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- EMDB-45614: T cell receptor complex -

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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 / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / Fc-gamma receptor signaling pathway ...regulation of lymphocyte apoptotic process / gamma-delta T cell receptor complex / Fc-gamma receptor III complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / CD4-positive, alpha-beta T cell proliferation / gamma-delta T cell activation / negative thymic T cell selection / Fc-gamma receptor signaling pathway / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of protein localization to cell surface / signal complex assembly / Nef and signal transduction / positive regulation of cell-matrix adhesion / T cell receptor complex / establishment or maintenance of cell polarity / smoothened signaling pathway / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / dendrite development / small molecule binding / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / FCGR activation / PD-1 signaling / Role of phospholipids in phagocytosis / T cell receptor binding / negative regulation of smoothened signaling pathway / positive regulation of T cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / T cell activation / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / FCGR3A-mediated IL10 synthesis / cerebellum development / protein tyrosine kinase binding / clathrin-coated endocytic vesicle membrane / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / calcium-mediated signaling / transmembrane signaling receptor activity / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / positive regulation of type II interferon production / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / Clathrin-mediated endocytosis / signaling receptor complex adaptor activity / protein transport / Downstream TCR signaling / protein complex oligomerization / T cell receptor signaling pathway / cell body / protein-containing complex assembly / regulation of apoptotic process / adaptive immune response / dendritic spine / cell surface receptor signaling pathway / protein heterodimerization activity / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 zeta subunit / : / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / Immunoreceptor tyrosine-based activation motif ...: / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 zeta subunit / : / Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 zeta chain / 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: To Be Published
Title: T cell receptor complex
Authors: Gully BS / Rossjohn J
History
DepositionJul 2, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45614.png

Downloads & links

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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
Voxel sizeX=Y=Z: 0.82 Å
Density
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 °

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Supplemental data

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Mask #1

Fileemd_45614_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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Histogram

Histogram (log scale)

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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

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Additional map: Non-sharpened overall map

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

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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Histogram

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Additional map: DeepEMhancer postprocessed main map

Fileemd_45614_additional_5.map
AnnotationDeepEMhancer postprocessed main map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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)

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Half map: Half-map B for overall map

Fileemd_45614_half_map_2.map
AnnotationHalf-map B for overall map
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Sample components

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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Image processing

Particle selectionNumber selected: 2663326
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)

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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

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