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- EMDB-9895: Structure of a protein -

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Basic information

Entry
Database: EMDB / ID: EMD-9895
TitleStructure of a protein
Map data
Samplecomplex
  • (T-cell surface glycoprotein CD3 ...) x 4
  • (T cell receptor ...T-cell receptor) x 2
Function / homology
Function and homology information


FCGR activation / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / PD-1 signaling / Role of phospholipids in phagocytosis / Regulation of actin dynamics for phagocytic cup formation / Generation of second messenger molecules / Nef and signal transduction / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains ...FCGR activation / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / PD-1 signaling / Role of phospholipids in phagocytosis / Regulation of actin dynamics for phagocytic cup formation / Generation of second messenger molecules / Nef and signal transduction / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of lymphocyte apoptotic process / interleukin-2 production / positive regulation of T cell anergy / alpha-beta T cell receptor complex / positive regulation of cell-cell adhesion mediated by integrin / negative regulation of smoothened signaling pathway / receptor signaling complex adaptor activity / negative thymic T cell selection / positive regulation of protein localization to cell surface / positive regulation of alpha-beta T cell proliferation / positive thymic T cell selection / establishment or maintenance of cell polarity / positive regulation of interleukin-4 production / signal complex assembly / positive regulation of cell-matrix adhesion / positive regulation of interleukin-2 biosynthetic process / positive regulation of calcium-mediated signaling / dendrite development / immunological synapse / T cell differentiation / T cell receptor complex / clathrin-coated vesicle membrane / protein homotrimerization / positive regulation of T cell proliferation / protein tyrosine kinase binding / cerebellum development / T cell activation / T cell receptor binding / apoptotic signaling pathway / response to nutrient / positive regulation of interferon-gamma production / T cell costimulation / cell body / regulation of defense response to virus by virus / SH3 domain binding / protein transport / transmembrane signaling receptor activity / cell-cell junction / protein-containing complex assembly / Fc-gamma receptor signaling pathway involved in phagocytosis / membrane organization / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane receptor protein tyrosine kinase signaling pathway / regulation of immune response / protein homooligomerization / regulation of apoptotic process / transcription coactivator activity / T cell receptor signaling pathway / adaptive immune response / cell surface receptor signaling pathway / dendritic spine / protein homotetramerization / negative regulation of gene expression / external side of plasma membrane / G protein-coupled receptor signaling pathway / positive regulation of gene expression / protein heterodimerization activity / protein kinase binding / integral component of plasma membrane / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / integral component of membrane / identical protein binding / plasma membrane / cytoplasm
Immunoreceptor tyrosine-based activation motif / Ig-like domain profile. / CD3 protein, epsilon/gamma/delta subunit / T-cell receptor alpha chain, constant domain / T-cell surface glycoprotein CD3 zeta subunit / Immunoglobulin-like fold / CD3 gamma/delta subunit, Ig-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin V-set domain / Immunoglobulin-like domain ...Immunoreceptor tyrosine-based activation motif / Ig-like domain profile. / CD3 protein, epsilon/gamma/delta subunit / T-cell receptor alpha chain, constant domain / T-cell surface glycoprotein CD3 zeta subunit / Immunoglobulin-like fold / CD3 gamma/delta subunit, Ig-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin C1-set domain / Immunoglobulin V-set domain / Domain of unknown function (DUF1968) / Immunoglobulin subtype / T-cell surface glycoprotein CD3 zeta chain / T-cell surface glycoprotein CD3 delta chain / ITAM motif mammalian type profile. / T-cell surface glycoprotein CD3 delta chain / Phosphorylated immunoreceptor signalling ITAM / Immunoglobulin C1-set / Immunoglobulin subtype 2 / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit
T-cell surface glycoprotein CD3 delta chain / M1-specific T cell receptor beta chain / T-cell surface glycoprotein CD3 gamma chain / T-cell surface glycoprotein CD3 epsilon chain / T cell receptor beta constant 2 / T cell receptor alpha constant / Possible J 11 gene segment / T cell receptor beta variable 6-5 / T cell receptor alpha variable 12-3 / T-cell surface glycoprotein CD3 zeta chain
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDong D / Zheng L / Lin J / Zhu Y / Li N / Zhang B / Xie S / Zheng J / Wang Y / Gao N / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Nature / Year: 2019
Title: Structural basis of assembly of the human T cell receptor-CD3 complex.
Authors: De Dong / Lvqin Zheng / Jianquan Lin / Bailing Zhang / Yuwei Zhu / Ningning Li / Shuangyu Xie / Yuhang Wang / Ning Gao / Zhiwei Huang /
Abstract: The αβ T cell receptor (TCR), in association with the CD3γε-CD3δε-CD3ζζ signalling hexamer, is the primary determinant of T cell development and activation, and of immune responses to foreign ...The αβ T cell receptor (TCR), in association with the CD3γε-CD3δε-CD3ζζ signalling hexamer, is the primary determinant of T cell development and activation, and of immune responses to foreign antigens. The mechanism of assembly of the TCR-CD3 complex remains unknown. Here we report a cryo-electron microscopy structure of human TCRαβ in complex with the CD3 hexamer at 3.7 Å resolution. The structure contains the complete extracellular domains and all the transmembrane helices of TCR-CD3. The octameric TCR-CD3 complex is assembled with 1:1:1:1 stoichiometry of TCRαβ:CD3γε:CD3δε:CD3ζζ. Assembly of the extracellular domains of TCR-CD3 is mediated by the constant domains and connecting peptides of TCRαβ that pack against CD3γε-CD3δε, forming a trimer-like structure proximal to the plasma membrane. The transmembrane segment of the CD3 complex adopts a barrel-like structure formed by interaction of the two transmembrane helices of CD3ζζ with those of CD3γε and CD3δε. Insertion of the transmembrane helices of TCRαβ into the barrel-like structure via both hydrophobic and ionic interactions results in transmembrane assembly of the TCR-CD3 complex. Together, our data reveal the structural basis for TCR-CD3 complex assembly, providing clues to TCR triggering and a foundation for rational design of immunotherapies that target the complex.
Validation ReportPDB-ID: 6jxr

SummaryFull reportAbout validation report
History
DepositionApr 24, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseSep 11, 2019-
UpdateSep 18, 2019-
Current statusSep 18, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0291
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0291
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6jxr
  • Surface level: 0.0291
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9895.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 295.96 Å
1.06 Å/pix.
x 280 pix.
= 295.96 Å
1.06 Å/pix.
x 280 pix.
= 295.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.057 Å
Density
Contour LevelBy AUTHOR: 0.0291 / Movie #1: 0.0291
Minimum - Maximum-0.10278036 - 0.15216365
Average (Standard dev.)0.00004511633 (±0.0028621645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 295.96002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0571.0571.057
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z295.960295.960295.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1030.1520.000

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Supplemental data

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Sample components

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Entire complex

EntireName: complex / Number of components: 7

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Component #1: protein, complex

ProteinName: complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, T-cell surface glycoprotein CD3 zeta chain

ProteinName: T-cell surface glycoprotein CD3 zeta chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 18.723439 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, T-cell surface glycoprotein CD3 delta chain

ProteinName: T-cell surface glycoprotein CD3 delta chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.949537 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, T-cell surface glycoprotein CD3 epsilon chain

ProteinName: T-cell surface glycoprotein CD3 epsilon chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.174227 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, T-cell surface glycoprotein CD3 gamma chain

ProteinName: T-cell surface glycoprotein CD3 gamma chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.493457 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, T cell receptor alpha variable 12-3,Possible J 11 gene s...

ProteinName: T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha constant
Details: fusion protein of residues 22-114 from A0A0B4J271, residues 116-132 from A0N4Z6 and residues 134-273 from P01848.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.308662 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, T cell receptor beta variable 6-5,M1-specific T cell rec...

ProteinName: T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2
Details: fusion protein of residues 22-112 from A0A0K0K1A5, residues 121-134 from P0DSE2 and residues 135-312 from A0A0G2JMB4.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.498463 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 64.4 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 197487
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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