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- PDB-6k60: Structural and functional basis for HLA-G isoform recognition of ... -

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基本情報

登録情報
データベース: PDB / ID: 6k60
タイトルStructural and functional basis for HLA-G isoform recognition of immune checkpoint receptor LILRBs
要素
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain G
  • Leukocyte immunoglobulin-like receptor subfamily B member 1
  • Peptide from Histone H2A.J
キーワードIMMUNE SYSTEM / HLA class I / HLAG / LILRB1/ILT2
機能・相同性
機能・相同性情報


peripheral B cell tolerance induction / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / positive regulation of tolerance induction / negative regulation of serotonin secretion / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation ...peripheral B cell tolerance induction / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / positive regulation of tolerance induction / negative regulation of serotonin secretion / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / MHC class Ib protein binding / negative regulation of T cell mediated cytotoxicity / immune response-regulating signaling pathway / negative regulation of CD8-positive, alpha-beta T cell activation / MHC class I receptor activity / cis-Golgi network membrane / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of immune response / negative regulation of cytokine production involved in immune response / positive regulation of T cell tolerance induction / dendritic cell differentiation / interleukin-10-mediated signaling pathway / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of G0 to G1 transition / negative regulation of interleukin-12 production / negative regulation of dendritic cell apoptotic process / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / filopodium membrane / T cell proliferation involved in immune response / positive regulation of macrophage cytokine production / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-10 production / CD8 receptor binding / protein homotrimerization / negative regulation of calcium ion transport / negative regulation of cell cycle / MHC class I protein binding / negative regulation of type II interferon production / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of endothelial cell apoptotic process / negative regulation of tumor necrosis factor production / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular defense response / negative regulation of T cell proliferation / Packaging Of Telomere Ends / positive regulation of defense response to virus by host / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of interleukin-12 production / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / SH2 domain binding / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / negative regulation of receptor binding / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / early endosome lumen / negative regulation of angiogenesis / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / transferrin transport / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / cellular response to iron ion / PRC2 methylates histones and DNA / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / peptide antigen assembly with MHC class II protein complex / RNA Polymerase I Promoter Escape / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Transcriptional regulation by small RNAs / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex
類似検索 - 分子機能
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
IODIDE ION / Leukocyte immunoglobulin like receptor B1 / Histone H2A / HLA class I histocompatibility antigen, alpha chain G / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 1 / Histone H2A.J
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.149 Å
データ登録者Kuroki, K. / Matsubara, H. / Kanda, R. / Miyashita, N. / Shiroishi, M. / Fukunaga, Y. / Kamishikiryo, J. / Fukunaga, A. / Hirose, K. / Sugita, Y. ...Kuroki, K. / Matsubara, H. / Kanda, R. / Miyashita, N. / Shiroishi, M. / Fukunaga, Y. / Kamishikiryo, J. / Fukunaga, A. / Hirose, K. / Sugita, Y. / Kita, S. / Ose, T. / Maenaka, K.
資金援助 日本, 3件
組織認可番号国
Japan Agency for Medical Research and Development (AMED)18am0101093j0002 日本
Japan Society for the Promotion of Science23770102 日本
Japan Society for the Promotion of Science25870019 日本
引用ジャーナル: J Immunol. / 年: 2019
タイトル: Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms.
著者: Kuroki, K. / Matsubara, H. / Kanda, R. / Miyashita, N. / Shiroishi, M. / Fukunaga, Y. / Kamishikiryo, J. / Fukunaga, A. / Fukuhara, H. / Hirose, K. / Hunt, J.S. / Sugita, Y. / Kita, S. / Ose, T. / Maenaka, K.
履歴
登録2019年5月31日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02019年11月27日Provider: repository / タイプ: Initial release
改定 1.12019年12月25日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.22023年11月22日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: HLA class I histocompatibility antigen, alpha chain G
B: Beta-2-microglobulin
C: Peptide from Histone H2A.J
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
E: HLA class I histocompatibility antigen, alpha chain G
F: Beta-2-microglobulin
G: Peptide from Histone H2A.J
H: Leukocyte immunoglobulin-like receptor subfamily B member 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,36516
ポリマ－134,3508
非ポリマー1,0158
水00
1
A: HLA class I histocompatibility antigen, alpha chain G
B: Beta-2-microglobulin
C: Peptide from Histone H2A.J
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,6838
ポリマ－67,1754
非ポリマー5084
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: HLA class I histocompatibility antigen, alpha chain G
F: Beta-2-microglobulin
G: Peptide from Histone H2A.J
H: Leukocyte immunoglobulin-like receptor subfamily B member 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,6838
ポリマ－67,1754
非ポリマー5084
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)164.378, 164.378, 326.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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要素

#1: タンパク質 HLA class I histocompatibility antigen, alpha chain G / HLA G antigen / MHC class I antigen G


分子量: 32017.492 Da / 分子数: 2 / 変異: C42S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-G, HLA-6.0, HLAG / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P17693
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61769
#3: タンパク質・ペプチド Peptide from Histone H2A.J


分子量: 1148.424 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: A0A0U1RRH7, UniProt: Q9BTM1*PLUS
#4: タンパク質 Leukocyte immunoglobulin-like receptor subfamily B member 1


分子量: 22129.842 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LILRB1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A0G2JQ44, UniProt: Q8NHL6*PLUS
#5: 化合物
ChemComp-IOD / IODIDE ION


分子量: 126.904 Da / 分子数: 8 / 由来タイプ: 合成 / 式: I
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.16 Å3/Da / 溶媒含有率: 67.21 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.2M sodium iodide, 0.1M Bis Tris propane (pH 8.5), 20% PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Photon Factory / ビームライン: BL-5A / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2012年3月9日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.149→32.806 Å / Num. obs: 29650 / % possible obs: 99.9 % / 冗長度: 7.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4
反射 シェル解像度: 3.15→3.26 Å / Rmerge(I) obs: 0.501 / Num. unique obs: 2852

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)精密化
HKL-2000データ削減
HKL-2000データスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2DYP and 3D2U

2dyp

3d2u


解像度: 3.149→32.806 Å / SU ML: 0.38 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 28.65 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2886 1504 5.09 %
Rwork0.2613 --
obs0.2628 29526 99.4 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.149→32.806 Å
タンパク質核酸リガンド溶媒全体
原子数7974 0 8 0 7982
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0058196
X-RAY DIFFRACTIONf_angle_d1.08111119
X-RAY DIFFRACTIONf_dihedral_angle_d18.9143055
X-RAY DIFFRACTIONf_chiral_restr0.0591149
X-RAY DIFFRACTIONf_plane_restr0.0071437
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1492-3.25080.40331450.36342426X-RAY DIFFRACTION97
3.2508-3.36680.32361440.30882533X-RAY DIFFRACTION100
3.3668-3.50150.32391360.29882530X-RAY DIFFRACTION100
3.5015-3.66070.30461310.27322544X-RAY DIFFRACTION100
3.6607-3.85340.30911480.27582516X-RAY DIFFRACTION99
3.8534-4.09440.30321200.25352545X-RAY DIFFRACTION100
4.0944-4.40980.27951220.24862556X-RAY DIFFRACTION99
4.4098-4.85230.26981480.22062527X-RAY DIFFRACTION99
4.8523-5.55150.27771420.23992558X-RAY DIFFRACTION100
5.5515-6.98320.27441380.27222589X-RAY DIFFRACTION100
6.9832-32.8080.25451300.25142698X-RAY DIFFRACTION100
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.198-1.9042-3.42214.67672.27039.312-0.38260.4604-0.3955-0.93340.47280.05130.731-0.4362-0.0960.6543-0.2334-0.03290.3799-0.04960.593248.683246.526642.2659
27.5683-1.3045-0.14945.7552.63574.2844-0.39031.0515-1.2967-0.36070.1841-0.41820.86910.34760.19630.8649-0.16460.17660.4803-0.17510.706954.440936.802739.7079
34.4273-0.1231-0.31184.9629-0.46281.4875-0.03070.5020.3266-0.77340.1761-0.4307-0.41610.2208-0.15130.9439-0.24140.03330.437-0.02040.46454.12157.136541.8582
43.05650.89252.52322.74120.50193.20520.11981.0383-0.8758-1.0240.1452-1.14020.02280.2048-0.20661.2152-0.2060.41310.9215-0.11810.63958.831338.751825.1416
54.8204-0.28710.25191.9806-1.89991.7736-0.43041.0956-0.0094-0.77790.22550.27040.4747-0.08860.18661.1084-0.1575-0.02861.0046-0.03040.450429.369540.675216.2326
61.35951.6566-0.9253.73550.96413.0844-0.23880.67860.3478-0.72090.21960.433-0.0783-1.2438-0.10220.8097-0.0906-0.0790.84940.05830.368530.110540.6520.2305
70.4271.00970.2872.94990.6950.1479-0.15171.0341-0.2355-2.0316-0.5427-0.187-0.17990.04090.57151.63810.17530.12672.15370.31630.527333.22141.58287.8108
82.5661-0.6943-0.99582.03261.66490.6788-0.14360.19310.231-0.38391.0399-0.9701-0.6456-0.1019-0.82221.0217-0.1325-0.07880.59520.03040.354931.025346.671535.6249
92.00038.559-7.08519.8084-7.53716.69950.031-0.1548-1.1407-2.2470.3398-1.40891.9529-0.4219-0.29461.1159-0.21610.12850.5782-0.06570.59230.022923.86925.2629
104.152.44682.94538.88951.44592.019-0.2419-0.4692-0.02640.0592-0.1066-0.2146-0.256-0.29690.42710.542-0.13610.09380.47950.03030.344831.975537.964138.2845
115.81640.0483-3.22098.3513-0.5286.0176-0.3868-1.08830.16540.24620.37440.35080.11070.53590.020.7856-0.17760.00310.3925-0.00970.544429.393128.733643.2435
124.0627-0.0230.47960.30531.13314.061-0.11480.1996-0.3485-1.34070.2813-0.4203-0.4639-0.0838-0.15660.7376-0.2341-0.00740.5456-0.00110.329938.603140.190636.1663
139.04224.38224.34698.73621.12155.20020.5195-0.9714-0.60650.4733-0.38820.92410.8469-1.6871-0.19330.6682-0.09830.12820.62640.13610.608121.930330.07635.8137
141.587-1.94363.19933.9564-2.88727.1135-0.8607-0.91890.62421.00960.54950.5588-1.5364-0.94530.25910.81930.03660.16410.5096-0.19240.568524.682247.927544.435
158.362-2.8023-2.71559.32697.65696.2631-0.18410.8334-0.4876-1.4150.21351.0659-0.98570.0375-0.04410.6129-0.0928-0.01440.68390.12760.506522.315335.21530.0408
166.471-4.5325-5.95816.22687.97132.0189-0.58350.14360.06461.06420.5265-1.41991.4758-0.2844-0.04270.87070.01190.09360.4030.1270.566359.682552.928843.7372
171.949-2.80470.17894.4586-1.98267.8651-0.887-0.21620.37710.421-0.0828-0.166-0.9606-1.2770.9930.67160.2182-0.04220.83260.02820.7662-0.214547.715631.2256
180.8361-1.0488-0.09976.20782.35721.05290.07230.60120.2704-2.33810.13430.3820.5134-1.266-0.14790.7942-0.1478-0.16550.9160.01870.55638.734143.515122.0959
193.823-0.9421-1.18242.9719-0.26441.7336-0.36780.67790.6392-0.6029-0.0466-0.0806-0.5104-0.55280.46020.67140.0541-0.13040.72620.14120.67277.683148.23331.2146
205.3737-1.54650.91286.68011.62987.0264-0.74750.32431.2167-0.19620.64550.0578-1.2191-0.21150.02330.9310.0042-0.24770.52050.08650.852518.534861.434736.2796
210.7332-0.99720.19092.7861-2.66713.7052-0.13810.01410.17670.2951-0.2121-0.3603-0.98920.74220.33470.793-0.32330.060.4891-0.00720.792430.89692.596443.2315
224.7635-0.2575.31462.9332-1.7782.0827-0.92530.3785-0.07430.13010.85340.2208-2.24520.66840.02190.9214-0.2180.01220.61080.02210.818224.085212.095344.3164
233.12650.7171-0.84743.7548-1.4471.49820.0718-0.27890.0231-0.19670.2467-0.0847-0.2318-0.0757-0.27430.7006-0.27540.08320.4445-0.06480.572128.5932-4.533149.6849
246.1239-2.21915.62741.4767-0.98217.58230.08410.68850.075-0.4499-0.32910.0004-0.47060.32350.24310.7937-0.2286-0.06280.46540.08360.6524.491-7.928432.3444
252.9782-0.40161.38815.0553-1.38181.79420.06670.045-0.1079-0.46130.18390.93170.2458-0.2249-0.24520.5841-0.22970.00190.4644-0.03580.46323.0881-7.637236.4902
265.845-0.9111-2.05853.8408-0.44525.95370.33490.3406-0.373-0.7848-0.1965-0.03530.33820.7067-0.08820.8708-0.1487-0.03430.5686-0.08660.379847.54735.045616.9606
271.6953-0.43850.34863.9191-0.10820.83770.35511.6214-0.2038-1.1881-0.1725-0.65181.12690.1719-0.3241.2808-0.00170.06470.985-0.18880.424350.68223.274910.1769
287.2314-0.9935-4.37163.92923.08884.8107-0.45142.285-0.514-0.81310.16240.57670.5554-1.21790.31220.9664-0.0742-0.17180.7521-0.01230.483439.20097.59079.3162
292.66511.4595-1.88544.2055-1.85982.63570.6376-0.33830.15610.2435-0.57330.4842-0.63520.6731-0.0290.6961-0.2318-0.03790.5152-0.09560.311248.30959.395431.8371
302.15440.46270.1434.7785-1.8013.52410.3131-0.18510.18520.73340.0890.1672-0.98750.038-0.35050.8388-0.51380.09140.6717-0.1730.511446.065411.855333.9401
312.56652.36110.59692.7520.95730.32060.3088-0.4592-0.51271.4139-0.3561-0.8295-0.7860.5342-0.01770.9482-0.7059-0.10111.1263-0.10830.460949.66787.849943.5102
328.5193-3.732-0.883.9037-3.15347.17610.7853-1.88921.21851.9421-0.1671-0.0618-0.7544-0.3653-0.57541.3665-0.58550.11630.8792-0.17490.848650.787219.32642.6134
337.1725-3.1991.39036.07884.91499.59520.75030.67710.738-1.18730.4565-1.1044-1.37860.2147-1.16920.5938-0.22770.16530.60290.02110.544237.1262-0.116638.2165
341.53460.64730.9592.7780.3880.64420.7823-0.89250.45280.7676-0.20320.1954-0.85050.3929-0.51631.063-0.45130.20010.5777-0.11910.631844.46113.861436.8456
351.2127-1.50620.7198.7219-1.50481.93750.6674-0.69390.39140.1783-0.9135-1.75-0.52860.45810.31940.8973-0.9123-0.2870.9958-0.16280.584456.835111.523537.9058
361.51411.3572-0.42252.15080.71944.75640.2908-0.12-0.23970.0506-0.2802-0.7748-0.96381.0361-0.0080.7973-0.37860.02450.6699-0.00180.565356.12912.073429.1721
374.4376-6.51295.03959.7717-7.37859.4548-0.29650.16640.27051.5795-0.05740.5075-1.38891.2090.35190.6394-0.1791-0.02040.4724-0.07770.607421.3799-5.962546.8329
384.1904-1.35883.63061.9901-1.62693.4791-0.355-0.05620.83530.2879-0.312-1.6829-0.59240.52270.72960.6802-0.3088-0.1521.34860.07241.345770.64613.306427.3594
392.76031.08242.57363.11230.62532.4561-0.2579-1.44940.4805-0.01760.4617-0.03790.55420.8498-0.14251.75970.5719-0.04352.4234-0.55131.059671.542511.626725.7659
402.72880.74410.25954.1333-0.51990.1111-0.82031.74760.8709-0.25450.12512.07330.007-1.04860.63430.6893-0.26550.00991.53030.1471.211466.7233.099528.6274
412.8377-0.6873-0.49011.22280.46062.4431-0.524-0.6282-0.955-0.0001-0.5182-0.48490.22771.29950.88670.5915-0.2898-0.06771.65540.43881.146460.6158-9.326537.9381
421.62-0.72460.12461.32082.07754.9058-0.22340.42730.39030.05040.23760.255-0.21211.5536-0.04010.5169-0.13230.05681.51940.09740.852261.1712-7.751935.1973
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 253 )
7X-RAY DIFFRACTION7chain 'A' and (resid 254 through 274 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 11 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 41 )
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 51 )
12X-RAY DIFFRACTION12chain 'B' and (resid 52 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 9 )
17X-RAY DIFFRACTION17chain 'D' and (resid 5 through 35 )
18X-RAY DIFFRACTION18chain 'D' and (resid 36 through 44 )
19X-RAY DIFFRACTION19chain 'D' and (resid 45 through 124 )
20X-RAY DIFFRACTION20chain 'D' and (resid 125 through 191 )
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 37 )
22X-RAY DIFFRACTION22chain 'E' and (resid 38 through 56 )
23X-RAY DIFFRACTION23chain 'E' and (resid 57 through 103 )
24X-RAY DIFFRACTION24chain 'E' and (resid 104 through 118 )
25X-RAY DIFFRACTION25chain 'E' and (resid 119 through 185 )
26X-RAY DIFFRACTION26chain 'E' and (resid 186 through 242 )
27X-RAY DIFFRACTION27chain 'E' and (resid 243 through 262 )
28X-RAY DIFFRACTION28chain 'E' and (resid 263 through 275 )
29X-RAY DIFFRACTION29chain 'F' and (resid 0 through 19 )
30X-RAY DIFFRACTION30chain 'F' and (resid 20 through 30 )
31X-RAY DIFFRACTION31chain 'F' and (resid 31 through 41 )
32X-RAY DIFFRACTION32chain 'F' and (resid 42 through 51 )
33X-RAY DIFFRACTION33chain 'F' and (resid 52 through 61 )
34X-RAY DIFFRACTION34chain 'F' and (resid 62 through 71 )
35X-RAY DIFFRACTION35chain 'F' and (resid 72 through 90 )
36X-RAY DIFFRACTION36chain 'F' and (resid 91 through 99 )
37X-RAY DIFFRACTION37chain 'G' and (resid 1 through 9 )
38X-RAY DIFFRACTION38chain 'H' and (resid 9 through 46 )
39X-RAY DIFFRACTION39chain 'H' and (resid 47 through 62 )
40X-RAY DIFFRACTION40chain 'H' and (resid 63 through 74 )
41X-RAY DIFFRACTION41chain 'H' and (resid 75 through 175 )
42X-RAY DIFFRACTION42chain 'H' and (resid 176 through 190 )

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る