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- PDB-9c42: Structure of human MR1-ellagic acid in complex with human MAIT A-... -

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基本情報

登録情報
データベース: PDB / ID: 9c42
タイトルStructure of human MR1-ellagic acid in complex with human MAIT A-F7 TCR
要素
  • Beta-2-microglobulin
  • MAIT T-cell receptor beta chain
  • Major histocompatibility complex class I-related gene protein
  • TRA@ protein
キーワードIMMUNE SYSTEM / T-cell receptor / MHC-like / Inhibitor / Antigen-presenting molecule
機能・相同性
機能・相同性情報


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / 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
類似検索 - ドメイン・相同性
ACETIC ACID / Chem-REF / Beta-2-microglobulin / TRA@ protein / Major histocompatibility complex class I-related gene protein
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: 2.69 Å
データ登録者Wang, C.J.H. / Le Nours, J. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)2008981 オーストラリア
引用ジャーナル: To Be Published
タイトル: Ellagic acid metabolism as a source of dietary MR1 ligands
著者: Wang, C.J.H. / Tang, J.S. / Stephens, R. / Faulkner, S. / Gell, K. / Li, Y. / Cait, A. / Rossjohn, J. / Le Nours, J. / Gasser, O.
履歴
登録2024年6月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年6月11日Provider: repository / タイプ: Initial release
改定 1.12025年6月18日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list

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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: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: TRA@ protein
E: MAIT T-cell receptor beta chain
F: Beta-2-microglobulin
G: TRA@ protein
H: MAIT T-cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)189,26520
ポリマ－188,1008
非ポリマー1,16512
水2,648147
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TRA@ protein
H: MAIT T-cell receptor beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,4819
ポリマ－94,0504
非ポリマー4315
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-81 kcal/mol
Surface area35900 Å2
手法PISA
2
C: Major histocompatibility complex class I-related gene protein
D: TRA@ protein
E: MAIT T-cell receptor beta chain
F: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,78411
ポリマ－94,0504
非ポリマー7347
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-55 kcal/mol
Surface area35550 Å2
手法PISA
単位格子
Length a, b, c (Å)215.810, 70.352, 143.434
Angle α, β, γ (deg.)90.00, 104.09, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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要素

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タンパク質 , 4種, 8分子 ACBFDGEH

#1: タンパク質 Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


分子量: 31711.670 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: MR1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q95460
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 2 / Fragment: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61769
#3: タンパク質 TRA@ protein


分子量: 22781.268 Da / 分子数: 2 / Fragment: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRA@ / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q6P4G7
#4: タンパク質 MAIT T-cell receptor beta chain


分子量: 27677.760 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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非ポリマー , 6種, 159分子

#5: 化合物 ChemComp-REF / 2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione / Ellagic acid, 4,4',5,5',6,6'-Hexahydroxydiphenic acid 2,6,2',6'-dilactone / エラグ酸


分子量: 302.193 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C14H6O8 / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Na
#7: 化合物 ChemComp-ACY / ACETIC ACID / 酢酸


分子量: 60.052 Da / 分子数: 3 / 由来タイプ: 天然 / 式: C2H4O2
#8: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#9: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C3H8O3
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 147 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 2.87 Å3/Da / 溶媒含有率: 57.1 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG 3350, bis-tris propane, sodium acetate / PH範囲: 6.1 - 6.5

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.954 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2024年8月2日
放射モノクロメーター: Channel-cut Si(111) liquid nitrogen cooled
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: 0.954 Å / 相対比: 1
反射解像度: 2.69→47.83 Å / Num. obs: 57901 / % possible obs: 99.7 % / 冗長度: 5.3 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.084 / Rrim(I) all: 0.2 / Net I/σ(I): 7
反射 シェル解像度: 2.7→2.77 Å / 冗長度: 4.7 % / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4476 / CC1/2: 0.599 / Rpim(I) all: 0.608 / Rrim(I) all: 1.32 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.18.2_3874: ???)精密化
XDSBUILT=20220110データ削減
Aimless0.2.1データスケーリング
PHENIX1.20.1-4487位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.69→47.78 Å / SU ML: 0.39 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.34 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2456 2958 5.11 %
Rwork0.1935 --
obs0.1961 57863 99.37 %
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: 2.69→47.78 Å
タンパク質核酸リガンド溶媒全体
原子数12374 0 85 147 12606
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00912898
X-RAY DIFFRACTIONf_angle_d1.15817622
X-RAY DIFFRACTIONf_dihedral_angle_d19.6894487
X-RAY DIFFRACTIONf_chiral_restr0.0631907
X-RAY DIFFRACTIONf_plane_restr0.0082274
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.740.3631200.30632490X-RAY DIFFRACTION96
2.74-2.780.39891460.30022633X-RAY DIFFRACTION100
2.78-2.840.34971230.27762631X-RAY DIFFRACTION100
2.84-2.890.32391460.26522563X-RAY DIFFRACTION100
2.89-2.950.32451580.26332608X-RAY DIFFRACTION100
2.95-3.010.31811250.24632632X-RAY DIFFRACTION100
3.01-3.080.26281330.24332615X-RAY DIFFRACTION100
3.08-3.160.2871500.23612607X-RAY DIFFRACTION100
3.16-3.250.29821470.23892585X-RAY DIFFRACTION100
3.25-3.340.28431370.22282644X-RAY DIFFRACTION100
3.34-3.450.27681540.20572559X-RAY DIFFRACTION99
3.45-3.570.26531320.19322625X-RAY DIFFRACTION99
3.57-3.720.2211370.18392589X-RAY DIFFRACTION99
3.72-3.880.27951330.18192628X-RAY DIFFRACTION99
3.88-4.090.21291380.17322597X-RAY DIFFRACTION99
4.09-4.340.19471490.14992627X-RAY DIFFRACTION100
4.34-4.680.17781320.13862634X-RAY DIFFRACTION100
4.68-5.150.1941360.14542644X-RAY DIFFRACTION99
5.15-5.890.24361570.17452621X-RAY DIFFRACTION100
5.9-7.420.24931550.20262635X-RAY DIFFRACTION99
7.42-47.780.20991500.18532738X-RAY DIFFRACTION99
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)
11.8511-0.64120.48812.72540.92312.2812-0.00370.06930.1612-0.26680.1544-0.3271-0.01840.3745-0.13180.2344-0.05920.04630.35340.01990.329750.892277.3325224.5446
22.2097-1.97030.30945.7536-1.35512.01270.0016-0.1933-0.15430.18370.05650.29020.0148-0.1286-0.07680.211-0.0366-0.02750.3216-0.00050.270238.704480.6124235.3891
32.83250.02271.37691.33910.25322.4437-0.1232-0.28420.28580.2780.227-0.2227-0.06970.2251-0.06470.33560.1021-0.05220.4776-0.05850.540564.775474.464247.7566
40.34110.7463-0.52443.70610.95572.9302-0.0968-0.74380.45980.54210.0471-0.2635-0.381-0.30420.07630.48720.1374-0.16770.8364-0.18510.629670.38179.7214262.0302
55.22770.9454-2.1082.46931.73855.095-0.23550.24230.57860.4434-0.1123-0.8494-0.24440.47420.32150.2782-0.0811-0.07050.48480.0360.589370.234987.8667239.7982
62.0177-0.55810.51141.33991.54321.93060.0753-0.09881.1459-0.3472-0.0027-1.0028-0.23660.7724-0.0770.3069-0.07910.05940.61660.08780.674968.941888.8317233.3555
76.94691.5627-0.61312.0062-1.67966.92230.29080.75391.126-0.3448-0.2510.1018-0.25260.5174-0.07720.435-0.18750.04071.1553-0.09780.775877.623489.5987228.0441
82.35961.83361.19452.7166-0.3461.82680.03110.278-0.5522-0.23290.0702-0.40360.08230.8044-0.11790.2545-0.01180.01520.537-0.02880.406164.484883.8667233.4794
92.66221.21461.23651.02291.02572.0536-0.32171.05910.89880.08950.151-0.3208-0.33930.90290.17630.4248-0.14830.00150.81740.15251.096873.652895.892234.4788
106.50811.9178-4.61413.9351.43445.58320.0589-0.5825-0.05630.3995-0.17530.245-0.39150.90120.09180.4628-0.1721-0.23170.55310.00061.063476.084593.811240.5874
111.83570.3285-0.72583.2206-0.55212.1824-0.10330.36650.1266-0.08770.08230.3006-0.1305-0.04910.04180.2328-0.0107-0.04210.36330.01360.4108-4.213862.9104161.035
123.24451.21931.79885.3227-0.35742.3520.0125-0.1622-0.03890.4871-0.2169-0.1218-0.0097-0.01510.19980.2475-0.03330.06060.3840.01150.24131.158151.1858171.6796
132.8039-0.7242-1.5610.62260.65941.9422-0.0098-0.2430.08530.071-0.0207-0.0419-0.21530.1917-0.01160.3539-0.0757-0.04330.32220.01780.2927-10.891470.19183.4636
145.27480.7181-0.79754.0578-1.75065.6290.2252-0.48790.01290.529-0.0735-0.2515-0.1709-0.0597-0.10840.38520.0783-0.04560.2899-0.07610.3956-19.271973.5084195.5218
153.609-0.0812-0.9541.41850.73652.20880.01540.20870.08820.03370.0684-0.1313-0.00540.0944-0.08590.294-0.092-0.01120.48240.10130.353530.257861.5592160.3246
166.4731-1.0644-4.12571.02041.32213.61690.3566-0.44240.2005-0.13070.222-0.3145-0.11230.4602-0.5840.3448-0.0656-0.03030.57130.0220.526146.683263.0646144.9858
177.9028-0.40181.3082.38421.78062.85140.2572-0.34340.17770.0040.2124-0.56720.05970.3356-0.51630.3973-0.02990.01130.7471-0.01930.542756.796962.0997139.0022
183.7601-0.284-1.61042.9437-1.07184.6566-0.08110.4187-0.0075-0.41830.01360.16910.2701-0.53650.08720.3214-0.1126-0.0630.57470.05790.289915.08261.7052139.9231
192.389-0.96271.08111.71770.62131.38350.22180.18580.0041-0.0549-0.03450.0163-0.044-0.3003-0.27250.3043-0.13490.01390.4250.03220.337322.958361.0749138.3848
206.934-1.95973.00412.7835-1.88143.82190.48530.4813-1.0581-0.35080.09750.35920.43720.1416-0.5920.4108-0.0309-0.05840.4333-0.01850.417544.640655.062129.0733
212.0078-2.42663.02352.00840.0512.00870.64650.1827-0.2498-0.79650.2496-1.05520.76980.388-0.84510.4661-0.0054-0.00110.3632-0.08630.5148-19.260649.5243171.7551
225.01062.24950.65142.7618-1.85073.6872-0.23190.13860.75490.276-0.06790.2941-0.6107-0.41160.30840.36090.1192-0.07380.3509-0.06270.3164-29.247473.3437178.1339
232.20081.06170.39524.8201-0.0322.4707-0.49160.44780.50340.01940.4379-0.2701-0.41310.41980.05270.3293-0.0087-0.10680.4665-0.02970.2822-25.010668.9092173.0936
249.4102-7.5141-1.17528.14071.48574.93840.37651.1286-0.0135-0.4047-0.6247-0.2032-0.3894-0.110.18110.2689-0.0269-0.04230.39690.01050.3841-26.239160.8583165.6982
252.0019-0.33871.95045.7831-1.1873.3454-1.05171.13981.8086-0.88520.54480.5435-0.1885-0.24380.48210.45480.0529-0.13570.71120.09170.527-31.761670.5903163.6515
266.4191-2.93722.75854.8382-3.25977.5239-0.25440.0750.4351-0.23660.1584-0.21740.4314-0.24830.15230.2672-0.0157-0.01310.3399-0.04790.3781-12.140760.2126170.2486
277.0802-5.7318-1.75212.03073.05246.66960.05710.20480.5165-1.22390.2826-0.313-0.5268-0.5539-0.35890.3691-0.0867-0.11050.4572-0.03960.5547-24.622270.5427169.5254
280.97440.61060.29120.38370.18160.08180.50860.54590.2714-0.731-0.78171.1198-0.4139-0.91490.28180.47040.2529-0.09790.6882-0.12820.8504-41.551574.7891174.8384
294.1771-3.208-0.86798.13840.84622.07920.17710.3579-0.3958-1.188-0.30350.7256-0.0668-0.33040.10990.2749-0.0112-0.08760.5026-0.07930.3975-30.783757.2296168.0457
309.2304-3.3508-2.69648.07332.60554.11130.2082-0.27310.78950.0958-0.30640.0774-0.1829-0.15110.09320.2898-0.03660.01980.5079-0.06120.2684-34.609266.2048177.2827
3122.000222.00011.10620.4861-1.47143.72810.272-0.1960.68511.03570.5066-0.29840.9870.36060.11710.9998-0.24140.9262-35.68769.6004186.6859
326.4993-2.7974-1.52832.16150.10291.5639-0.1666-0.5278-0.2021-0.02780.098-0.0768-0.15440.29070.07190.4133-0.0669-0.01670.25110.04810.274821.016150.2776220.7822
335.48852.11394.66853.75231.87095.47540.3530.365-0.60650.0860.0178-0.17360.32010.5455-0.38270.2729-0.0089-0.04850.29870.01750.312426.601558.2186221.7501
341.2182-0.16681.18750.75180.50571.7732-0.3120.08280.75220.22130.02720.052-0.3860.03530.32840.4091-0.07530.00060.30020.02310.446322.323464.6078227.4474
356.01491.41443.15081.00351.51683.03340.01880.0035-0.30740.08860.0243-0.17880.1637-0.0909-0.05530.4051-0.104-0.04390.22360.04680.33423.794757.0435230.6137
362.01272.90953.81653.50071.14225.81420.07910.38560.6031-0.2320.02360.370.0464-0.4249-0.15170.34780.0023-0.0450.25910.07450.350417.368658.1508219.6745
376.36661.76251.632.7970.65852.85860.0364-0.1604-0.2837-0.1411-0.0161-0.2929-0.5220.1246-0.00880.3667-0.0329-0.00770.36180.01230.218128.267757.1859218.5053
384.5260.9826-0.24442.5312-1.01453.31080.12480.172-0.0276-0.59170.15880.22910.2042-0.4601-0.32920.47120.0273-0.10070.27250.06030.4471-2.44745.5365199.2725
398.3575-0.3872-4.6914.2814-0.5957.7325-0.2433-0.7806-0.433-0.12540.0999-0.31670.99770.75480.12660.44680.0359-0.10360.2981-0.00270.42196.855340.3824203.0116
406.57110.6533-1.60691.7022-0.44585.11040.336-0.59170.5705-0.35020.2194-0.0966-0.5188-0.0206-0.53090.3817-0.03630.01430.30350.07420.39440.076252.3547205.7235
414.18440.8228-1.08041.40841.6577.898-0.17450.1101-0.8672-0.58770.2608-0.03741.65820.076-0.03620.74730.04120.01430.30950.02210.4971-1.916835.5997199.2148
422.9542-0.17231.40594.06322.83952.83090.04380.44320.0434-0.4302-0.0789-0.0567-0.36050.21730.01760.3505-0.05280.00130.41850.09630.240134.3666.4284204.3151
434.2661-0.6617-0.17095.3583.11281.84030.09490.32610.2814-0.09750.0442-0.21120.00640.2189-0.11790.4624-0.1068-0.11040.45260.12370.256534.281968.2604206.0364
443.54590.47291.39960.58121.62716.78120.1094-0.085-0.21780.46860.3408-0.28931.04180.8857-0.38080.57380.0727-0.16370.460.00290.420926.40353.9038189.1121
458.0722-0.9832-2.79551.29780.18172.6106-0.1334-0.0869-0.0846-0.12630.0080.036-0.16880.09490.1220.4017-0.036-0.06680.24730.02310.23742.825853.4325194.7787
466.6177-0.7687-1.67111.0653-0.1694.8294-0.4111-0.5493-0.20010.26610.1152-0.0509-0.00090.62820.40050.3373-0.0543-0.04660.30660.02090.340112.291952.1012196.8737
474.35750.3107-2.34630.7137-0.26692.68690.15830.21470.2685-0.1778-0.02860.1426-0.1240.0081-0.14970.37-0.0472-0.07630.23330.01840.27717.394758.4601188.8675
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 19 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 71 )
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 90 )
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 97 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 84 )
12X-RAY DIFFRACTION12chain 'C' and (resid 85 through 146 )
13X-RAY DIFFRACTION13chain 'C' and (resid 147 through 237 )
14X-RAY DIFFRACTION14chain 'C' and (resid 238 through 270 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 91 )
16X-RAY DIFFRACTION16chain 'D' and (resid 92 through 150 )
17X-RAY DIFFRACTION17chain 'D' and (resid 151 through 199 )
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 94 )
19X-RAY DIFFRACTION19chain 'E' and (resid 95 through 124 )
20X-RAY DIFFRACTION20chain 'E' and (resid 125 through 243 )
21X-RAY DIFFRACTION21chain 'F' and (resid 0 through 5 )
22X-RAY DIFFRACTION22chain 'F' and (resid 6 through 19 )
23X-RAY DIFFRACTION23chain 'F' and (resid 20 through 30 )
24X-RAY DIFFRACTION24chain 'F' and (resid 31 through 41 )
25X-RAY DIFFRACTION25chain 'F' and (resid 42 through 51 )
26X-RAY DIFFRACTION26chain 'F' and (resid 52 through 61 )
27X-RAY DIFFRACTION27chain 'F' and (resid 62 through 71 )
28X-RAY DIFFRACTION28chain 'F' and (resid 72 through 77 )
29X-RAY DIFFRACTION29chain 'F' and (resid 78 through 90 )
30X-RAY DIFFRACTION30chain 'F' and (resid 91 through 98 )
31X-RAY DIFFRACTION31chain 'F' and (resid 99 through 99 )
32X-RAY DIFFRACTION32chain 'G' and (resid 1 through 17 )
33X-RAY DIFFRACTION33chain 'G' and (resid 18 through 42 )
34X-RAY DIFFRACTION34chain 'G' and (resid 43 through 59 )
35X-RAY DIFFRACTION35chain 'G' and (resid 60 through 75 )
36X-RAY DIFFRACTION36chain 'G' and (resid 76 through 91 )
37X-RAY DIFFRACTION37chain 'G' and (resid 92 through 108 )
38X-RAY DIFFRACTION38chain 'G' and (resid 109 through 135 )
39X-RAY DIFFRACTION39chain 'G' and (resid 136 through 156 )
40X-RAY DIFFRACTION40chain 'G' and (resid 157 through 175 )
41X-RAY DIFFRACTION41chain 'G' and (resid 176 through 201 )
42X-RAY DIFFRACTION42chain 'H' and (resid 1 through 63 )
43X-RAY DIFFRACTION43chain 'H' and (resid 64 through 109 )
44X-RAY DIFFRACTION44chain 'H' and (resid 110 through 124 )
45X-RAY DIFFRACTION45chain 'H' and (resid 125 through 162 )
46X-RAY DIFFRACTION46chain 'H' and (resid 163 through 188 )
47X-RAY DIFFRACTION47chain 'H' and (resid 189 through 244 )

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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