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- EMDB-70157: 1C5H TCR bound to R-phycoerythrin -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-70157
Title1C5H TCR bound to R-phycoerythrin
Map dataComposite Map
Sample
  • Complex: 1C5H TCR bound to R-phycoerythrin
    • Complex: R-phycoerythrin
      • Protein or peptide: R-phycoerythrin class I alpha subunit
      • Protein or peptide: R-phycoerythrin class I beta subunit
    • Complex: 1C5H TCR
      • Protein or peptide: 1C5H TCR delta chain
      • Protein or peptide: TCR gamma chain
  • Ligand: PHYCOERYTHROBILIN
  • Ligand: PHYCOUROBILIN
KeywordsT-cell / gamma delta TCR / phycoerythrin / direct / IMMUNE SYSTEM
Function / homologyPhycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / phycobilisome / chloroplast thylakoid membrane / photosynthesis / Globin-like superfamily / R-phycoerythrin class I beta subunit / R-phycoerythrin class I alpha subunit
Function and homology information
Biological speciesHomo sapiens (human) / Ceramium secundatum (eukaryote) / Pyropia tenera (asakusa nori)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.03 Å
AuthorsRashleigh L / Venugopal H / Rossjohn J / Gully BS
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230102073 Australia
CitationJournal: Structure / Year: 2025
Title: Antibody-like recognition of a γδ T cell receptor toward a foreign antigen.
Authors: Liam Rashleigh / Hariprasad Venugopal / Michael T Rice / Sachith D Gunasinghe / Chhon Ling Sok / Nicholas A Gherardin / Catarina F Almeida / Ildiko Van Rhijn / D Branch Moody / Dale I ...Authors: Liam Rashleigh / Hariprasad Venugopal / Michael T Rice / Sachith D Gunasinghe / Chhon Ling Sok / Nicholas A Gherardin / Catarina F Almeida / Ildiko Van Rhijn / D Branch Moody / Dale I Godfrey / Jamie Rossjohn / Benjamin S Gully /
Abstract: The antigen recognition principles of B cells and αβ T cells have been well described compared to those of the γδ T cell. By way of their specificity conferring receptor (γδTCR), γδ T cells ...The antigen recognition principles of B cells and αβ T cells have been well described compared to those of the γδ T cell. By way of their specificity conferring receptor (γδTCR), γδ T cells can directly bind proteinaceous antigens. A known γδ T cell and B cell model antigen is phycoerythrin (PE), a light harvesting protein from rhodophytes and cyanobacteria. Here we probed human γδTCR reactivity to PE, in which a Vδ1Vγ5 TCR bound directly to induce proximal signaling and cellular activation. We determined the cryoelectron microscopy (cryo-EM) structure of the γδTCR-phycoerythrin immune complex. We then determined the cryo-EM structures of an antibody fragment and an αβTCR bound to PE. This revealed convergent use of apical aromatic residues to mediate contacts with a common PE epitope. Comparative analyses of the γδTCR revealed multiple antibody-like characteristics, including an enrichment of apical aromatic residues. Our findings reveal further distinct facets of antigen recognition by the γδTCR.
History
DepositionApr 10, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70157.png

Downloads & links

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Map

FileDownload / File: emd_70157.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 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: 3.7
Minimum - Maximum-32.661034000000001 - 45.701813000000001
Average (Standard dev.)0.003115483 (±1.0355191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 1C5H TCR bound to R-phycoerythrin

EntireName: 1C5H TCR bound to R-phycoerythrin
Components
  • Complex: 1C5H TCR bound to R-phycoerythrin
    • Complex: R-phycoerythrin
      • Protein or peptide: R-phycoerythrin class I alpha subunit
      • Protein or peptide: R-phycoerythrin class I beta subunit
    • Complex: 1C5H TCR
      • Protein or peptide: 1C5H TCR delta chain
      • Protein or peptide: TCR gamma chain
  • Ligand: PHYCOERYTHROBILIN
  • Ligand: PHYCOUROBILIN

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Supramolecule #1: 1C5H TCR bound to R-phycoerythrin

SupramoleculeName: 1C5H TCR bound to R-phycoerythrin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: R-phycoerythrin

SupramoleculeName: R-phycoerythrin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Ceramium secundatum (eukaryote)

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Supramolecule #3: 1C5H TCR

SupramoleculeName: 1C5H TCR / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: R-phycoerythrin class I alpha subunit

MacromoleculeName: R-phycoerythrin class I alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pyropia tenera (asakusa nori)
Molecular weightTheoretical: 17.707906 KDa
SequenceString:
MKSVITTTIS AADAAGRFPS SSDLESVQGN IQRAASRLEA AEKLAGNHEA VVKEAGDACF AKYPYLKNPG EAGDSQEKIN KCYRDIDHY MRLINYSLVV GGTGPLDEWG IAGAREVYRA LNLPGSSYIA AFVFTRDRLC VPRDMSAQAA VEFSGALDYV I NSLC

UniProtKB: R-phycoerythrin class I alpha subunit

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Macromolecule #2: R-phycoerythrin class I beta subunit

MacromoleculeName: R-phycoerythrin class I beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pyropia tenera (asakusa nori)
Molecular weightTheoretical: 18.33685 KDa
SequenceString:
MLDAFSRVVV NSDSKAAYVS GSDLQALKTF IADGNKRLDA VNSIVSNASC IVSDAVSGMI CENPGLIAPG GNCYTNRRMA ACLRDGEII LRYTSYALLA GDSSVLEDRC LNGLKETYIA LGVPTNSTAR AVSIMKSSAV AFISNTAPQR KMATAAGDCS A LSSEVASY CDKVSAAI

UniProtKB: R-phycoerythrin class I beta subunit

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Macromolecule #3: 1C5H TCR delta chain

MacromoleculeName: 1C5H TCR delta chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.886508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AQKVTQAQSS VSMPVRKAVT LNCLYETSWW SYYIFWYKQL PSKEMIFLIR QGSDEQNAKS GRYSVNFKKA AKSVALTISA LQLEDSAKY FCALGAPHTY WGISTDLSSW DTRQMFFGTG IKLFVEPRSQ PHTKPSVFVM KNGTNVACLV KEFYPKDIRI N LVSSKKIT ...String:
AQKVTQAQSS VSMPVRKAVT LNCLYETSWW SYYIFWYKQL PSKEMIFLIR QGSDEQNAKS GRYSVNFKKA AKSVALTISA LQLEDSAKY FCALGAPHTY WGISTDLSSW DTRQMFFGTG IKLFVEPRSQ PHTKPSVFVM KNGTNVACLV KEFYPKDIRI N LVSSKKIT EFDPAIVISP SGKYNAVKLG KYEDSNSVTC SVQHDNKTVH STDFEVKTDS TDHVKPKETE NTKQPSKSAS G

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Macromolecule #4: TCR gamma chain

MacromoleculeName: TCR gamma chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.014568 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSNLEGGTKS VTRPTRSSAE ITCDLTVINA FYIHWYLHQE GKAPQRLLYY DVSNSKDVLE SGLSPGKYYT HTPRRWSWIL ILRNLIEND SGVYYCATWD RPSKLFGSGT TLVVTDKQLD ADVSPKPTIF LPSIAETKLQ KAGTYLCLLE KFFPDVIKIH W QEKKSNTI ...String:
SSNLEGGTKS VTRPTRSSAE ITCDLTVINA FYIHWYLHQE GKAPQRLLYY DVSNSKDVLE SGLSPGKYYT HTPRRWSWIL ILRNLIEND SGVYYCATWD RPSKLFGSGT TLVVTDKQLD ADVSPKPTIF LPSIAETKLQ KAGTYLCLLE KFFPDVIKIH W QEKKSNTI LGSQEGNTMK TNDTYMKFSW LTVPEESLDK EHRCIVRHEN NKNGVDQEII FPPIKTDVIT MDPKDNASG

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Macromolecule #5: PHYCOERYTHROBILIN

MacromoleculeName: PHYCOERYTHROBILIN / type: ligand / ID: 5 / Number of copies: 24 / Formula: PEB
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-PEB:
PHYCOERYTHROBILIN

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Macromolecule #6: PHYCOUROBILIN

MacromoleculeName: PHYCOUROBILIN / type: ligand / ID: 6 / Number of copies: 6 / Formula: PUB
Molecular weightTheoretical: 590.71 Da
Chemical component information

ChemComp-CYB:
PHYCOUROBILIN

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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: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.03 Å / Resolution method: OTHER / Number images used: 45513
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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