- PDB-8d5k: The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYL... -
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基本情報
登録情報
データベース: PDB / ID: 8d5k
タイトル
The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYLQVASHV Presented by H2-Kd
要素
Beta-2-microglobulin
H-2 class I histocompatibility antigen, K-D alpha chain
Pre-mRNA-processing factor 19
キーワード
IMMUNE SYSTEM / Complex / MHC
機能・相同性
機能・相同性情報
Formation of TC-NER Pre-Incision Complex / mRNA Splicing - Major Pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication factor A complex / positive regulation of astrocyte differentiation / Prp19 complex / U2-type catalytic step 1 spliceosome / U2-type catalytic step 2 spliceosome / Endosomal/Vacuolar pathway ...Formation of TC-NER Pre-Incision Complex / mRNA Splicing - Major Pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication factor A complex / positive regulation of astrocyte differentiation / Prp19 complex / U2-type catalytic step 1 spliceosome / U2-type catalytic step 2 spliceosome / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of mRNA splicing, via spliceosome / ER-Phagosome pathway / DAP12 signaling / ubiquitin-ubiquitin ligase activity / lipid biosynthetic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / spliceosomal complex assembly / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / protein K63-linked ubiquitination / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / spliceosomal tri-snRNP complex assembly / proteasomal protein catabolic process / beta-2-microglobulin binding / cellular defense response / positive regulation of neuron differentiation / Neutrophil degranulation / catalytic step 2 spliceosome / lipid droplet / peptide binding / DNA damage checkpoint signaling / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / spliceosomal complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / RING-type E3 ubiquitin transferase / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / mRNA splicing, via spliceosome / MHC class II protein complex / spindle / double-strand break repair via nonhomologous end joining / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / protein polyubiquitination / phagocytic vesicle membrane / ubiquitin-protein transferase activity / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / ubiquitin protein ligase activity / positive regulation of T cell activation / protein localization / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / site of double-strand break / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / nuclear speck / defense response to bacterium / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能
解像度: 2.066→41.349 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.527 / SU ML: 0.146 / 交差検証法: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.191 / 詳細: Hydrogens have not been used
Rfactor
反射数
%反射
Rfree
0.2335
1254
5.272 %
Rwork
0.2027
22530
-
all
0.204
-
-
obs
-
23784
90.245 %
溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT
原子変位パラメータ
Biso mean: 46.908 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.426 Å2
0 Å2
0.163 Å2
2-
-
3.235 Å2
0 Å2
3-
-
-
-2.812 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.066→41.349 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
3139
0
0
55
3194
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.011
3236
X-RAY DIFFRACTION
r_angle_refined_deg
1.874
1.654
4402
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.677
5
378
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
5.714
10
28
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.067
10
510
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
17.388
10
173
X-RAY DIFFRACTION
r_chiral_restr
0.12
0.2
446
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
2537
X-RAY DIFFRACTION
r_nbd_refined
0.225
0.2
1368
X-RAY DIFFRACTION
r_nbtor_refined
0.316
0.2
2181
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.157
0.2
169
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.501
0.2
53
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.326
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
3.064
3.668
1524
X-RAY DIFFRACTION
r_mcangle_it
4.188
5.474
1898
X-RAY DIFFRACTION
r_scbond_it
4.248
3.999
1712
X-RAY DIFFRACTION
r_scangle_it
5.805
5.856
2504
X-RAY DIFFRACTION
r_lrange_it
8.08
72.071
13089
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20