9MKO | pdb_00009mko

4D4 TCR bound to R-phycoerythrin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antibody-like recognition of a gamma delta T cell receptor toward a foreign antigen.

Rashleigh, L.Venugopal, H.Rice, M.T.Gunasinghe, S.D.Sok, C.L.Gherardin, N.A.Almeida, C.F.Van Rhijn, I.Moody, D.B.Godfrey, D.I.Rossjohn, J.Gully, B.S.

(2025) Structure 33: 1649

  • DOI: https://doi.org/10.1016/j.str.2025.07.006
  • Primary Citation of Related Structures:  
    9MGB, 9MKO, 9O60, 9O61, 9O62

  • PubMed 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 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.


  • Organizational Affiliation
    • Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
R-phycoerythrin class I alpha subunit164Ceramium secundatumMutation(s): 0 
UniProt
Find proteins for O36005 (Griffithsia monilis)
Explore O36005 
Go to UniProtKB:  O36005
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UniProt GroupO36005
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
R-phycoerythrin class I beta subunit176Ceramium secundatumMutation(s): 0 
UniProt
Find proteins for P51367 (Porphyra purpurea)
Explore P51367 
Go to UniProtKB:  P51367
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UniProt GroupP51367
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
4D4 TCR alpha chainM [auth a]196Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
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UniProt GroupP01848
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
4D4 TCR beta chainN [auth b]237Mus musculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PUB (Subject of Investigation/LOI)
Query on PUB

Download Ideal Coordinates CCD File 
AA [auth G]
HA [auth J]
KA [auth M]
PA [auth Q]
Q [auth B]
AA [auth G],
HA [auth J],
KA [auth M],
PA [auth Q],
Q [auth B],
V [auth D]
PHYCOUROBILIN
C33 H42 N4 O6
KDCCOOGTVSRCHX-YYVBKQGDSA-N
PEB (Subject of Investigation/LOI)
Query on PEB

Download Ideal Coordinates CCD File 
BA [auth G]
CA [auth G]
DA [auth I]
EA [auth I]
FA [auth J]
BA [auth G],
CA [auth G],
DA [auth I],
EA [auth I],
FA [auth J],
GA [auth J],
IA [auth L],
JA [auth L],
LA [auth M],
MA [auth M],
NA [auth O],
O [auth A],
OA [auth O],
P [auth A],
QA [auth Q],
R [auth B],
RA [auth Q],
S [auth B],
T [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth F],
Z [auth F]
PHYCOERYTHROBILIN
C33 H40 N4 O6
NKCBCVIFPXGHAV-WAVSMFBNSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP230102073

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references
  • Version 1.2: 2025-10-15
    Changes: Data collection, Database references