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- EMDB-45814: Dimeric 9C2 gamma delta TCR bound by Fab 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-45814
TitleDimeric 9C2 gamma delta TCR bound by Fab 3
Map data
Sample
  • Complex: G115 gamma delta TCR/CD3 complex bound by OKT3 Fab
    • Protein or peptide: 9C2 TCR delta chain
    • Protein or peptide: 9C2 TCR gamma chain
    • Protein or peptide: anti TCR variable delta 1 Fab heavy chain Fab 3
    • Protein or peptide: anti TCR variable delta 1 Fab light chain Fab 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
KeywordsTCR / CD3 / gamma delta / Fab / OKT3 / immune receptor / T cell / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 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_45814.png

Downloads & links

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Map

FileDownload / File: emd_45814.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 402.72 Å		0.84 Å/pix.
x 480 pix.
= 402.72 Å		0.84 Å/pix.
x 480 pix.
= 402.72 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: 0.151
Minimum - Maximum-0.57296455 - 0.88558376
Average (Standard dev.)-0.00026515857 (±0.014744278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 402.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45814_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45814_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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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: 9C2 TCR delta chain
    • Protein or peptide: 9C2 TCR gamma chain
    • Protein or peptide: anti TCR variable delta 1 Fab heavy chain Fab 3
    • Protein or peptide: anti TCR variable delta 1 Fab light chain Fab 3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose

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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: 9C2 TCR delta chain

MacromoleculeName: 9C2 TCR delta chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.2801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AQKVTQAQSS VSMPVRKAVT LNCLYETSWW SYYIFWYKQL PSKEMIFLIR QGSDEQNAKS GRYSVNFKKA AKSVALTISA LQLEDSAKY FCALGDPGGL NTDKLIFGKG TRVTVEPRSQ PHTKPSVFVM KNGTNVACLV KEFYPKDIRI NLVSSKKITE F DPAIVISP ...String:
AQKVTQAQSS VSMPVRKAVT LNCLYETSWW SYYIFWYKQL PSKEMIFLIR QGSDEQNAKS GRYSVNFKKA AKSVALTISA LQLEDSAKY FCALGDPGGL NTDKLIFGKG TRVTVEPRSQ PHTKPSVFVM KNGTNVACLV KEFYPKDIRI NLVSSKKITE F DPAIVISP SGKYNAVKLG KYEDSNSVTC SVQHDNKTVH STDFEVKTDS TDHVKPKETE NTKQPSKSCH KPKAIVHTEK VN MMSLTVL GLRMLFAKTV AVNFLLTAKL FFLSRGRAKR GSG

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Macromolecule #2: 9C2 TCR gamma chain

MacromoleculeName: 9C2 TCR gamma chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.697551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSNLEGGTKS VTRPTRSSAE ITCDLTVINA FYIHWYLHQE GKAPQRLLYY DVSNSKDVLE SGLSPGKYYT HTPRRWSWIL ILRNLIEND SGVYYCATWD RGNPKTHYYK KLFGSGTTLV VTDKQLDADV SPKPTIFLPS IAETKLQKAG TYLCLLEKFF P DVIKIHWQ ...String:
SSNLEGGTKS VTRPTRSSAE ITCDLTVINA FYIHWYLHQE GKAPQRLLYY DVSNSKDVLE SGLSPGKYYT HTPRRWSWIL ILRNLIEND SGVYYCATWD RGNPKTHYYK KLFGSGTTLV VTDKQLDADV SPKPTIFLPS IAETKLQKAG TYLCLLEKFF P DVIKIHWQ EKKSNTILGS QEGNTMKTND TYMKFSWLTV PEKSLDKEHR CIVRHENNKN GVDQEIIFPP IKTDVITMDP KD NCSKDAN DTLLLQLTNT SAYYMYLLLL LKSVVYFAII TCCLLRRTAF CCNGEKS

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Macromolecule #3: anti TCR variable delta 1 Fab heavy chain Fab 3

MacromoleculeName: anti TCR variable delta 1 Fab heavy chain Fab 3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.193801 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLQQPGAD LVRPGTSVKL SCKASGYTFT SYWMHWVQQR PGQGLEWIGV IDPSDSYTNY NQKFKGKATL TVDTSSSTAY MQLSSLTSE DSAVYYCARS DDYDEGYFFD QWGQGTTLTV SAAKTTPPSV YPLAPGSAAQ TNSMVTLGCL VKGYFPEPVT V TWNSGSLS ...String:
QVQLQQPGAD LVRPGTSVKL SCKASGYTFT SYWMHWVQQR PGQGLEWIGV IDPSDSYTNY NQKFKGKATL TVDTSSSTAY MQLSSLTSE DSAVYYCARS DDYDEGYFFD QWGQGTTLTV SAAKTTPPSV YPLAPGSAAQ TNSMVTLGCL VKGYFPEPVT V TWNSGSLS SGVHTFPAVL QSDLYTLSSS VTVPSSTWPS ETVTCNVAHP ASSTKVDKKI VPRDCG

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Macromolecule #4: anti TCR variable delta 1 Fab light chain Fab 3

MacromoleculeName: anti TCR variable delta 1 Fab light chain Fab 3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.032916 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DVVMTQTPLT LSVTVGQPAS ISCKSSQSLL HSNGKTYLNW LLQRPGQSPK LLIYLVSKVE SGVPDRFSGS GSGTDFTLKI SRVEAEDLG LYYCLQVTHF PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
DVVMTQTPLT LSVTVGQPAS ISCKSSQSLL HSNGKTYLNW LLQRPGQSPK LLIYLVSKVE SGVPDRFSGS GSGTDFTLKI SRVEAEDLG LYYCLQVTHF PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRGE C

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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: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 7 / Number of copies: 2 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29351
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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