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- PDB-1zgl: Crystal structure of 3A6 TCR bound to MBP/HLA-DR2a -

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Basic information

Entry
Database: PDB / ID: 1zgl
TitleCrystal structure of 3A6 TCR bound to MBP/HLA-DR2a
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • Myelin basic protein
  • T cell receptor alpha chain
  • T cell receptor beta chain
  • major histocompatibility complex, class II, DR beta 5
KeywordsIMMUNE SYSTEM / TCR-peptide-MHC complex
Function / homology
Function and homology information


positive regulation of metalloendopeptidase activity / compact myelin / structural constituent of myelin sheath / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / 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 metalloendopeptidase activity / compact myelin / structural constituent of myelin sheath / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / 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 / EGR2 and SOX10-mediated initiation of Schwann cell myelination / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / membrane organization / alpha-beta T cell receptor complex / positive regulation of chemokine (C-X-C motif) ligand 2 production / transport vesicle membrane / maintenance of blood-brain barrier / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / myelination / MHC class II antigen presentation / substantia nigra development / central nervous system development / trans-Golgi network membrane / cell periphery / lumenal side of endoplasmic reticulum membrane / response to bacterium / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / sensory perception of sound / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / positive regulation of interleukin-6 production / positive regulation of T cell mediated cytotoxicity / response to toxic substance / cognition / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / myelin sheath / MAPK cascade / protease binding / early endosome membrane / chemical synaptic transmission / adaptive immune response / calmodulin binding / lysosome / immune response / Golgi membrane / lysosomal membrane / neuronal cell body / synapse / lipid binding / cell surface / protein-containing complex / extracellular exosome / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / 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 ...Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant / T cell receptor beta constant 1 / HLA class II histocompatibility antigen, DR alpha chain / Myelin basic protein / HLA class II histocompatibility antigen, DR beta 5 chain / HLA class II histocompatibility antigen, DR beta 5 chain / Myelin basic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, Y. / Huang, Y. / Lue, J. / Quandt, J.A. / Martin, R. / Mariuzza, R.A.
CitationJournal: Embo J. / Year: 2005
Title: Structure of a human autoimmune TCR bound to a myelin basic protein self-peptide and a multiple sclerosis-associated MHC class II molecule.
Authors: Li, Y. / Huang, Y. / Lue, J. / Quandt, J.A. / Martin, R. / Mariuzza, R.A.
History
DepositionApr 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 19, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn ...entity / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _pdbx_entity_src_syn.details ..._entity.pdbx_fragment / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: major histocompatibility complex, class II, DR beta 5
C: Myelin basic protein
M: T cell receptor alpha chain
P: T cell receptor beta chain
D: HLA class II histocompatibility antigen, DR alpha chain
E: major histocompatibility complex, class II, DR beta 5
F: Myelin basic protein
Q: T cell receptor alpha chain
R: T cell receptor beta chain
G: HLA class II histocompatibility antigen, DR alpha chain
H: major histocompatibility complex, class II, DR beta 5
I: Myelin basic protein
S: T cell receptor alpha chain
T: T cell receptor beta chain
J: HLA class II histocompatibility antigen, DR alpha chain
K: major histocompatibility complex, class II, DR beta 5
L: Myelin basic protein
U: T cell receptor alpha chain
V: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)383,72620
Polymers383,72620
Non-polymers00
Water00
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: major histocompatibility complex, class II, DR beta 5
C: Myelin basic protein
M: T cell receptor alpha chain
P: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,9325
Polymers95,9325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: major histocompatibility complex, class II, DR beta 5
F: Myelin basic protein
Q: T cell receptor alpha chain
R: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,9325
Polymers95,9325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: HLA class II histocompatibility antigen, DR alpha chain
H: major histocompatibility complex, class II, DR beta 5
I: Myelin basic protein
S: T cell receptor alpha chain
T: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,9325
Polymers95,9325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: HLA class II histocompatibility antigen, DR alpha chain
K: major histocompatibility complex, class II, DR beta 5
L: Myelin basic protein
U: T cell receptor alpha chain
V: T cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,9325
Polymers95,9325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.480, 97.690, 124.020
Angle α, β, γ (deg.)74.39, 83.19, 61.55
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21084.826 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / References: UniProt: P01903
#2: Protein
major histocompatibility complex, class II, DR beta 5


Mass: 22446.783 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / References: UniProt: Q29787, UniProt: Q30154*PLUS
#3: Protein/peptide
Myelin basic protein / MBP


Mass: 1672.946 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens / References: UniProt: Q6AI64, UniProt: P02686*PLUS
#4: Protein
T cell receptor alpha chain


Mass: 22932.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / References: UniProt: P01848
#5: Protein
T cell receptor beta chain


Mass: 27794.729 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-26b / Production host: Escherichia coli (E. coli) / References: UniProt: P01850
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: 2.58 Å3/Da / Density % sol: 52.29 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 177348 / Num. obs: 81551 / % possible obs: 0.863 % / Observed criterion σ(F): 5.9 / Observed criterion σ(I): 5.9 / Rmerge(I) obs: 0.08 / Rsym value: 0.08
Reflection shellResolution: 2.8→2.92 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.284 / % possible all: 86.5

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 1617 -Random
Rwork0.28 ---
all-94436 --
obs-81551 86.4 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23456 0 0 0 23456

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