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- PDB-9mgb: scFv antibody CL33 bound to R-phycoerythrin -

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Basic information

Entry
Database: PDB / ID: 9mgb
TitlescFv antibody CL33 bound to R-phycoerythrin
Components
  • CL33 scFv
  • R-phycoerythrin alpha chain
  • R-phycoerythrin beta chain
KeywordsIMMUNE SYSTEM / Phycoerythrin / antibody / scFv / immunity
Function / homologyPHYCOERYTHROBILIN / PHYCOUROBILIN
Function and homology information
Biological speciesMus musculus (house mouse)
Neopyropia tenera (asakusa nori)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsRashleigh, L. / 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
DepositionDec 10, 2024Deposition 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 alpha chain
B: R-phycoerythrin beta chain
C: R-phycoerythrin alpha chain
D: R-phycoerythrin beta chain
F: R-phycoerythrin alpha chain
G: R-phycoerythrin beta chain
I: R-phycoerythrin alpha chain
J: R-phycoerythrin beta chain
L: R-phycoerythrin alpha chain
M: R-phycoerythrin beta chain
O: R-phycoerythrin alpha chain
Q: R-phycoerythrin beta chain
a: CL33 scFv
c: CL33 scFv
e: CL33 scFv
g: CL33 scFv
i: CL33 scFv
k: CL33 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,96948
Polymers382,29618
Non-polymers17,67330
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
R-phycoerythrin alpha chain


Mass: 17707.906 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Neopyropia tenera (asakusa nori)
#2: Protein
R-phycoerythrin beta chain


Mass: 18398.875 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Neopyropia tenera (asakusa nori)
#3: Antibody
CL33 scFv


Mass: 27609.285 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN


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


Mass: 590.710 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H42N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1R-phycoerythrin bound by CL33 scFvCOMPLEX#1-#30MULTIPLE SOURCES
2R-phycoerythrinCOMPLEX#1-#21NATURAL
3CL33 scFVCOMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Neopyropia tenera (asakusa nori)2785
43Mus musculus (house mouse)10090
Source (recombinant)Organism: Escherichia coli (E. coli)
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k 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: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327384
ELECTRON MICROSCOPYf_angle_d0.53237240
ELECTRON MICROSCOPYf_dihedral_angle_d7.945212
ELECTRON MICROSCOPYf_chiral_restr0.0374062
ELECTRON MICROSCOPYf_plane_restr0.0034774

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