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- PDB-9o61: R-phycoerythrin -

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Basic information

Entry
Database: PDB / ID: 9o61
TitleR-phycoerythrin
Components
  • R-phycoerythrin class I alpha subunit
  • R-phycoerythrin class I beta subunit
KeywordsIMMUNE SYSTEM / T-cell / gamma delta TCR / phycoerythrin / direct
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOERYTHROBILIN / PHYCOUROBILIN / R-phycoerythrin class I beta subunit / R-phycoerythrin class I alpha subunit
Similarity search - Component
Biological speciesPyropia tenera (asakusa nori)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.68 Å
AuthorsRashleigh, L. / Venugopal, H. / Rossjohn, J. / Gully, B.S.
Funding support Australia, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Oct 15, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R-phycoerythrin class I alpha subunit
B: R-phycoerythrin class I beta subunit
C: R-phycoerythrin class I alpha subunit
D: R-phycoerythrin class I beta subunit
E: R-phycoerythrin class I alpha subunit
F: R-phycoerythrin class I beta subunit
G: R-phycoerythrin class I alpha subunit
H: R-phycoerythrin class I beta subunit
I: R-phycoerythrin class I alpha subunit
J: R-phycoerythrin class I beta subunit
K: R-phycoerythrin class I alpha subunit
L: R-phycoerythrin class I beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,94142
Polymers216,26912
Non-polymers17,67330
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
R-phycoerythrin class I alpha subunit


Mass: 17707.906 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pyropia tenera (asakusa nori) / References: UniProt: A0A1C9C9A7
#2: Protein
R-phycoerythrin class I beta subunit


Mass: 18336.850 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pyropia tenera (asakusa nori) / References: UniProt: A0A1C9C989
#3: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PUB / PHYCOUROBILIN


Mass: 590.710 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H42N4O6
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: R-phycoerythrin / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 211282 / Symmetry type: POINT

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