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- PDB-2iam: Structural basis for recognition of mutant self by a tumor-specif... -

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Basic information

Entry
Database: PDB / ID: 2iam
TitleStructural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR
Components
  • (CD4+ T cell receptor E8 ...) x 2
  • (HLA class II histocompatibility antigen, ...) x 2
  • 15-mer peptide from Triosephosphate isomerase
KeywordsIMMUNE SYSTEM / major histocompatibility complex / T cell receptor / T cell stimulation / melanoma / tumor antigen
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / 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 ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / 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 / 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 / triose-phosphate isomerase / triose-phosphate isomerase activity / alpha-beta T cell receptor complex / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / Gluconeogenesis / CD4 receptor binding / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / Glycolysis / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / 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 / alpha-beta T cell activation / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / glycolytic process / gluconeogenesis / lumenal side of endoplasmic reticulum membrane / response to bacterium / protein tetramerization / 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 / ER to Golgi transport vesicle membrane / 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 / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / positive regulation of protein phosphorylation / 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 / early endosome membrane / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / nucleus / membrane / plasma membrane / cytosol
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) / Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase ...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) / Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / 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 / Aldolase-type TIM barrel / 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 / HLA class II histocompatibility antigen, DRB1 beta chain / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDeng, L. / Langley, R.J. / Mariuzza, R.A.
CitationJournal: Nat.Immunol. / Year: 2007
Title: Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor
Authors: Deng, L. / Langley, R.J. / Brown, P.H. / Xu, G. / Teng, L. / Wang, Q. / Gonzales, M.I. / Callender, G.G. / Nishimura, M.I. / Topalian, S.L. / Mariuzza, R.A.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, DRB1-1 beta chain
P: 15-mer peptide from Triosephosphate isomerase
C: CD4+ T cell receptor E8 alpha chain
D: CD4+ T cell receptor E8 beta chain


Theoretical massNumber of molelcules
Total (without water)94,2065
Polymers94,2065
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-74 kcal/mol
Surface area36030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.391, 270.542, 97.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
DetailsEach asymmetric unit contains one biological unit.

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Components

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

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA / major histocompatibility complex class II HLA-DR1 alpha chain


Mass: 21155.904 Da / Num. of mol.: 1 / Fragment: residues 1-182 (26-207)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class I antigen DRB1*1 / DR-1 / DR1 / major histocompatibility complex class II HLA-DR1 beta chain


Mass: 22080.664 Da / Num. of mol.: 1 / Fragment: residues 1-190 (30-219)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04229, UniProt: P01911*PLUS

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CD4+ T cell receptor E8 ... , 2 types, 2 molecules CD

#4: Protein CD4+ T cell receptor E8 alpha chain


Mass: 22399.682 Da / Num. of mol.: 1 / Mutation: T156C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01848
#5: Protein CD4+ T cell receptor E8 beta chain


Mass: 27088.197 Da / Num. of mol.: 1 / Mutation: S167C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01850

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Protein/peptide / Non-polymers , 2 types, 41 molecules P

#3: Protein/peptide 15-mer peptide from Triosephosphate isomerase


Mass: 1481.713 Da / Num. of mol.: 1 / Fragment: residues 23-37 (22-36) / Mutation: T28I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPI1, TPI / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60174, triose-phosphate isomerase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 26581 / % possible obs: 92.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.7
Reflection shellResolution: 2.8→2.94 Å / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3 / Num. unique all: 5639 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FYT, 1IAL

1fyt

1ial


Resolution: 2.8→41.91 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 25.523 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.747 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27915 1329 5 %RANDOM
Rwork0.20693 ---
obs0.21051 25046 92.16 %-
all-26375 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.39 Å20 Å20 Å2
2--4.95 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 0 40 6551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9369110
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.925807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54724.265340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.109151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.691542
X-RAY DIFFRACTIONr_chiral_restr0.1170.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025221
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.22923
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24441
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0430.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7521.54164
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27826594
X-RAY DIFFRACTIONr_scbond_it1.90832909
X-RAY DIFFRACTIONr_scangle_it2.9444.52516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 90 -
Rwork0.272 1825 -
obs--91.5 %

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