[English] 日本語
Yorodumi
- PDB-3t0e: Crystal structure of a complete ternary complex of T cell recepto... -

+
Open data


ID or keywords:

Loading...

-
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


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of interleukin-4 production / 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 / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of interleukin-4 production / 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 / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / T cell selection / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / alpha-beta T cell receptor complex / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Alpha-defensins / inflammatory response to antigenic stimulus / positive regulation of kinase activity / regulation of T cell activation / transport vesicle membrane / intermediate filament / T cell receptor complex / extracellular matrix structural constituent / polysaccharide binding / T-helper 1 type immune response / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of calcium ion transport / alpha-beta T cell activation / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / epidermis development / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / T cell receptor binding / positive regulation of calcium-mediated signaling / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / immunoglobulin complex, circulating / immunoglobulin receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / MHC class II antigen presentation / positive regulation of interleukin-2 production / protein tyrosine kinase binding / trans-Golgi network membrane / complement activation, classical pathway / Vpu mediated degradation of CD4 / calcium-mediated signaling / lumenal side of endoplasmic reticulum membrane / protein tetramerization / antigen binding / response to bacterium / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / transmembrane signaling receptor activity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / positive regulation of peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / MHC class II protein complex binding / Clathrin-mediated endocytosis / late endosome membrane / virus receptor activity / signaling receptor activity / T cell receptor signaling pathway / early endosome membrane / antibacterial humoral response / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium
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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://pdbjlvh1.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