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- PDB-3qaz: IL-2 mutant D10 ternary complex -

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基本情報

登録情報
データベース: PDB / ID: 3qaz
タイトルIL-2 mutant D10 ternary complex
要素
  • Cytokine receptor common subunit gamma
  • Interleukin-2
  • Interleukin-2 receptor subunit beta
キーワードSIGNALING PROTEIN/Cytokine / cytokine receptor signaling complex / SIGNALING PROTEIN-Cytokine complex
機能・相同性
機能・相同性情報


interleukin-2 receptor complex / interleukin-2 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation ...interleukin-2 receptor complex / interleukin-2 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / negative regulation of lymphocyte proliferation / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling / positive regulation of T cell differentiation in thymus / lymphocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / leukocyte activation involved in immune response / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / activated T cell proliferation / cellular homeostasis / STAT3 nuclear events downstream of ALK signaling / Interleukin-15 signaling / cytokine receptor activity / cell surface receptor signaling pathway via STAT / kinase activator activity / natural killer cell activation / Interleukin-2 signaling / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / cytokine binding / positive regulation of dendritic spine development / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / immunoglobulin mediated immune response / T cell differentiation / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of B cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / Interleukin-7 signaling / positive regulation of phagocytosis / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / positive regulation of inflammatory response / cytokine-mediated signaling pathway / cell-cell signaling / T cell differentiation in thymus / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / RAF/MAP kinase cascade / positive regulation of cell growth / protein-containing complex assembly / response to ethanol / Interleukin-4 and Interleukin-13 signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / adaptive immune response / transcription by RNA polymerase II / receptor complex / cell adhesion / endosome / immune response / external side of plasma membrane / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
類似検索 - 分子機能
Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. ...Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Short hematopoietin receptor family 1 signature. / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
Interleukin-2 receptor subunit beta / Cytokine receptor common subunit gamma / Interleukin-2
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: 3.802 Å
データ登録者Levin, A.M. / Bates, D.L. / Ring, A.M. / Lin, J.T. / Su, L. / Krieg, C. / Bowman, G.R. / Novick, P. / Pande, V.S. / Khort, H.E. ...Levin, A.M. / Bates, D.L. / Ring, A.M. / Lin, J.T. / Su, L. / Krieg, C. / Bowman, G.R. / Novick, P. / Pande, V.S. / Khort, H.E. / Boyman, O. / Gathman, C.G. / Garcia, K.C.
引用ジャーナル: Nature / 年: 2012
タイトル: Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'
著者: Levin, A.M. / Bates, D.L. / Ring, A.M. / Krieg, C. / Lin, J.T. / Su, L. / Moraga, I. / Raeber, M.E. / Bowman, G.R. / Novick, P. / Pande, V.S. / Fathman, C.G. / Boyman, O. / Garcia, K.C.
履歴
登録2011年1月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年4月11日Provider: repository / タイプ: Initial release
改定 1.12014年10月15日Group: Structure summary
改定 1.22020年7月29日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.32024年10月30日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Interleukin-2
B: Interleukin-2 receptor subunit beta
C: Cytokine receptor common subunit gamma
D: Interleukin-2
E: Interleukin-2 receptor subunit beta
F: Cytokine receptor common subunit gamma
G: Interleukin-2
H: Interleukin-2 receptor subunit beta
I: Cytokine receptor common subunit gamma
J: Interleukin-2
K: Interleukin-2 receptor subunit beta
L: Cytokine receptor common subunit gamma
M: Interleukin-2
N: Interleukin-2 receptor subunit beta
O: Cytokine receptor common subunit gamma
P: Interleukin-2
Q: Interleukin-2 receptor subunit beta
R: Cytokine receptor common subunit gamma
S: Interleukin-2
T: Interleukin-2 receptor subunit beta
U: Cytokine receptor common subunit gamma
V: Interleukin-2
W: Interleukin-2 receptor subunit beta
X: Cytokine receptor common subunit gamma
Y: Interleukin-2
Z: Interleukin-2 receptor subunit beta
a: Cytokine receptor common subunit gamma
b: Interleukin-2
c: Interleukin-2 receptor subunit beta
d: Cytokine receptor common subunit gamma
e: Interleukin-2
f: Interleukin-2 receptor subunit beta
g: Cytokine receptor common subunit gamma
h: Interleukin-2
i: Interleukin-2 receptor subunit beta
j: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)791,55590
ポリマ－779,61036
非ポリマー11,94554
水00
1
A: Interleukin-2
B: Interleukin-2 receptor subunit beta
C: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,2959
ポリマ－64,9683
非ポリマー1,3276
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Interleukin-2
E: Interleukin-2 receptor subunit beta
F: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,2959
ポリマ－64,9683
非ポリマー1,3276
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: Interleukin-2
H: Interleukin-2 receptor subunit beta
I: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,2959
ポリマ－64,9683
非ポリマー1,3276
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
J: Interleukin-2
K: Interleukin-2 receptor subunit beta
L: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,2959
ポリマ－64,9683
非ポリマー1,3276
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
M: Interleukin-2
N: Interleukin-2 receptor subunit beta
O: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,2959
ポリマ－64,9683
非ポリマー1,3276
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
P: Interleukin-2
Q: Interleukin-2 receptor subunit beta
R: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)66,2959
ポリマ－64,9683
非ポリマー1,3276
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
S: Interleukin-2
T: Interleukin-2 receptor subunit beta
U: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,6316
ポリマ－64,9683
非ポリマー6643
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
V: Interleukin-2
W: Interleukin-2 receptor subunit beta
X: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,6316
ポリマ－64,9683
非ポリマー6643
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
9
Y: Interleukin-2
Z: Interleukin-2 receptor subunit beta
a: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,6316
ポリマ－64,9683
非ポリマー6643
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
10
b: Interleukin-2
c: Interleukin-2 receptor subunit beta
d: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,6316
ポリマ－64,9683
非ポリマー6643
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
11
e: Interleukin-2
f: Interleukin-2 receptor subunit beta
g: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,6316
ポリマ－64,9683
非ポリマー6643
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
12
h: Interleukin-2
i: Interleukin-2 receptor subunit beta
j: Cytokine receptor common subunit gamma
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)65,6316
ポリマ－64,9683
非ポリマー6643
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)118.226, 118.099, 236.115
Angle α, β, γ (deg.)99.86, 99.86, 99.74
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Interleukin-2 / IL-2 / T-cell growth factor / TCGF


分子量: 15727.153 Da / 分子数: 12 / 断片: unp residues 21-153 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL2 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P60568
#2: タンパク質
Interleukin-2 receptor subunit beta / IL-2 receptor subunit beta / IL-2R subunit beta / IL-2RB / High affinity IL-2 receptor subunit beta ...IL-2 receptor subunit beta / IL-2R subunit beta / IL-2RB / High affinity IL-2 receptor subunit beta / p70-75 / p75


分子量: 25044.402 Da / 分子数: 12 / 断片: unp residues 24-240 / Mutation: N29Q, N43Q, N71Q / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL2RB / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P14784
#3: タンパク質
Cytokine receptor common subunit gamma / Interleukin-2 receptor subunit gamma / IL-2 receptor subunit gamma / IL-2R subunit gamma / IL-2RG / p64


分子量: 24195.963 Da / 分子数: 12 / 断片: unp residues 56-254 / Mutation: N75Q / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IL2RG / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P31785
#4: 糖...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 54 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 4.02 Å3/Da / 溶媒含有率: 69.39 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5
詳細: 100 mM Bis-Tris, 200 mM NH4SO4, 25% PEG-3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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データ収集

回折平均測定温度: 200 K
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 8.2.2 / 波長: 0.97 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2010年9月20日
放射モノクロメーター: U50 Undulator / 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: 0.97 Å / 相対比: 1
反射解像度: 3.8→52.2 Å / Num. all: 112967 / Num. obs: 111113 / % possible obs: 93.4 % / Observed criterion σ(F): 1.97 / Observed criterion σ(I): 2.08 / 冗長度: 2.1 %
反射 シェル解像度: 3.8023→3.9381 Å / 冗長度: 2.1 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.08 / Num. unique all: 112735 / Rsym value: 0.229 / % possible all: 98.7

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
PHASER位相決定
PHENIX(phenix.refine: dev_621)精密化
HKL-2000データ削減
SCALEPACKデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 3.802→52.191 Å / SU ML: 0.57 / σ(F): 1.97 / 位相誤差: 44.21 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.344 1854 1.67 %RANDOM
Rwork0.291 ---
obs0.292 111113 93.2 %-
all-112967 --
溶媒の処理減衰半径: 0.16 Å / VDWプローブ半径: 0.5 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 50.719 Å2 / ksol: 0.309 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--9.721 Å25.4178 Å21.2927 Å2
2---7.0751 Å22.2275 Å2
3---4.676 Å2
精密化ステップサイクル: LAST / 解像度: 3.802→52.191 Å
タンパク質核酸リガンド溶媒全体
原子数50806 0 756 0 51562
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00653246
X-RAY DIFFRACTIONf_angle_d1.08572229
X-RAY DIFFRACTIONf_dihedral_angle_d16.5119627
X-RAY DIFFRACTIONf_chiral_restr0.0737957
X-RAY DIFFRACTIONf_plane_restr0.0059030
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8023-3.93810.35981170.32176472X-RAY DIFFRACTION55
3.9381-4.09570.33371710.297311382X-RAY DIFFRACTION97
4.0957-4.28210.33082050.288711555X-RAY DIFFRACTION99
4.2821-4.50770.341990.285311631X-RAY DIFFRACTION99
4.5077-4.790.32781970.268311597X-RAY DIFFRACTION99
4.79-5.15950.33522120.252711638X-RAY DIFFRACTION99
5.1595-5.67810.31741960.257811639X-RAY DIFFRACTION99
5.6781-6.49850.40321960.281511584X-RAY DIFFRACTION99
6.4985-8.18230.33271910.278111650X-RAY DIFFRACTION99
8.1823-52.1960.35061700.331410111X-RAY DIFFRACTION86
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)
10.2363-0.01310.2429-0.0137-0.0370.27440.09690.12180.07540.1099-0.00780.0529-0.11860.4438-0.11320.24720.33830.46380.7901-0.42930.0656-37.18855.87144.7166
20.63060.15370.10010.2890.12040.0361-0.277-0.58020.11750.378-0.1160.03270.2055-0.17040.1337-0.15830.38330.6475-0.0911-0.6675-0.4362-37.11414.92464.5589
30.0631-0.00920.0870.20210.11850.1366-0.2945-0.08050.02190.1168-0.06220.0670.0936-0.09560.04150.14451.46280.17750.0641-0.75620.1191-37.9447-19.2358-14.054
4-0.0071-0.14950.0074-0.01870.10280.08450.41310.14060.0602-0.10480.0202-0.0405-0.3517-0.2054-0.02740.00431.4516-0.3038-0.4226-0.6668-0.4359-41.6915-10.41-18.2624
50.2173-0.2029-0.05260.4292-0.07350.0695-0.07580.0476-0.0848-0.11490.11350.13220.26060.1392-0.04010.79020.3685-0.18910.5938-0.22690.6756-50.59592.4637-30.9238
60.24820.0631-0.25360.0342-0.00040.8288-0.1770.0245-0.22330.0417-0.17850.06530.1918-0.29230.13270.0428-0.5959-0.73980.53770.02360.9595-48.0359-2.6369-27.7893
70.29180.41290.070.76520.32540.3382-0.1468-0.09240.087-0.1431-0.24490.2564-0.21140.05480.13050.97960.70640.22840.58360.00980.9689-37.233137.66153.5005
80.08360.06620.01130.2266-0.13360.0998-0.0698-0.0304-0.01240.1679-0.1291-0.1871-0.19890.13540.08320.2461-1.00860.5039-0.14380.57730.0409-36.575432.00494.669
90.0007-0.03560.00940.4531-0.14780.0690.11080.05470.02070.1201-0.0775-0.0221-0.0989-0.0594-0.03091.10340.166-0.34291.17160.16141.0587-42.915920.1201-26.9144
100.0646-0.0555-0.01160.1116-0.02440.0205-0.01080.0769-0.031-0.1117-0.12320.06320.033-0.0840.00640.1240.1609-0.8902-0.1968-0.20060.2843-47.770717.9668-27.4069
110.10810.0032-0.03790.15040.24090.3998-0.03110.054-0.07760.1312-0.0076-0.21170.16730.0020.09961.2378-0.14930.36820.668-0.070.6178-43.276323.1316-16.7268
120.1206-0.07250.06260.1202-0.0008-0.0651-0.1291-0.0122-0.05830.1654-0.0651-0.34910.1160.15510.0475-1.1016-0.222-1.4088-0.8803-0.0668-0.7705-83.9312-0.7536-38.6775
130.16130.0160.08170.29540.24310.35920.0715-0.1182-0.37860.4895-0.1230.12060.5141-0.0141-0.00720.41120.2613-0.0817-0.6187-1.1629-0.4497-83.869-0.6485-39.5889
140.04890.06180.1240.03160.08790.22150.13650.3634-0.02120.08670.0265-0.1010.270.1218-0.09570.4637-0.5163-0.32571.20040.24480.3642-97.0287-3.5607-67.0931
150.13490.15190.16110.47240.05220.22390.18920.5768-0.0751-0.31150.29760.1539-0.3820.1412-0.18371.4333-0.2576-0.1576-0.1754-0.04560.0855-102.0964-8.4044-59.318
160.03690.0287-0.07460.0771-0.1070.3297-0.1880.2124-0.1618-0.39880.26380.1040.3464-0.18560.10360.2937-0.3615-0.2631-0.5657-0.73390.0296-115.4045-19.7752-49.3329
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990.22370.03690.20740.1042-0.01790.20310.0286-0.0620.06260.0837-0.0849-0.05270.0254-0.01630.01070.7534-0.1593-0.18260.84940.48790.8788-10.181965.503710.6414
1000.43070.03130.1690.01080.0310.03970.1289-0.63580.1745-0.00280.18390.18410.1065-0.5076-0.06850.41670.0081-0.47260.10190.4417-0.2929-117.60819.503328.559
1011.289-0.639-0.08920.7195-0.19240.72820.09520.29260.15140.1795-0.2913-0.3124-0.15340.07510.09060.9522-0.24230.11790.6838-0.02620.703-117.88148.267528.4479
1020.0364-0.0083-0.03160.0116-0.0046-0.00120.26420.05140.1001-0.0632-0.04370.0927-0.0529-0.0094-0.05790.2636-0.23830.5450.56620.64050.603-99.2519-15.04135.5766
1030.3274-0.205-0.13560.1790.09950.09230.1895-0.00460.3512-0.11870.131-0.3125-0.13270.108-0.09460.47830.43690.82580.60180.43770.1037-94.471-7.436830.3079
1040.0437-0.01780.0226-0.044-0.01010.09790.1146-0.0185-0.10130.0875-0.0273-0.19130.0275-0.06080.0107-1.0054-0.8557-0.27840.0961-0.1675-0.7672-80.71682.906720.0187
1050.0812-0.00280.0308-0.0487-0.02510.10260.14550.10660.09260.07970.00010.07780.00610.0131-0.0231-0.54910.6381-0.19970.0460.37210.1359-84.1619-1.329523.2738
1060.15310.1028-0.17020.1032-0.19350.38110.02080.0174-0.10240.1129-0.3158-0.02580.07270.13390.17411.33650.2631-0.04170.96350.36251.3122-115.835640.645519.9564
1070.1111-0.09250.17150.0795-0.12910.2375-0.2-0.0698-0.08590.1176-0.0617-0.07180.17270.09660.17471.06620.18190.21780.1286-0.14030.9857-116.836134.843422.5352
1080.2331-0.18220.12990.42690.43061.0188-0.2135-0.07690.04950.0544-0.1191-0.09040.2925-0.06220.23010.6913-0.16650.10540.42440.01480.5155-84.92621.790623.2268
1090.11960.1265-0.17670.3546-0.04120.46760.0653-0.0546-0.0748-0.08130.0875-0.1124-0.03590.1835-0.00361.3489-0.46870.48591.4330.34031.5222-84.009318.632718.7478
1100.0008-0.0068-0.02130.35340.35080.7112-0.1289-0.22860.1016-0.04470.1316-0.5927-0.03510.3645-0.09270.39670.24190.56040.86970.24271.0474-95.030424.802820.8868
1110.0552-0.03650.16510.0343-0.0661-0.06740.0541-0.28550.3070.4401-0.1974-0.2285-0.48430.15450.0492-3.7339-0.7511-1.1103-3.15630.8251-0.9026-108.485-7.6179197.4256
1120.6031-0.21930.45620.1538-0.27450.60860.2175-0.5745-0.01940.48450.32960.43660.5787-0.5011-0.1369-1.70891.3539-1.4903-2.1460.4806-0.9993-108.0498-7.3618196.6099
1130.0647-0.0101-0.0407-0.0172-0.0457-0.0383-0.01840.30060.1833-0.27580.1404-0.1925-0.22340.2626-0.017-2.39412.13-0.1715-1.2045-0.5472-1.1117-99.778912.4566174.8423
1140.02030.09950.17030.34930.15030.86260.0811-0.2140.28470.04390.07740.7432-0.0456-1.29940.1082-1.70230.9528-0.4867-1.0012-0.8824-0.3347-107.306716.0994181.2417
1150.30730.18390.11140.10960.07860.05330.1136-0.18120.02910.06020.2071-0.14470.13460.1188-0.10250.39960.29790.17480.9845-0.04931.4393-121.686127.4367189.1752
1160.6769-0.37350.37460.1908-0.17840.14760.14450.0645-0.10060.05890.3116-0.14680.00930.5184-0.269-0.033-0.2396-0.08740.3656-0.21550.7897-116.972724.711185.7774
1170.08630.0183-0.0130.11780.21210.34680.1371-0.0043-0.09030.01050.1119-0.00340.01870.175-0.07180.7930.72140.25140.6743-0.00550.3661-122.8494-8.1207226.4209
1180.492-0.16970.70390.2011-0.39441.10440.377-0.00010.0557-0.20010.2426-0.05110.3065-0.4665-0.12730.99030.09840.50211.3315-0.1850.8373-119.2286-8.5847221.2881
1190.1195-0.0361-0.0040.34640.20850.1108-0.0474-0.09260.12090.20910.0512-0.2530.09160.1499-0.04140.60790.3152-0.10860.8165-0.4650.8068-121.777523.2659208.2635
1200.2676-0.2113-0.06640.16330.03740.0276-0.062-0.043-0.05460.0646-0.00120.1357-0.0336-0.01010.00111.18540.46570.52441.12970.48471.2654-125.533223.5689204.2181
1210.0524-0.0553-0.11620.14170.10130.3008-0.1834-0.1181-0.0001-0.0623-0.0808-0.00890.2573-0.03350.07141.1086-0.1722-0.23230.7592-0.25690.7084-122.868912.9059210.8543
1220.40080.16150.09730.01970.05640.01190.02270.129-0.2662-0.1612-0.0602-0.03760.01960.2142-0.04130.5746-0.5141-0.22080.1078-0.13480.3655-41.365154.2107101.663
1230.45360.2372-0.35790.2119-0.20040.2173-0.4141-0.4581-0.39780.284-0.1893-0.03790.301-0.01640.0981-0.4676-1.36770.7304-0.9236-0.2302-0.9155-42.366154.4928101.7443
1240.1588-0.03680.04150.0132-0.04680.1509-0.00170.04990.06090.05630.12940.1899-0.2829-0.0870.0501-0.06230.2634-1.15150.14140.0638-0.3973-68.858858.2188116.7254
1250.69860.54720.19440.4090.25710.95550.836-0.03960.02990.59150.5651-0.08490.44760.1412-0.25350.5842-0.6381-0.5589-0.5866-0.2494-0.1529-62.050551.7944121.4882
1260.03320.0412-0.00970.9044-0.03210.021-0.0605-0.0634-0.10080.0279-0.0635-0.0013-0.3865-0.0380.09912.2406-0.09850.5520.16660.3041.0754-54.225238.5818134.3045
1270.6560.1464-0.39510.0992-0.2680.6860.01480.10910.249-0.08870.1690.0842-0.22660.0505-0.11540.7346-0.34850.12070.81660.45510.8682-57.87542.6018130.8857
1280.01070.010.00850.03970.01250.0023-0.0306-0.0726-0.18410.0549-0.0097-0.17380.08560.0940.047-0.01360.3418-0.0745-0.36990.47410.4577-10.82843.7701106.9918
1290.3927-0.22010.2090.1731-0.04360.1386-0.2897-0.58640.14470.3020.210.086-0.1916-0.27610.05740.16890.61380.0020.506-0.10980.256-16.368246.7813105.5603
1300.0624-0.0095-0.06040.12070.07120.0561-0.12710.0306-0.0022-0.075-0.13030.0187-0.20780.06320.05950.8460.4194-0.56970.3178-0.02550.7597-35.131241.8056134.148
1310.09490.101-0.33660.1273-0.39411.191-0.158-0.0943-0.2501-0.0414-0.0783-0.23310.24510.14990.09540.20990.2273-0.6173-0.21630.15170.596-38.321937.4779133.4618
1320.25060.0038-0.05890.0674-0.09990.2960.1117-0.06020.05050.1087-0.0104-0.056-0.006-0.1102-0.07420.31150.2235-0.13261.15470.17950.7123-30.217341.4175124.401
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:68)
2X-RAY DIFFRACTION2chain 'A' and (resseq 69:133)
3X-RAY DIFFRACTION3chain 'B' and (resseq 6:71)
4X-RAY DIFFRACTION4chain 'B' and (resseq 72:131)
5X-RAY DIFFRACTION5chain 'B' and (resseq 132:181)
6X-RAY DIFFRACTION6chain 'B' and (resseq 182:207)
7X-RAY DIFFRACTION7chain 'C' and (resseq 34:93)
8X-RAY DIFFRACTION8chain 'C' and (resseq 94:133)
9X-RAY DIFFRACTION9chain 'C' and (resseq 134:173)
10X-RAY DIFFRACTION10chain 'C' and (resseq 174:203)
11X-RAY DIFFRACTION11chain 'C' and (resseq 204:224)
12X-RAY DIFFRACTION12chain 'D' and (resseq 6:68)
13X-RAY DIFFRACTION13chain 'D' and (resseq 69:133)
14X-RAY DIFFRACTION14chain 'E' and (resseq 6:71)
15X-RAY DIFFRACTION15chain 'E' and (resseq 72:131)
16X-RAY DIFFRACTION16chain 'E' and (resseq 132:181)
17X-RAY DIFFRACTION17chain 'E' and (resseq 182:207)
18X-RAY DIFFRACTION18chain 'F' and (resseq 34:93)
19X-RAY DIFFRACTION19chain 'F' and (resseq 94:133)
20X-RAY DIFFRACTION20chain 'F' and (resseq 134:173)
21X-RAY DIFFRACTION21chain 'F' and (resseq 174:203)
22X-RAY DIFFRACTION22chain 'F' and (resseq 204:224)
23X-RAY DIFFRACTION23chain 'G' and (resseq 6:68)
24X-RAY DIFFRACTION24chain 'G' and (resseq 69:133)
25X-RAY DIFFRACTION25chain 'H' and (resseq 6:71)
26X-RAY DIFFRACTION26chain 'H' and (resseq 72:131)
27X-RAY DIFFRACTION27chain 'H' and (resseq 132:181)
28X-RAY DIFFRACTION28chain 'H' and (resseq 182:207)
29X-RAY DIFFRACTION29chain 'I' and (resseq 34:93)
30X-RAY DIFFRACTION30chain 'I' and (resseq 94:133)
31X-RAY DIFFRACTION31chain 'I' and (resseq 134:173)
32X-RAY DIFFRACTION32chain 'I' and (resseq 174:203)
33X-RAY DIFFRACTION33chain 'I' and (resseq 204:224)
34X-RAY DIFFRACTION34chain 'J' and (resseq 6:68)
35X-RAY DIFFRACTION35chain 'J' and (resseq 69:133)
36X-RAY DIFFRACTION36chain 'K' and (resseq 6:71)
37X-RAY DIFFRACTION37chain 'K' and (resseq 72:131)
38X-RAY DIFFRACTION38chain 'K' and (resseq 132:181)
39X-RAY DIFFRACTION39chain 'K' and (resseq 182:207)
40X-RAY DIFFRACTION40chain 'L' and (resseq 34:93)
41X-RAY DIFFRACTION41chain 'L' and (resseq 94:133)
42X-RAY DIFFRACTION42chain 'L' and (resseq 134:173)
43X-RAY DIFFRACTION43chain 'L' and (resseq 174:203)
44X-RAY DIFFRACTION44chain 'L' and (resseq 204:224)
45X-RAY DIFFRACTION45chain 'M' and (resseq 6:68)
46X-RAY DIFFRACTION46chain 'M' and (resseq 69:133)
47X-RAY DIFFRACTION47chain 'N' and (resseq 6:71)
48X-RAY DIFFRACTION48chain 'N' and (resseq 72:131)
49X-RAY DIFFRACTION49chain 'N' and (resseq 132:181)
50X-RAY DIFFRACTION50chain 'N' and (resseq 182:207)
51X-RAY DIFFRACTION51chain 'O' and (resseq 34:93)
52X-RAY DIFFRACTION52chain 'O' and (resseq 94:133)
53X-RAY DIFFRACTION53chain 'O' and (resseq 134:173)
54X-RAY DIFFRACTION54chain 'O' and (resseq 174:203)
55X-RAY DIFFRACTION55chain 'O' and (resseq 204:224)
56X-RAY DIFFRACTION56chain 'P' and (resseq 6:68)
57X-RAY DIFFRACTION57chain 'P' and (resseq 69:133)
58X-RAY DIFFRACTION58chain 'Q' and (resseq 6:71)
59X-RAY DIFFRACTION59chain 'Q' and (resseq 72:131)
60X-RAY DIFFRACTION60chain 'Q' and (resseq 132:181)
61X-RAY DIFFRACTION61chain 'Q' and (resseq 182:207)
62X-RAY DIFFRACTION62chain 'R' and (resseq 34:93)
63X-RAY DIFFRACTION63chain 'R' and (resseq 94:133)
64X-RAY DIFFRACTION64chain 'R' and (resseq 134:173)
65X-RAY DIFFRACTION65chain 'R' and (resseq 174:203)
66X-RAY DIFFRACTION66chain 'R' and (resseq 204:224)
67X-RAY DIFFRACTION67chain 'S' and (resseq 6:68)
68X-RAY DIFFRACTION68chain 'S' and (resseq 69:133)
69X-RAY DIFFRACTION69chain 'T' and (resseq 6:71)
70X-RAY DIFFRACTION70chain 'T' and (resseq 72:131)
71X-RAY DIFFRACTION71chain 'T' and (resseq 132:181)
72X-RAY DIFFRACTION72chain 'T' and (resseq 182:207)
73X-RAY DIFFRACTION73chain 'U' and (resseq 34:93)
74X-RAY DIFFRACTION74chain 'U' and (resseq 94:133)
75X-RAY DIFFRACTION75chain 'U' and (resseq 134:173)
76X-RAY DIFFRACTION76chain 'U' and (resseq 174:203)
77X-RAY DIFFRACTION77chain 'U' and (resseq 204:224)
78X-RAY DIFFRACTION78chain 'V' and (resseq 6:68)
79X-RAY DIFFRACTION79chain 'V' and (resseq 69:133)
80X-RAY DIFFRACTION80chain 'W' and (resseq 6:71)
81X-RAY DIFFRACTION81chain 'W' and (resseq 72:131)
82X-RAY DIFFRACTION82chain 'W' and (resseq 132:181)
83X-RAY DIFFRACTION83chain 'W' and (resseq 182:207)
84X-RAY DIFFRACTION84chain 'X' and (resseq 34:93)
85X-RAY DIFFRACTION85chain 'X' and (resseq 94:133)
86X-RAY DIFFRACTION86chain 'X' and (resseq 134:173)
87X-RAY DIFFRACTION87chain 'X' and (resseq 174:203)
88X-RAY DIFFRACTION88chain 'X' and (resseq 204:224)
89X-RAY DIFFRACTION89chain 'Y' and (resseq 6:68)
90X-RAY DIFFRACTION90chain 'Y' and (resseq 69:133)
91X-RAY DIFFRACTION91chain 'Z' and (resseq 6:71)
92X-RAY DIFFRACTION92chain 'Z' and (resseq 72:131)
93X-RAY DIFFRACTION93chain 'Z' and (resseq 132:181)
94X-RAY DIFFRACTION94chain 'Z' and (resseq 182:207)
95X-RAY DIFFRACTION95chain 'a' and (resseq 34:93)
96X-RAY DIFFRACTION96chain 'a' and (resseq 94:133)
97X-RAY DIFFRACTION97chain 'a' and (resseq 134:173)
98X-RAY DIFFRACTION98chain 'a' and (resseq 174:203)
99X-RAY DIFFRACTION99chain 'a' and (resseq 204:224)
100X-RAY DIFFRACTION100chain 'b' and (resseq 6:68)
101X-RAY DIFFRACTION101chain 'b' and (resseq 69:133)
102X-RAY DIFFRACTION102chain 'c' and (resseq 6:71)
103X-RAY DIFFRACTION103chain 'c' and (resseq 72:131)
104X-RAY DIFFRACTION104chain 'c' and (resseq 132:181)
105X-RAY DIFFRACTION105chain 'c' and (resseq 182:207)
106X-RAY DIFFRACTION106chain 'd' and (resseq 34:93)
107X-RAY DIFFRACTION107chain 'd' and (resseq 94:133)
108X-RAY DIFFRACTION108chain 'd' and (resseq 134:173)
109X-RAY DIFFRACTION109chain 'd' and (resseq 174:203)
110X-RAY DIFFRACTION110chain 'd' and (resseq 204:224)
111X-RAY DIFFRACTION111chain 'e' and (resseq 6:68)
112X-RAY DIFFRACTION112chain 'e' and (resseq 69:133)
113X-RAY DIFFRACTION113chain 'f' and (resseq 6:71)
114X-RAY DIFFRACTION114chain 'f' and (resseq 72:131)
115X-RAY DIFFRACTION115chain 'f' and (resseq 132:181)
116X-RAY DIFFRACTION116chain 'f' and (resseq 182:207)
117X-RAY DIFFRACTION117chain 'g' and (resseq 34:93)
118X-RAY DIFFRACTION118chain 'g' and (resseq 94:133)
119X-RAY DIFFRACTION119chain 'g' and (resseq 134:173)
120X-RAY DIFFRACTION120chain 'g' and (resseq 174:203)
121X-RAY DIFFRACTION121chain 'g' and (resseq 204:224)
122X-RAY DIFFRACTION122chain 'h' and (resseq 6:68)
123X-RAY DIFFRACTION123chain 'h' and (resseq 69:133)
124X-RAY DIFFRACTION124chain 'i' and (resseq 6:71)
125X-RAY DIFFRACTION125chain 'i' and (resseq 72:131)
126X-RAY DIFFRACTION126chain 'i' and (resseq 132:181)
127X-RAY DIFFRACTION127chain 'i' and (resseq 182:207)
128X-RAY DIFFRACTION128chain 'j' and (resseq 34:93)
129X-RAY DIFFRACTION129chain 'j' and (resseq 94:133)
130X-RAY DIFFRACTION130chain 'j' and (resseq 134:173)
131X-RAY DIFFRACTION131chain 'j' and (resseq 174:203)
132X-RAY DIFFRACTION132chain 'j' and (resseq 204:224)

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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。

-
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