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- EMDB-48248: scFv antibody CL33 bound to R-phycoerythrin -

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Basic information

Entry
Database: EMDB / ID: EMD-48248
TitlescFv antibody CL33 bound to R-phycoerythrin
Map data
Sample
  • Complex: R-phycoerythrin bound by CL33 scFv
    • Complex: R-phycoerythrin
      • Protein or peptide: R-phycoerythrin alpha chain
      • Protein or peptide: R-phycoerythrin beta chain
    • Complex: CL33 scFV
      • Protein or peptide: CL33 scFv
  • Ligand: PHYCOERYTHROBILIN
  • Ligand: PHYCOUROBILIN
KeywordsPhycoerythrin / antibody / scFv / immunity / IMMUNE SYSTEM
Biological speciesNeopyropia tenera (asakusa nori) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsRashleigh L / 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
DepositionDec 10, 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_48248.png

Downloads & links

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Map

FileDownload / File: emd_48248.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-1.1080183 - 3.1931717
Average (Standard dev.)-0.0017352074 (±0.0977761)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_48248_additional_1.map
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Half map: #1

Fileemd_48248_half_map_1.map
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Half map: #2

Fileemd_48248_half_map_2.map
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Sample components

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Entire : R-phycoerythrin bound by CL33 scFv

EntireName: R-phycoerythrin bound by CL33 scFv
Components
  • Complex: R-phycoerythrin bound by CL33 scFv
    • Complex: R-phycoerythrin
      • Protein or peptide: R-phycoerythrin alpha chain
      • Protein or peptide: R-phycoerythrin beta chain
    • Complex: CL33 scFV
      • Protein or peptide: CL33 scFv
  • Ligand: PHYCOERYTHROBILIN
  • Ligand: PHYCOUROBILIN

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Supramolecule #1: R-phycoerythrin bound by CL33 scFv

SupramoleculeName: R-phycoerythrin bound by CL33 scFv / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: R-phycoerythrin

SupramoleculeName: R-phycoerythrin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Neopyropia tenera (asakusa nori)

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Supramolecule #3: CL33 scFV

SupramoleculeName: CL33 scFV / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: R-phycoerythrin alpha chain

MacromoleculeName: R-phycoerythrin alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Neopyropia 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

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Macromolecule #2: R-phycoerythrin beta chain

MacromoleculeName: R-phycoerythrin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Neopyropia tenera (asakusa nori)
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

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Macromolecule #3: CL33 scFv

MacromoleculeName: CL33 scFv / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.609285 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVHSEVQLQQ SGAELARPGA SVKLSCKASG YTFTSYGISW VKQRTGQGLE WIGEIYPRSG NTYYNEKFKG KATLTADKSS STAYMELRS LTSEDSAVYF CARQGYYANS QFTYWGQGTL VTVSAAAGGG GSGGGGSGGG GSVHSDIQMT QTTSSLSASL G DRVTISCS ...String:
MVHSEVQLQQ SGAELARPGA SVKLSCKASG YTFTSYGISW VKQRTGQGLE WIGEIYPRSG NTYYNEKFKG KATLTADKSS STAYMELRS LTSEDSAVYF CARQGYYANS QFTYWGQGTL VTVSAAAGGG GSGGGGSGGG GSVHSDIQMT QTTSSLSASL G DRVTISCS ASQGISNYLN WYQQKPDGTV KLLIYYTSSL HSGVPSRFSG SGSGTDYSLT ISNLEPEDIA TYYCQQYSKL PW TFGGGTN LEIKHHHHHH

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Macromolecule #4: PHYCOERYTHROBILIN

MacromoleculeName: PHYCOERYTHROBILIN / type: ligand / ID: 4 / Number of copies: 24 / Formula: PEB
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-PEB:
PHYCOERYTHROBILIN

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Macromolecule #5: PHYCOUROBILIN

MacromoleculeName: PHYCOUROBILIN / type: ligand / ID: 5 / 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

MicroscopeFEI TALOS ARCTICA
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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