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- EMDB-48332: 4D4 TCR bound to R-phycoerythrin -

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Basic information

Entry
Database: EMDB / ID: EMD-48332
Title4D4 TCR bound to R-phycoerythrin
Map data4D4 TCR bound to R-phycoerythrin
Sample
  • Complex: ternary complex of 4D4 alpha/beta TCR bound to R-phycoerythrin
    • Complex: 4D4 alpha beta TCR
      • Protein or peptide: 4D4 TCR alpha chain
      • Protein or peptide: 4D4 TCR beta chain
    • Complex: R-phycoerythrin
      • Protein or peptide: R-phycoerythrin class I alpha subunit
      • Protein or peptide: R-phycoerythrin class I beta subunit
  • Ligand: PHYCOERYTHROBILIN
  • Ligand: PHYCOUROBILIN
KeywordsTCR / phycoerythrin / immunity / direct recognition / 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 speciesMus musculus (house mouse) / Ceramium secundatum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsRashleigh L / Gully BS / Rossjohn J
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
DepositionDec 17, 2024-
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_48332.png

Downloads & links

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Map

FileDownload / File: emd_48332.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation4D4 TCR bound to R-phycoerythrin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 320 pix.
= 310.4 Å		0.97 Å/pix.
x 320 pix.
= 310.4 Å		0.97 Å/pix.
x 320 pix.
= 310.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.2439429 - 2.6633794
Average (Standard dev.)-0.00002341884 (±0.09003175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 310.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_48332_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48332_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48332_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ternary complex of 4D4 alpha/beta TCR bound to R-phycoerythrin

EntireName: ternary complex of 4D4 alpha/beta TCR bound to R-phycoerythrin
Components
  • Complex: ternary complex of 4D4 alpha/beta TCR bound to R-phycoerythrin
    • Complex: 4D4 alpha beta TCR
      • Protein or peptide: 4D4 TCR alpha chain
      • Protein or peptide: 4D4 TCR beta chain
    • Complex: R-phycoerythrin
      • Protein or peptide: R-phycoerythrin class I alpha subunit
      • Protein or peptide: R-phycoerythrin class I beta subunit
  • Ligand: PHYCOERYTHROBILIN
  • Ligand: PHYCOUROBILIN

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Supramolecule #1: ternary complex of 4D4 alpha/beta TCR bound to R-phycoerythrin

SupramoleculeName: ternary complex of 4D4 alpha/beta TCR bound to R-phycoerythrin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4, #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: 4D4 alpha beta TCR

SupramoleculeName: 4D4 alpha beta TCR / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: R-phycoerythrin

SupramoleculeName: R-phycoerythrin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Ceramium secundatum (eukaryote)

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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: Ceramium secundatum (eukaryote)
Molecular weightTheoretical: 17.753998 KDa
SequenceString:
MKSVITTTIS AADAAGRFPS SSDLESVQGN IQRAASRLEA AEKLAGNHEA VVKEAGDACF AKYPYLKNPG EAGDSQEKIN KCYRDIDHY MRLINYSLVV GGTGPLDEWC 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: Ceramium secundatum (eukaryote)
Molecular weightTheoretical: 18.398875 KDa
SequenceString:
MLDAFSRVVV NSDSKAAYVS GSDLQALKTF IADGNKRLDA VNSIVSNASC IVSDAVSGMI CENPGLIAPG GNCYTNRRMA ACLRDGEII LRYTSYALLA GDSSVLEDRC LNGLKETYIA LGVPTNSTVR AVSIMKSSAV AFISNTASQR KMATADGDCS A LSSEVASY CDKVSAAI

UniProtKB: R-phycoerythrin class I beta subunit

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Macromolecule #3: 4D4 TCR alpha chain

MacromoleculeName: 4D4 TCR alpha chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.728928 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVEQSPSALS LHEGTSSALR CNFTTTTRSV QWFRQNSRGS LINLFYLASG TKENGRLKSA FDSKELYSTL HIRDAQLEDS GTYFCAAEA GSFNKLTFGA GTRLAVSPYI QNPDPAVYQL RDSKSSDKSV CLFTDFDSQT NVSQSKDSDV YITDKCVLDM R SMDFKSNS ...String:
QVEQSPSALS LHEGTSSALR CNFTTTTRSV QWFRQNSRGS LINLFYLASG TKENGRLKSA FDSKELYSTL HIRDAQLEDS GTYFCAAEA GSFNKLTFGA GTRLAVSPYI QNPDPAVYQL RDSKSSDKSV CLFTDFDSQT NVSQSKDSDV YITDKCVLDM R SMDFKSNS AVAWSNKSDF ACANAFNNSI IPEDTFFP

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Macromolecule #4: 4D4 TCR beta chain

MacromoleculeName: 4D4 TCR beta chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.083371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TAVFQTPNYH VTQVGNEVSF NCKQTLGHDT MYWYKQDSKK LLKIMFSYNN KQLIVNETVP RRFSPQSSDK AHLNLRIKSV EPEDSAVYL CASSFRWVGE QYFGPGTRLT VLEDLKNVFP PEVAVFEPSA AAASHTQKAT LVCLATGFYP DHVELSWWVN G KEVHSGVC ...String:
TAVFQTPNYH VTQVGNEVSF NCKQTLGHDT MYWYKQDSKK LLKIMFSYNN KQLIVNETVP RRFSPQSSDK AHLNLRIKSV EPEDSAVYL CASSFRWVGE QYFGPGTRLT VLEDLKNVFP PEVAVFEPSA AAASHTQKAT LVCLATGFYP DHVELSWWVN G KEVHSGVC TDPQPLKEQP ALNDSRYALS SRLRVSATFW QNPRNHFRCQ VQFYGLSEND EWTQDRAKPV TQIVSAEAW

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27700
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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