAPGSAAQ TNSMVTLGCL VKGYFPEPVT V TWNSGSLS ...String:
QVQLQQPGAE LVKPGASVKL SCKASGYTFT NHWISWVKQR PGQGLEWIGN IFPGSSSPNY NEKFKSKATL TVDTSSSTAY MQLSSLTSD ASAVYYCTRW GNYGYYYAMD YWGQGTSVTV SSAKTTPPSV YPLAPGSAAQ TNSMVTLGCL VKGYFPEPVT V TWNSGSLS SGVHTFPAVL QSDLYTLSSS VTVPSSTWPS ETVTCNVAHP ASSTKVDKKI VPRDCG

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Macromolecule #4: anti TCR variable delta 2 Fab light chain

MacromoleculeName: anti TCR variable delta 2 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.224613 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QIVLTQSPAI MSASLGEEIT LTCSASSRVN YMHWYQQKSG TSPKLLIYST SNLASGVPSR FSGSGSGTFY SLTIISVEAE DAADYYCHQ WSSYPTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN S WTDQDSKD ...String:
QIVLTQSPAI MSASLGEEIT LTCSASSRVN YMHWYQQKSG TSPKLLIYST SNLASGVPSR FSGSGSGTFY SLTIISVEAE DAADYYCHQ WSSYPTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN S WTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RGEC

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156210
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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