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- PDB-1ymm: TCR/HLA-DR2b/MBP-peptide complex -

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Basic information

Entry
Database: PDB / ID: 1ymm
TitleTCR/HLA-DR2b/MBP-peptide complex
Components
  • (HLA class II histocompatibility antigen, DR ...) x 2
  • MBP peptide
  • T cell receptor alpha chain
  • T-cell receptor beta chain
KeywordsIMMUNE SYSTEM / protein-protein complex / T cell repertoire / auto-immunity
Function / homology
Function and homology information


compact myelin / structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II ...compact myelin / structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 T cell mediated immune response to tumor cell / positive regulation of kinase activity / membrane organization / positive regulation of memory T cell differentiation / CD4 receptor binding / alpha-beta T cell receptor complex / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / positive regulation of chemokine (C-X-C motif) ligand 2 production / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / maintenance of blood-brain barrier / 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 / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / substantia nigra development / myelination / MHC class II antigen presentation / central nervous system development / trans-Golgi network membrane / cell periphery / lumenal side of endoplasmic reticulum membrane / protein tetramerization / response to bacterium / peptide antigen assembly with MHC class II protein complex / sensory perception of sound / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / 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 interleukin-6 production / positive regulation of T cell activation / cognition / response to toxic substance / 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 / MAPK cascade / Downstream TCR signaling / myelin sheath / T cell receptor signaling pathway / positive regulation of protein phosphorylation / protease binding / early endosome membrane / chemical synaptic transmission / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / calmodulin binding / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / neuronal cell body / synapse / lipid binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / protein-containing complex
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 / HLA class II histocompatibility antigen, DRB1 beta chain / Myelin basic protein / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHahn, M. / Nicholson, M.J. / Pyrdol, J. / Wucherpfennig, K.W.
CitationJournal: NAT.IMMUNOL. / Year: 2005
Title: Unconventional topology of self peptide-major histocompatibility complex binding by a human autoimmune T cell receptor.
Authors: Hahn, M. / Nicholson, M.J. / Pyrdol, J. / Wucherpfennig, K.W.
History
DepositionJan 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE These mutations are located in the hypervariable region of the chain and are unique to ...SEQUENCE These mutations are located in the hypervariable region of the chain and are unique to specific T cell receptor.

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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, DR beta chain
C: MBP peptide
D: T cell receptor alpha chain
E: T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5206
Polymers98,2985
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.340, 212.620, 278.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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HLA class II histocompatibility antigen, DR ... , 2 types, 2 molecules AB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / HLA-DR2b alpha


Mass: 22107.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Plasmid: pAcDB3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SF9 / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DR beta chain / HLA-DR2b beta


Mass: 22991.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcDB3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SF9 / References: UniProt: Q29790, UniProt: P01911*PLUS

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Protein , 2 types, 2 molecules DE

#4: Protein T cell receptor alpha chain / TCR Ob.1A12 alpha


Mass: 22978.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcDB3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SF9 / References: GenBank: 29293741, UniProt: P01848*PLUS
#5: Protein T-cell receptor beta chain / TCR Ob.1A12 beta


Mass: 27934.092 Da / Num. of mol.: 1 / Mutation: C13S, C193S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcDB3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SF9 / References: UniProt: P01850

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Protein/peptide / Sugars , 2 types, 2 molecules C

#3: Protein/peptide MBP peptide


Mass: 2286.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P02686
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 6 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 7
Details: Na-tartrate, ammonium formate, HEPES, pH 7.0, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC / Detector: CCD / Date: Nov 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 35129 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.103 / Χ2: 1.096
Reflection shell
Resolution (Å)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3.1-3.2129950.949182.1
3.21-3.3434511.007192.90.787
3.34-3.4935061.097195.60.586
3.49-3.6736101.111197.60.382
3.67-3.935931.184197.30.259
3.9-4.235911.14196.80.162
4.2-4.6235881.0721970.097
4.62-5.2736131.097196.90.08
5.27-6.6136111.174196.20.075
6.61-2035711.057192.80.041

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNS1refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→19.72 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3765203.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1236 5 %RANDOM
Rwork0.274 ---
all0.276 24725 --
obs0.276 24725 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.858 Å2 / ksol: 0.229 e/Å3
Displacement parametersBiso mean: 71.5 Å2
Baniso -1Baniso -2Baniso -3
1-13.28 Å20 Å20 Å2
2--2.19 Å20 Å2
3----15.47 Å2
Refinement stepCycle: LAST / Resolution: 3.5→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5774 0 15 0 5789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d27.04
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 221 5.4 %
Rwork0.344 3899 -
obs--97.6 %

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