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- PDB-3o6f: Crystal structure of a human autoimmune TCR MS2-3C8 bound to MHC ... -

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Basic information

Entry
Database: PDB / ID: 3o6f
TitleCrystal structure of a human autoimmune TCR MS2-3C8 bound to MHC class II self-ligand MBP/HLA-DR4
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-4 beta chain
  • T-cell receptor alpha chain C region
  • T-cell receptor beta-1 chain C region
KeywordsIMMUNE SYSTEM / Autoimmunity / Multiple sclerosis / T cell receptor / HLA class II / protein-protein complex / Immunoglobulin fold / Membrane
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor 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 / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor 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 / 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 / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / alpha-beta T cell receptor complex / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / 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 / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / response to bacterium / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
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 ...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 / MHC classes I/II-like antigen recognition protein / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor beta constant 2 / 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: 2.8 Å
AuthorsYin, Y. / Li, Y. / Martin, R. / Mariuzza, R.A.
CitationJournal: Embo J. / Year: 2011
Title: Structure of a TCR with high affinity for self-antigen reveals basis for escape from negative selection.
Authors: Yin, Y. / Li, Y. / Kerzic, M.C. / Martin, R. / Mariuzza, R.A.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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 C region
D: T-cell receptor beta-1 chain C region
E: HLA class II histocompatibility antigen, DR alpha chain
F: HLA class II histocompatibility antigen, DRB1-4 beta chain
G: T-cell receptor alpha chain C region
H: T-cell receptor beta-1 chain C region


Theoretical massNumber of molelcules
Total (without water)193,2018
Polymers193,2018
Non-polymers00
Water48627
1
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 C region
D: T-cell receptor beta-1 chain C region


Theoretical massNumber of molelcules
Total (without water)96,6004
Polymers96,6004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HLA class II histocompatibility antigen, DR alpha chain
F: HLA class II histocompatibility antigen, DRB1-4 beta chain
G: T-cell receptor alpha chain C region
H: T-cell receptor beta-1 chain C region


Theoretical massNumber of molelcules
Total (without water)96,6004
Polymers96,6004
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.480, 218.403, 98.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.: 2 / 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.: 2 / Fragment: unp residues 30-220
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 C region


Mass: 22743.068 Da / Num. of mol.: 2 / Fragment: unp residues 1-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAC, TCRA / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848
#4: Protein T-cell receptor beta-1 chain C region


Mass: 27531.672 Da / Num. of mol.: 2 / Fragment: unp residues 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBC1 / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A5B9
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 10% (w/v) polyethylene glycol 8000, 0.2 M calcium acetate, and 0.1 M imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2009
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL SAGITTAL FOCUSING MONOCHROMETER AND VERTICAL FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.8→49.2 Å / Num. obs: 55156 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBG ENTRIES 1J8H, 1YMM, 3DX9, 1KGC

1j8h

1ymm

3dx9

1kgc


Resolution: 2.8→49.2 Å / SU ML: 0.39 / σ(F): 1.33 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 2782 5.05 %
Rwork0.239 --
obs0.239 55100 99.8 %
all-55256 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.97 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5903 Å20 Å2-0 Å2
2--9.5502 Å20 Å2
3----5.9599 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12860 0 0 27 12887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113230
X-RAY DIFFRACTIONf_angle_d1.33918009
X-RAY DIFFRACTIONf_dihedral_angle_d14.8914686
X-RAY DIFFRACTIONf_chiral_restr0.0841963
X-RAY DIFFRACTIONf_plane_restr0.0072358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.36692670.32025094X-RAY DIFFRACTION99
2.9001-3.01620.38412910.31095160X-RAY DIFFRACTION100
3.0162-3.15340.34442470.27845197X-RAY DIFFRACTION100
3.1534-3.31960.35743040.27895162X-RAY DIFFRACTION100
3.3196-3.52760.30362620.26135209X-RAY DIFFRACTION100
3.5276-3.79980.28722520.25035233X-RAY DIFFRACTION100
3.7998-4.18210.28923020.2295174X-RAY DIFFRACTION100
4.1821-4.78680.23362660.1965283X-RAY DIFFRACTION100
4.7868-6.02910.23752900.20775305X-RAY DIFFRACTION100
6.0291-49.21360.24183010.23455501X-RAY DIFFRACTION100

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