[English] 日本語
Yorodumi
- PDB-9mko: 4D4 TCR bound to R-phycoerythrin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mko
Title4D4 TCR bound to R-phycoerythrin
Components
  • (R-phycoerythrin class I ...) x 2
  • 4D4 TCR alpha chain
  • 4D4 TCR beta chain
KeywordsIMMUNE SYSTEM / TCR / phycoerythrin / immunity / direct recognition
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 speciesMus musculus (house mouse)
Ceramium secundatum (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsRashleigh, L. / Gully, B.S. / Rossjohn, J.
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 17, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
F: R-phycoerythrin class I alpha subunit
G: R-phycoerythrin class I beta subunit
I: R-phycoerythrin class I alpha subunit
J: R-phycoerythrin class I beta subunit
L: R-phycoerythrin class I alpha subunit
M: R-phycoerythrin class I beta subunit
O: R-phycoerythrin class I alpha subunit
Q: R-phycoerythrin class I beta subunit
a: 4D4 TCR alpha chain
b: 4D4 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,40244
Polymers265,73014
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

-
Components

-
R-phycoerythrin class I ... , 2 types, 12 molecules ACFILOBDGJMQ

#1: Protein
R-phycoerythrin class I alpha subunit


Mass: 17753.998 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Ceramium secundatum (eukaryote) / References: UniProt: A0A1C9C9A7
#2: Protein
R-phycoerythrin class I beta subunit


Mass: 18398.875 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Ceramium secundatum (eukaryote) / References: UniProt: A0A1C9C989

-
Protein , 2 types, 2 molecules ab

#3: Protein 4D4 TCR alpha chain


Mass: 21728.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Protein 4D4 TCR beta chain


Mass: 27083.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 2 types, 30 molecules

#5: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN


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


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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1ternary complex of 4D4 alpha/beta TCR bound to R-phycoerythrinCOMPLEX#3-#4, #1-#20RECOMBINANT
24D4 alpha beta TCRCOMPLEX#3-#41RECOMBINANT
3R-phycoerythrinCOMPLEX#1-#21NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
32Mus musculus (house mouse)10090
43Ceramium secundatum (eukaryote)193556
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
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)

-
Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27700 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more