- PDB-8w83: HLA-DQ2.5-alpha1 gliadin peptide in complex with DQN0344AE02 -
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データベース: PDB / ID: 8w83
タイトル
HLA-DQ2.5-alpha1 gliadin peptide in complex with DQN0344AE02
要素
DQN0344AE02 Fab heavy chain
DQN0344AE02 Fab light chain
HLA class II histocompatibility antigen, DQ alpha 1 chain
MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein
キーワード
IMMUNE SYSTEM / CELIAC DISEASE / ANTIBODY
機能・相同性
機能・相同性情報
MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / ER to Golgi transport vesicle membrane / clathrin-coated endocytic 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 / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / membrane / plasma membrane 類似検索 - 分子機能
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 ...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 / Immunoglobulin-like fold 類似検索 - ドメイン・相同性
MHC class II HLA-DQ-beta-1 / HLA class II histocompatibility antigen, DQ alpha 1 chain 類似検索 - 構成要素
A: DQN0344AE02 Fab heavy chain B: DQN0344AE02 Fab light chain C: HLA class II histocompatibility antigen, DQ alpha 1 chain D: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein E: DQN0344AE02 Fab heavy chain F: DQN0344AE02 Fab light chain G: HLA class II histocompatibility antigen, DQ alpha 1 chain H: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein I: DQN0344AE02 Fab heavy chain J: DQN0344AE02 Fab light chain K: HLA class II histocompatibility antigen, DQ alpha 1 chain L: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein M: DQN0344AE02 Fab heavy chain N: DQN0344AE02 Fab light chain O: HLA class II histocompatibility antigen, DQ alpha 1 chain P: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein ヘテロ分子
A: DQN0344AE02 Fab heavy chain B: DQN0344AE02 Fab light chain C: HLA class II histocompatibility antigen, DQ alpha 1 chain D: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein ヘテロ分子
E: DQN0344AE02 Fab heavy chain F: DQN0344AE02 Fab light chain G: HLA class II histocompatibility antigen, DQ alpha 1 chain H: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein ヘテロ分子
I: DQN0344AE02 Fab heavy chain J: DQN0344AE02 Fab light chain K: HLA class II histocompatibility antigen, DQ alpha 1 chain L: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein ヘテロ分子
M: DQN0344AE02 Fab heavy chain N: DQN0344AE02 Fab light chain O: HLA class II histocompatibility antigen, DQ alpha 1 chain P: MHC class II HLA-DQ-beta-1 - alpha1 gliadin peptide chimeric protein ヘテロ分子
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.98 Å / 相対比: 1
反射
解像度: 2.818→129.458 Å / Num. obs: 44543 / % possible obs: 92.7 % / 冗長度: 6.41 % 詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary! CC1/2: 0.9 / CC1/2 anomalous: 0.22 / Rmerge(I) obs: 0.5004 / Rpim(I) all: 0.2174 / Rrim(I) all: 0.5466 / AbsDiff over sigma anomalous: 0.843 / Baniso tensor eigenvalue 1: 93.6 Å2 / Baniso tensor eigenvalue 2: 55.4 Å2 / Baniso tensor eigenvalue 3: 27 Å2 / Baniso tensor eigenvector 1 ortho1: 0.7173 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.6968 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.6968 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.7173 / Aniso diffraction limit 1: 4.256 Å / Aniso diffraction limit 2: 3.653 Å / Aniso diffraction limit 3: 2.817 Å / Aniso diffraction limit axis 1 ortho1: 0.75744 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.65284 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.65284 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.75744 / Net I/σ(I): 4.68 / Num. measured all: 285587 / Orthogonalization convention: pdb / % possible anomalous: 91.6 / % possible ellipsoidal: 92.7 / % possible ellipsoidal anomalous: 91.6 / % possible spherical: 47.7 / % possible spherical anomalous: 46.8 / Redundancy anomalous: 3.28