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- PDB-3t0e: Crystal structure of a complete ternary complex of T cell recepto... -

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Basic information

Entry
Database: PDB / ID: 3t0e
TitleCrystal structure of a complete ternary complex of T cell receptor, peptide-MHC and CD4
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-4 beta chain
  • T-cell receptor alpha chain
  • T-cell receptor beta chain
  • T-cell surface glycoprotein CD4
KeywordsIMMUNE SYSTEM / CD4 / T cell receptor / TCR / HLA class II / MHC / autoimmunity / T cell activation / Immunoglobulin fold / Membrane
Function / homology
Function and homology information


regulation of interleukin-4 production / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of interleukin-10 production / maintenance of protein location in cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation ...regulation of interleukin-4 production / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of interleukin-10 production / maintenance of protein location in cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / T cell selection / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / MHC class II protein binding / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / CD4 receptor binding / alpha-beta T cell receptor complex / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / Nef Mediated CD4 Down-regulation / Alpha-defensins / regulation of T cell activation / Other interleukin signaling / intermediate filament / extracellular matrix structural constituent / T-helper 1 type immune response / T cell receptor complex / transport vesicle membrane / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / alpha-beta T cell activation / regulation of calcium ion transport / Generation of second messenger molecules / T cell differentiation / immunological synapse / Co-inhibition by PD-1 / epidermis development / positive regulation of protein kinase activity / Binding and entry of HIV virion / detection of bacterium / T cell receptor binding / coreceptor activity / negative regulation of T cell proliferation / MHC class II antigen presentation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Vpu mediated degradation of CD4 / response to bacterium / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / T cell receptor signaling pathway / signaling receptor activity / Clathrin-mediated endocytosis / positive regulation of protein phosphorylation / virus receptor activity / early endosome membrane / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / early endosome / lysosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade
Similarity search - Function
CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor beta constant 2 / T-cell surface glycoprotein CD4 / T cell receptor alpha chain constant / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsYin, Y. / Mariuzza, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of a complete ternary complex of T-cell receptor, peptide-MHC, and CD4.
Authors: Yin, Y. / Wang, X.X. / Mariuzza, R.A.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-4 beta chain
C: T-cell receptor alpha chain
D: T-cell receptor beta chain
E: T-cell surface glycoprotein CD4


Theoretical massNumber of molelcules
Total (without water)138,3155
Polymers138,3155
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20760 Å2
Unit cell
Length a, b, c (Å)146.151, 146.151, 231.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21155.904 Da / Num. of mol.: 1 / Fragment: unp residues 26-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-4 beta chain / MHC class II antigen DRB1*4 / DR-4 / DR4


Mass: 25169.824 Da / Num. of mol.: 1 / Fragment: unp residues 30-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pET-26b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13760, UniProt: P01911*PLUS
#3: Protein T-cell receptor alpha chain


Mass: 22743.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#4: Protein T-cell receptor beta chain


Mass: 27531.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A5B9*PLUS
#5: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 41714.750 Da / Num. of mol.: 1 / Fragment: unp residues 26-398 / Mutation: Q40Y, T45W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Plasmid: pAcGP67B / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01730
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8
Details: 10 mM Tris-HCl pH8, 10 mM NaAc pH5.2, 5 mM NaCl, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→47.672 Å / Num. all: 21831 / Num. obs: 21818 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.099

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→47.672 Å / SU ML: 1.1 / σ(F): 1.34 / Phase error: 31.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3047 1066 4.89 %
Rwork0.2383 --
obs0.2417 21818 99.79 %
all-21831 -
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 181.97 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.2812 Å20 Å2-0 Å2
2--8.2812 Å20 Å2
3----16.5623 Å2
Refinement stepCycle: LAST / Resolution: 4→47.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9259 0 0 0 9259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059493
X-RAY DIFFRACTIONf_angle_d1.10312900
X-RAY DIFFRACTIONf_dihedral_angle_d17.133423
X-RAY DIFFRACTIONf_chiral_restr0.0751432
X-RAY DIFFRACTIONf_plane_restr0.0041671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.1820.39971430.37162527X-RAY DIFFRACTION100
4.182-4.40230.37091380.32422535X-RAY DIFFRACTION100
4.4023-4.67790.31561210.26142561X-RAY DIFFRACTION100
4.6779-5.03880.27931120.22712588X-RAY DIFFRACTION100
5.0388-5.54510.3261110.22352591X-RAY DIFFRACTION100
5.5451-6.34590.34831490.26542583X-RAY DIFFRACTION100
6.3459-7.98910.32891470.21112620X-RAY DIFFRACTION100
7.9891-47.67560.25861450.21542747X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.65360.1402-0.61411.3447-1.41018.1827-0.2822-1.04090.37890.74830.181-0.1632-0.25790.610101.64690.1258-0.05951.8356-0.09191.81715.509146.0548-14.9675
25.5732-1.03261.73984.7125-1.19290.89070.44490.50991.0002-0.99980.4174-0.5701-0.15160.187101.9782-0.16130.17311.7350.05111.95863.361749.6265-26.9411
32.32421.84961.4973.36243.7573.9529-0.4050.58180.9445-0.62040.36890.1290.22360.2275-01.861-0.0190.15331.85720.5042.314420.164755.5693-41.2249
41.945-0.4511-2.48813.30041.73833.38590.1125-0.9943-0.4127-0.32310.2297-0.0294-0.02751.08301.818-0.1636-0.06921.68970.13631.696335.921635.8124-37.2283
56.1348-1.585-1.64234.9288-1.75731.187-0.5631-0.338-1.29680.83750.2699-0.30910.7073-0.8306-01.6508-0.0743-0.0411.7963-0.02851.7593-20.519330.2272-13.4572
67.60832.1719-1.40131.461-0.07623.9106-0.21060.70660.7152-0.5416-0.1638-0.36750.5571-0.042801.8492-0.2555-0.21232.4927-0.09351.9497-54.834331.3643-8.5559
75.2970.49520.55565.3023-2.66154.2120.04360.31791.7139-0.48630.0660.2510.6591-1.0322-01.8835-0.06460.04341.93140.2172.1928-24.012651.5787-24.3677
81.90230.57490.23695.5086-2.92871.50740.31920.23090.39270.228-0.390.2059-0.19490.059501.8899-0.0636-0.02492.6768-0.01522.3616-51.272448.2009-9.3938
93.77020.17112.25215.49191.59083.86520.8160.2069-0.0551-0.3336-0.35610.0050.0180.181902.03920.09220.32771.9158-0.06482.034540.437857.4493-25.1327
103.34512.93191.25142.64681.9754.23950.5454-1.1735-0.0195-0.4607-0.0298-0.1893-0.24750.4448-0.00012.3270.379-0.27261.8939-0.0952.062436.957863.64676.2193
113.40223.4857-1.05043.3808-1.47492.71690.2045-0.41930.0203-0.20660.21560.2957-0.4761-1.643-02.00090.4666-0.24082.0587-0.03252.29517.028856.620934.2973
120.70530.0108-0.89-0.1192-0.05221.0145-0.02280.08310.0042-0.5240.05850.418-0.08510.3586-03.09620.27850.02742.9394-0.34512.117514.770577.465156.6298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and ((resseq 1:122))
2X-RAY DIFFRACTION2chain 'A' and resseq 1:83
3X-RAY DIFFRACTION3chain 'A' and resseq 84:181
4X-RAY DIFFRACTION4chain 'B' and resseq 123:219
5X-RAY DIFFRACTION5chain 'C' and resseq 1:109
6X-RAY DIFFRACTION6chain 'C' and resseq 110:199
7X-RAY DIFFRACTION7chain 'D' and resseq 1:115
8X-RAY DIFFRACTION8chain 'D' and resseq 116:245
9X-RAY DIFFRACTION9chain 'E' and resseq 1:97
10X-RAY DIFFRACTION10chain 'E' and resseq 98:177
11X-RAY DIFFRACTION11chain 'E' and resseq 178:290
12X-RAY DIFFRACTION12chain 'E' and resseq 291:365

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