[English] 日本語
Yorodumi
- EMDB-45614: T cell receptor complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45614
TitleT cell receptor complex
Map dataMain B-factor sharpened overall map
Sample
  • Complex: T cell receptor complex
    • Protein or peptide: UCHT1 Fab
    • Protein or peptide: UCHT1 Fab chain 2
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
    • Protein or peptide: T cell receptor delta constant
    • Protein or peptide: T cell receptor gamma constant 1
KeywordsT cell receptor T cell immunity / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of lymphocyte apoptotic process / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / positive regulation of cell-cell adhesion mediated by integrin / positive thymic T cell selection / signal complex assembly / Nef and signal transduction / alpha-beta T cell receptor complex / T cell receptor complex ...regulation of lymphocyte apoptotic process / Fc-gamma receptor III complex / Fc-gamma receptor signaling pathway / gamma-delta T cell activation / positive regulation of cell-cell adhesion mediated by integrin / positive thymic T cell selection / signal complex assembly / Nef and signal transduction / alpha-beta T cell receptor complex / T cell receptor complex / positive regulation of cell-matrix adhesion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / dendrite development / small molecule binding / protein complex oligomerization / establishment or maintenance of cell polarity / alpha-beta T cell activation / Generation of second messenger molecules / FCGR activation / immunological synapse / Co-inhibition by PD-1 / Role of phospholipids in phagocytosis / T cell receptor binding / cerebellum development / positive regulation of T cell proliferation / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / T cell activation / FCGR3A-mediated phagocytosis / clathrin-coated endocytic vesicle membrane / SH3 domain binding / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / transmembrane signaling receptor activity / T cell receptor signaling pathway / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / signaling receptor complex adaptor activity / protein-containing complex assembly / cell body / regulation of apoptotic process / dendritic spine / adaptive immune response / protein-macromolecule adaptor activity / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / protein heterodimerization activity / negative regulation of gene expression / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / Golgi apparatus / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / : / T-cell surface glycoprotein CD3 zeta subunit / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif ...: / : / T-cell surface glycoprotein CD3 zeta subunit / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T cell receptor delta constant / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 epsilon chain / T-cell surface glycoprotein CD3 gamma chain / T cell receptor gamma constant 1 / T-cell surface glycoprotein CD3 zeta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsGully BS / Rossjohn J
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230102073 Australia
CitationJournal: Nature / Year: 2024
Title: Structure of a fully assembled γδ T cell antigen receptor.
Authors: Benjamin S Gully / João Ferreira Fernandes / Sachith D Gunasinghe / Mai T Vuong / Yuan Lui / Michael T Rice / Liam Rashleigh / Chan-Sien Lay / Dene R Littler / Sumana Sharma / Ana Mafalda ...Authors: Benjamin S Gully / João Ferreira Fernandes / Sachith D Gunasinghe / Mai T Vuong / Yuan Lui / Michael T Rice / Liam Rashleigh / Chan-Sien Lay / Dene R Littler / Sumana Sharma / Ana Mafalda Santos / Hariprasad Venugopal / Jamie Rossjohn / Simon J Davis /
Abstract: T cells in jawed vertebrates comprise two lineages, αβ T cells and γδ T cells, defined by the antigen receptors they express-that is, αβ and γδ T cell receptors (TCRs), respectively. ...T cells in jawed vertebrates comprise two lineages, αβ T cells and γδ T cells, defined by the antigen receptors they express-that is, αβ and γδ T cell receptors (TCRs), respectively. The two lineages have different immunological roles, requiring that γδ TCRs recognize more structurally diverse ligands. Nevertheless, the receptors use shared CD3 subunits to initiate signalling. Whereas the structural organization of αβ TCRs is understood, the architecture of γδ TCRs is unknown. Here, we used cryogenic electron microscopy to determine the structure of a fully assembled, MR1-reactive, human Vγ8Vδ3 TCR-CD3δγεζ complex bound by anti-CD3ε antibody Fab fragments. The arrangement of CD3 subunits in γδ and αβ TCRs is conserved and, although the transmembrane α-helices of the TCR-γδ and -αβ subunits differ markedly in sequence, packing of the eight transmembrane-helix bundles is similar. However, in contrast to the apparently rigid αβ TCR, the γδ TCR exhibits considerable conformational heterogeneity owing to the ligand-binding TCR-γδ subunits being tethered to the CD3 subunits by their transmembrane regions only. Reducing this conformational heterogeneity by transfer of the Vγ8Vδ3 TCR variable domains to an αβ TCR enhanced receptor signalling, suggesting that γδ TCR organization reflects a compromise between efficient signalling and the ability to engage structurally diverse ligands. Our findings reveal the marked structural plasticity of the TCR on evolutionary timescales, and recast it as a highly versatile receptor capable of initiating signalling as either a rigid or flexible structure.
History
DepositionJul 2, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45614.png

Downloads & links

-
Map

FileDownload / File: emd_45614.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain B-factor sharpened overall map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å		0.82 Å/pix.
x 480 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.2221788 - 1.9033381
Average (Standard dev.)-0.00011048855 (±0.017357197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_45614_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local B-factor sharpened refinement of the transmembrane region

Fileemd_45614_additional_1.map
AnnotationLocal B-factor sharpened refinement of the transmembrane region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local non-sharpened refinement of the transmembrane region

Fileemd_45614_additional_2.map
AnnotationLocal non-sharpened refinement of the transmembrane region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-sharpened overall map

Fileemd_45614_additional_3.map
AnnotationNon-sharpened overall map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Ab initio reconstruction for the TCR extracellular domain

Fileemd_45614_additional_4.map
AnnotationAb initio reconstruction for the TCR extracellular domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: DeepEMhancer postprocessed main map

Fileemd_45614_additional_5.map
AnnotationDeepEMhancer postprocessed main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map A for overall map

Fileemd_45614_half_map_1.map
AnnotationHalf-map A for overall map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map B for overall map

Fileemd_45614_half_map_2.map
AnnotationHalf-map B for overall map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : T cell receptor complex

EntireName: T cell receptor complex
Components
  • Complex: T cell receptor complex
    • Protein or peptide: UCHT1 Fab
    • Protein or peptide: UCHT1 Fab chain 2
    • Protein or peptide: T-cell surface glycoprotein CD3 zeta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 delta chain
    • Protein or peptide: T-cell surface glycoprotein CD3 epsilon chain
    • Protein or peptide: T-cell surface glycoprotein CD3 gamma chain
    • Protein or peptide: T cell receptor delta constant
    • Protein or peptide: T cell receptor gamma constant 1

-
Supramolecule #1: T cell receptor complex

SupramoleculeName: T cell receptor complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

-
Macromolecule #1: UCHT1 Fab

MacromoleculeName: UCHT1 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.614113 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDIQMTQTTS SLSASLGDRV TISCRASQDI RNYLNWYQQK PDGTVKLLIY YTSRLHSGVP SKFSGSGSGT DYSLTISNLE QEDIATYFC QQGNTLPWTF AGGTKLEI(UNK)(UNK) RADAAPTVSI FPPASEQLTS GGASVVCFLN NFYPKSINSK WKI DGSERQ ...String:
MDIQMTQTTS SLSASLGDRV TISCRASQDI RNYLNWYQQK PDGTVKLLIY YTSRLHSGVP SKFSGSGSGT DYSLTISNLE QEDIATYFC QQGNTLPWTF AGGTKLEI(UNK)(UNK) RADAAPTVSI FPPASEQLTS GGASVVCFLN NFYPKSINSK WKI DGSERQ NGVLNSWTDQ DSKDSTYSMS STLTLTKNEY ERHNSYTCEA THK(UNK)(UNK)(UNK)SPIV KSFNRS

-
Macromolecule #2: UCHT1 Fab chain 2

MacromoleculeName: UCHT1 Fab chain 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.766975 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLQQSGPE LVKPGASMKI SCKASGYSFT GYTMNWVKQS HGKNLEWMGL INPYKGVSTY NQKFKDKATL TVDKSSSTAY MELLSLTSE DSAVYYCARS GYYGDSDWYF DVWGQGTTLT VFSAKTTPPS VYPLAPGS(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)MVTLG ...String:
EVQLQQSGPE LVKPGASMKI SCKASGYSFT GYTMNWVKQS HGKNLEWMGL INPYKGVSTY NQKFKDKATL TVDKSSSTAY MELLSLTSE DSAVYYCARS GYYGDSDWYF DVWGQGTTLT VFSAKTTPPS VYPLAPGS(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)MVTLG CLVKGYFPEP VTVTWNSGSL SSGVHTFPAV LKSDLYTLSS SVTV(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)VTCNVA HPASSTTVDK KIVPR

-
Macromolecule #3: T-cell surface glycoprotein CD3 zeta chain

MacromoleculeName: T-cell surface glycoprotein CD3 zeta chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.605425 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
LDPKLCYLLD GILFIYGVIL TALFLRVKFS R

UniProtKB: T-cell surface glycoprotein CD3 zeta chain

-
Macromolecule #4: T-cell surface glycoprotein CD3 delta chain

MacromoleculeName: T-cell surface glycoprotein CD3 delta chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.693529 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
FKIPIEELED RVFVNCNTSI TWVEGTVGTL LSDITRLDLG KRILDPRGIY RCNGTDIYKD KESTVQVHYR MCQSCVELDP ATVAGIIVT DVIATLLLAL GVFCFA

UniProtKB: T-cell surface glycoprotein CD3 delta chain

-
Macromolecule #5: T-cell surface glycoprotein CD3 epsilon chain

MacromoleculeName: T-cell surface glycoprotein CD3 epsilon chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.111933 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QTPYKVSISG TTVILTCPQY PGSEILWQHN DKNIGGDEDD KNIGSDEDHL SLKEFSELEQ SGYYVCYPRG SKPEDANFYL YLRARVCEN CMEMDVMSVA TIVIVDICIT GGLLLLVYYW SKNRK

UniProtKB: T-cell surface glycoprotein CD3 epsilon chain

-
Macromolecule #6: T-cell surface glycoprotein CD3 gamma chain

MacromoleculeName: T-cell surface glycoprotein CD3 gamma chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.900892 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
SIKGNHLVKV YDYQEDGSVL LTCDAEAKNI TWFKDGKMIG FLTEDKKKWN LGSNAKDPRG MYQCKGSQNK SKPLQVYYRM CQNCIELNA ATISGFLFAE IVSIFVLAVG VYFIAG

UniProtKB: T-cell surface glycoprotein CD3 gamma chain

-
Macromolecule #7: T cell receptor delta constant

MacromoleculeName: T cell receptor delta constant / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.104061 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
HTEKVNMMSL TVLGLRMLFA KTVAVNFLLT AKLFFL

UniProtKB: T cell receptor delta constant

-
Macromolecule #8: T cell receptor gamma constant 1

MacromoleculeName: T cell receptor gamma constant 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.403386 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
TLLLQLTNTS AYYMYLLLLL KSVVYFAIIT CCLLRRTA

UniProtKB: T cell receptor gamma constant 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.4 / Details: Hepes buffer saline
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum ER / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2663326
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7phr

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.0) / Number images used: 193581
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.2.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7phr


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9ci8:
T cell receptor complex

+
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