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- PDB-6jxr: Structure of a protein -

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Basic information

Entry
Database: PDB / ID: 6jxr
TitleStructure of a protein
Components
  • (T cell receptor ...T-cell receptor) x 2
  • (T-cell surface glycoprotein CD3 ...) x 4
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


FCGR activation / Regulation of actin dynamics for phagocytic cup formation / Role of phospholipids in phagocytosis / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / PD-1 signaling / Cargo recognition for clathrin-mediated endocytosis / Generation of second messenger molecules / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...FCGR activation / Regulation of actin dynamics for phagocytic cup formation / Role of phospholipids in phagocytosis / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / PD-1 signaling / Cargo recognition for clathrin-mediated endocytosis / Generation of second messenger molecules / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Clathrin-mediated endocytosis / Nef and signal transduction / 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
Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoglobulin V-set domain / Immunoglobulin C1-set domain / Immunoglobulin-like domain superfamily / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 delta chain / T-cell receptor alpha chain, constant domain ...Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoglobulin V-set domain / Immunoglobulin C1-set domain / Immunoglobulin-like domain superfamily / CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 zeta subunit / T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit / T-cell surface glycoprotein CD3 delta chain / T-cell receptor alpha chain, constant domain / T-cell surface glycoprotein CD3 zeta chain / Immunoglobulin-like fold / Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin subtype 2 / Immunoglobulin C1-set / Phosphorylated immunoreceptor signalling ITAM / Domain of unknown function (DUF1968) / Immunoreceptor tyrosine-based activation motif / T-cell surface glycoprotein CD3 delta chain / ITAM motif mammalian type profile. / Ig-like domain profile.
T cell receptor alpha variable 12-3 / T cell receptor beta constant 2 / T cell receptor beta variable 6-5 / Possible J 11 gene segment / T cell receptor alpha constant / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 epsilon chain / T-cell surface glycoprotein CD3 gamma chain / M1-specific T cell receptor beta chain / T-cell surface glycoprotein CD3 zeta chain
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / 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, 1items
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 Report
SummaryFull reportAbout validation report
History
DepositionApr 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

Deposited unit
a: T-cell surface glycoprotein CD3 zeta chain
b: T-cell surface glycoprotein CD3 zeta chain
d: T-cell surface glycoprotein CD3 delta chain
f: T-cell surface glycoprotein CD3 epsilon chain
g: T-cell surface glycoprotein CD3 gamma chain
m: T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha constant
n: T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2
e: T-cell surface glycoprotein CD3 epsilon chain


Theoretical massNumber of molelcules
Total (without water)184,0458
Polymers184,0458
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26000 Å2
ΔGint-169 kcal/mol
Surface area52040 Å2

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Components

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T-cell surface glycoprotein CD3 ... , 4 types, 6 molecules abdfeg

#1: Protein/peptide T-cell surface glycoprotein CD3 zeta chain / T-cell receptor T3 zeta chain


Mass: 18723.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD247, CD3Z, T3Z, TCRZ / Production host: Homo sapiens (human) / References: UniProt: P20963
#2: Protein/peptide T-cell surface glycoprotein CD3 delta chain / T-cell receptor T3 delta chain


Mass: 18949.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD3D, T3D / Production host: Homo sapiens (human) / References: UniProt: P04234
#3: Protein/peptide T-cell surface glycoprotein CD3 epsilon chain / T-cell surface antigen T3/Leu-4 epsilon chain


Mass: 23174.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD3E, T3E / Production host: Homo sapiens (human) / References: UniProt: P07766
#4: Protein/peptide T-cell surface glycoprotein CD3 gamma chain / T-cell receptor T3 gamma chain


Mass: 20493.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD3G, T3G / Production host: Homo sapiens (human) / References: UniProt: P09693

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T cell receptor ... , 2 types, 2 molecules mn

#5: Protein/peptide T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha constant


Mass: 28308.662 Da / Num. of mol.: 1
Details: fusion protein of residues 22-114 from A0A0B4J271, residues 116-132 from A0N4Z6 and residues ...fusion protein of residues 22-114 from A0A0B4J271, residues 116-132 from A0N4Z6 and residues 134-273 from P01848.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV12-3, Tcr-alpha, TRAC, TCRA / Production host: Homo sapiens (human)
References: UniProt: A0A0B4J271, UniProt: A0N4Z6, UniProt: P01848
#6: Protein/peptide T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 / TR beta chain TRBV19*01J2S7*01C*02


Mass: 32498.463 Da / Num. of mol.: 1
Details: fusion protein of residues 22-112 from A0A0K0K1A5, residues 121-134 from P0DSE2 and residues ...fusion protein of residues 22-112 from A0A0K0K1A5, residues 121-134 from P0DSE2 and residues 135-312 from A0A0G2JMB4.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV6-5, TRB, TRBC2 / Production host: Homo sapiens (human)
References: UniProt: A0A0K0K1A5, UniProt: P0DSE2, UniProt: A0A0G2JMB4

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: complex / Type: COMPLEX / Entity ID: 1,2,3,4,5,6 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD
Image recordingElectron dose: 64.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197487 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0078633
f_angle_d0.98111715
f_dihedral_angle_d8.1725134
f_chiral_restr0.0571309
f_plane_restr0.0071492

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