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- PDB-9o60: Local refinement of 1C5H TCR bound to R-phycoerythrin (gamma chai... -

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Basic information

Entry
Database: PDB / ID: 9o60
TitleLocal refinement of 1C5H TCR bound to R-phycoerythrin (gamma chain dimer)
Components
  • 1C5H TCR delta chain
  • 1C5H TCR gamma chain
KeywordsIMMUNE SYSTEM / T-cell / gamma delta TCR / phycoerythrin / direct
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 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 gamma delta T cell receptor toward a foreign antigen
Authors: 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.
History
DepositionApr 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1C5H TCR gamma chain
a: 1C5H TCR delta chain
b: 1C5H TCR gamma chain


Theoretical massNumber of molelcules
Total (without water)80,9163
Polymers80,9163
Non-polymers00
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 1C5H TCR gamma chain


Mass: 27014.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein 1C5H TCR delta chain


Mass: 26886.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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

ComponentName: 1C5H TCR / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
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: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45513 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044182
ELECTRON MICROSCOPYf_angle_d0.6185680
ELECTRON MICROSCOPYf_dihedral_angle_d6.895564
ELECTRON MICROSCOPYf_chiral_restr0.046623
ELECTRON MICROSCOPYf_plane_restr0.005710

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