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- PDB-7n2q: AS4.3-YEIH-HLA*B27 -

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基本情報

登録情報
データベース: PDB / ID: 7n2q
タイトルAS4.3-YEIH-HLA*B27
要素
  • (AS4.3 T cell receptor ...) x 2
  • Beta-2-microglobulin
  • Human leukocyte antigen B27
  • YeiH protein
キーワードIMMUNE SYSTEM / TCR MHC HLA-B27
機能・相同性
機能・相同性情報


: / : / 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 ...: / : / 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 / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / 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
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 / 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 / : ...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 / 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 / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
MHC class I antigen / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å
データ登録者Yang, X. / Jude, K.M. / Garcia, K.C.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI103867 米国
引用ジャーナル: Nature / 年: 2022
タイトル: Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides.
著者: Yang, X. / Garner, L.I. / Zvyagin, I.V. / Paley, M.A. / Komech, E.A. / Jude, K.M. / Zhao, X. / Fernandes, R.A. / Hassman, L.M. / Paley, G.L. / Savvides, C.S. / Brackenridge, S. / Quastel, M.N. ...著者: Yang, X. / Garner, L.I. / Zvyagin, I.V. / Paley, M.A. / Komech, E.A. / Jude, K.M. / Zhao, X. / Fernandes, R.A. / Hassman, L.M. / Paley, G.L. / Savvides, C.S. / Brackenridge, S. / Quastel, M.N. / Chudakov, D.M. / Bowness, P. / Yokoyama, W.M. / McMichael, A.J. / Gillespie, G.M. / Garcia, K.C.
履歴
登録2021年5月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年12月7日Provider: repository / タイプ: Initial release
改定 1.12022年12月21日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22023年1月4日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
D: AS4.3 T cell receptor alpha chain
F: AS4.3 T cell receptor beta chain
A: Human leukocyte antigen B27
B: Beta-2-microglobulin
C: YeiH protein
E: AS4.3 T cell receptor alpha chain
G: AS4.3 T cell receptor beta chain
H: Human leukocyte antigen B27
I: Beta-2-microglobulin
J: YeiH protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)191,42023
ポリマ－189,43210
非ポリマー1,98813
水1,26170
1
D: AS4.3 T cell receptor alpha chain
F: AS4.3 T cell receptor beta chain
A: Human leukocyte antigen B27
B: Beta-2-microglobulin
C: YeiH protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,4769
ポリマ－94,7165
非ポリマー7604
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: AS4.3 T cell receptor alpha chain
G: AS4.3 T cell receptor beta chain
H: Human leukocyte antigen B27
I: Beta-2-microglobulin
J: YeiH protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)95,94414
ポリマ－94,7165
非ポリマー1,2289
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)54.977, 97.412, 175.484
Angle α, β, γ (deg.)90.000, 92.325, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "A"
d_2ens_1chain "H"
d_1ens_2(chain "B" and resid 1 through 99)
d_2ens_2chain "I"
d_1ens_3chain "C"
d_2ens_3chain "J"
d_1ens_4chain "D"
d_2ens_4(chain "E" and (resid 2 through 202 or resid 203 through 204))
d_1ens_5(chain "F" and resid 4 through 241)
d_2ens_5(chain "G" and resid 4 through 241)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYPROF1 - 276
d_21ens_1GLYPROQ1 - 276
d_11ens_2ILEMETG2 - 100
d_21ens_2ILEMETR1 - 99
d_11ens_3LEUPHEH1 - 9
d_21ens_3LEUPHES1 - 9
d_11ens_4LYSPROA1 - 201
d_12ens_4NAGNAGB
d_13ens_4NAGNAGC
d_21ens_4LYSPROI1 - 201
d_22ens_4NAGNAGJ
d_23ens_4NAGNAGK
d_11ens_5VALGLYD1 - 238
d_21ens_5VALGLYM1 - 238

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixベクター
1given(-0.998834108168, 0.0322566264658, 0.0359156568708), (-0.0381497387598, -0.983322983811, -0.177821559272), (0.0295807672647, -0.178984411495, 0.983407117449)25.1896501777, -11.7842865317, 85.6154546454
2given(-0.997695587904, 0.0523998104151, 0.04310189955), (-0.0600233997916, -0.977828974686, -0.200618263731), (0.0316339272587, -0.202743079125, 0.978720868539)25.1804050726, -11.8284255169, 85.8683098563
3given(-0.999469739359, 0.0199556677793, 0.0257295827625), (-0.0244923720699, -0.981436862958, -0.190215161693), (0.0214560904183, -0.190744476593, 0.981405207258)25.2983549386, -11.4091535961, 85.4079762566
4given(-0.999616728101, 0.0112463964777, 0.0252965504993), (-0.0170886489306, -0.969569098132, -0.244220683041), (0.0217801510239, -0.244559363987, 0.969389675264)25.2508387214, -10.6779387517, 84.6235562821
5given(-0.999922442317, 0.00228050882178, 0.0122437180323), (-0.00515627417751, -0.970683848981, -0.240304552939), (0.0113367626926, -0.240349047441, 0.97062032392)25.2321422358, -11.0661979471, 85.1417515988

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要素

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AS4.3 T cell receptor ... , 2種, 4分子 DEFG

#1: タンパク質 AS4.3 T cell receptor alpha chain


分子量: 22399.701 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: Homo sapiens (ヒト)
#2: タンパク質 AS4.3 T cell receptor beta chain


分子量: 27272.215 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: Homo sapiens (ヒト)

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タンパク質 , 2種, 4分子 AHBI

#3: タンパク質 Human leukocyte antigen B27 / HLA-B27


分子量: 32086.250 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 (大腸菌) / 参照: UniProt: A3F718
#4: 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 (大腸菌) / 参照: UniProt: P61769

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タンパク質・ペプチド / 糖 , 2種, 8分子 CJ

#5: タンパク質・ペプチド YeiH protein


分子量: 1078.413 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli (大腸菌)
#6: 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: 6 / 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

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非ポリマー , 3種, 77分子

#7: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 合成 / 式: SO4
#8: 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
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 70 / 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N
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: 2.48 Å3/Da / 溶媒含有率: 50.36 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 25% PEG3350 with 0.2M Ammonium sulfate and 0.1M BIS-TRIS pH 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: SSRL / ビームライン: BL12-1 / 波長: 0.97946 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年12月19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: 0.97946 Å / 相対比: 1
反射解像度: 2.7→48.71 Å / Num. obs: 49539 / % possible obs: 97.4 % / 冗長度: 3.4 % / Biso Wilson estimate: 60.1 Å2 / CC1/2: 0.938 / Net I/σ(I): 2.7
反射 シェル解像度: 2.7→2.79 Å / Num. unique obs: 4552 / CC1/2: 0.346

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.1_4122+SVN精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5KSB 1JGE

5ksb

1jge


解像度: 2.7→47.42 Å / SU ML: 0.4019 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.4083
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.264 2001 4.04 %
Rwork0.2134 47470 -
obs0.2155 49471 97.01 %
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
原子変位パラメータBiso mean: 77.17 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→47.42 Å
タンパク質核酸リガンド溶媒全体
原子数13219 0 122 70 13411
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00213670
X-RAY DIFFRACTIONf_angle_d0.524118583
X-RAY DIFFRACTIONf_chiral_restr0.04011993
X-RAY DIFFRACTIONf_plane_restr0.00372436
X-RAY DIFFRACTIONf_dihedral_angle_d12.48115008
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2FX-RAY DIFFRACTIONTorsion NCS0.902674852099
ens_2d_2GX-RAY DIFFRACTIONTorsion NCS0.968548365154
ens_3d_2HX-RAY DIFFRACTIONTorsion NCS0.253952559572
ens_4d_2AX-RAY DIFFRACTIONTorsion NCS2.20771751368
ens_5d_2DX-RAY DIFFRACTIONTorsion NCS0.81721534694
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.341420.3063367X-RAY DIFFRACTION96.61
2.77-2.840.371390.29683268X-RAY DIFFRACTION95.03
2.84-2.930.32961420.28193426X-RAY DIFFRACTION97.83
2.93-3.020.31191500.27983407X-RAY DIFFRACTION98.4
3.02-3.130.3951460.27853422X-RAY DIFFRACTION98.05
3.13-3.250.34431330.25993440X-RAY DIFFRACTION98.19
3.25-3.40.2871460.23993389X-RAY DIFFRACTION97.6
3.4-3.580.27581480.23513362X-RAY DIFFRACTION96.99
3.58-3.810.29161360.22573294X-RAY DIFFRACTION94.91
3.81-4.10.25151390.20193462X-RAY DIFFRACTION98.5
4.1-4.510.23281430.17173424X-RAY DIFFRACTION97.97
4.51-5.160.21221500.16893393X-RAY DIFFRACTION96.83
5.16-6.50.25011390.1983386X-RAY DIFFRACTION95.76
6.5-47.420.20031480.18263430X-RAY DIFFRACTION95.62
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)
10.48562093507-0.1116857348340.3554775810040.0796129007444-0.1401439257450.335332624125-0.204205860232-0.368344655194-0.652847867879-0.0784448031655-0.0752293313757-0.2414521177820.13458923156-0.0333400395521-0.06917143440270.367554714681-0.04582848533960.1390275979180.2933443775680.007174240058680.6390310551114.7314314478-16.2417685370.283038926288
20.0891739594039-0.006421209172310.07397404224550.0622723304692-0.0715477526360.0435737012546-0.08779927130590.0734236154776-0.01392451653240.1010618447680.206305987672-0.0735661010340.268010979724-0.0262066338972-0.05301992775681.283978952820.1216606794670.5865198237740.650584554485-0.1270589562071.1076294760141.2040341138-15.7375774154-23.3352055861
30.01696684301560.01318564291-0.02954296681390.179665025192-0.2256107777360.303435570979-0.357595898510.226527958638-0.2023243629770.160965916314-0.193730797971-0.007700002342110.4638031158280.266416217443-0.0292920880931.24148983940.1073791344330.427168519060.683033953897-0.1068169557640.97558501322641.1364155291-16.6270799789-23.0348322404
40.1199524306950.173771734084-0.1883814193980.070528274028-0.1552450575110.164869187126-0.1136070567170.2136393325230.0216064918096-0.0742431868790.125355629724-0.0458644574263-0.0926286752314-0.1438498733982.06133718783E-50.2917901346490.01763101164650.02714863828210.3301627979730.04842603760060.31907808499310.91389068935.69860427258-3.36183318356
50.0314079516183-0.01438252426710.007464023022850.0327487294499-0.02029515420350.0209227958034-0.111609335071-0.151655589976-0.212193930454-0.08829223221980.00691767258052-0.140101763630.1742987543910.0970926275816-2.11533616777E-50.421094902961-0.04356949805190.06535705477450.57718896741-0.07985456787360.41227026165232.74927646878.27805491238-16.2103217996
60.05119110741180.02279813805380.04771708775070.152987929513-0.1224679765480.213128990626-0.460093852551-0.121555921063-0.378445922032-0.2468934060650.0471903185667-0.1191888565150.445975486472-0.288935834555-0.5051800789410.336461632083-0.1999013170431.044105775790.701782507542-0.5016921574990.32693359634631.1964359207-8.15840023437-28.5912689633
7-0.001768216361020.01069422180470.008065750318890.002115869802770.003988330598020.0107106153879-0.115480246354-0.00383279514983-0.1062308729950.181757611258-0.131461360296-0.05555342000490.02659048466730.07553545213276.43116832326E-50.879824599950.07034914188320.1697776620880.770075324864-0.009234465616630.88251929886539.16583937750.850061450905-11.8960115542
80.05536388510610.04402181403610.04280244506790.03117759517910.04513943956470.215083796973-0.2582556439240.0718829680635-0.168551700702-0.173626518105-0.0009597329953450.02242844096180.101227609672-0.261183705184-0.1714921794030.756540958585-0.1177230791680.3194338924260.62485961501-0.2605181482350.67287963690630.40757305262.089987642-28.724446658
90.6275587137830.04038596003170.004157111054610.0797201583079-0.06948463195550.2215331236610.0382063454315-0.05902521774840.00929656958720.160541893387-0.1171650814060.0705085853697-0.07565817051320.0570725122629-1.03206318512E-50.381271096415-0.0835105678609-0.01439315370890.4527089661550.02315024110140.319652428092-10.652162701-7.7458760777718.2829420097
100.4101928293160.4388510208120.06834105792180.089111909585-0.07294623134720.0916714385958-0.0005789951407760.0622306722162-0.1034199122090.01979830931020.09212619093520.09125015908820.04756201553960.03666453315920.004321366226540.374403055417-0.03888042659820.03267063114820.3580421515860.02423126438560.435850088293-15.8534373074-18.656383899416.704473555
110.0308942388612-0.0336763036194-0.03702501112850.03038984710550.01390337557560.03707736041760.217114894063-0.0031958128670.1158145011350.2480136740940.006912996431210.3999855272340.10621025888-0.04975391912880.0007432150179490.545938924192-0.164811012216-0.02577607105850.5849001394490.117944169360.536871920457-35.3443769268-26.36258754635.7577601633
120.003998454313250.03942160268740.0150591703750.04198404785680.02798307771620.01519470580370.08771082723060.4134769644680.137863231833-0.0142773962813-0.1511083991430.202314935835-0.157568543499-0.1282475760830.0001851779214350.410437990395-0.02074100611440.01751969724080.571503304551-0.01360167829280.671867428486-31.0223713922-6.6498786838527.0079294689
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140.000964264418943-0.00725021266754-0.00326022264290.001048093945980.01283641233390.008989485421160.1570457277070.2563194615940.3445719417440.152874144742-0.0349700808280.266891529448-0.1178743231610.00474507379567-5.61948577343E-60.727920801395-0.04653529145410.1941592702050.5584089650070.00414037251370.473085519914-26.61934953861.2551855601630.8740485239
150.004666016145030.00767240173861-0.002658231552590.005843114021450.004400418951490.00474717217393-0.0994061881727-0.057048103791-0.02335679604650.109835395838-0.129203276565-0.102268284947-0.07925314481460.01876415106250.0002351828753761.25891497411-0.073984138110.1286518748770.686920551454-0.2129170708360.696294301803-22.93967236312.8813740700741.6423951735
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170.001568622223520.0195556317088-0.04353372695740.0106451700265-0.006907298267990.04830654288430.304313740951-0.1183221806310.1242609531570.330759433159-0.0531374456740.0181461983503-0.271980755536-0.270959161997-0.0002349998687740.75463994737-0.08790001354780.09784604047010.514040281918-0.002142062113940.387586212316-28.7396055678-2.1955815613437.4727818684
180.0476095039102-0.02172436431630.01723238413350.0311997419601-0.001434175307080.106285610881-0.0595065376117-0.0394241781487-0.0309458004917-0.0154355488689-0.0953879902027-0.0236998592567-0.01177019618170.0562814257503-0.1353969437870.742027544310.02019965926350.4873417273130.5255065585530.09630566755230.593360091148-35.6841030015-7.5336007362241.0589137622
190.01565316439050.01844604411850.002332265124920.00245459995885-0.00194557718422-0.003778223321720.0329585621752-0.03134826445050.0121773297372-0.226949286714-0.179105171582-0.0481389436940.0342133656919-0.09488145562841.4000962733E-50.426412370151-0.0221479689403-0.03479432345360.4575423600370.03562693476190.41530808392-5.40497909765-9.2471297641110.5279946519
200.05749564835230.040702103880.05621690194170.1586364590860.1585044909210.171972530961-0.01988153437880.01872038358680.0940308700326-0.03754635296220.01357241150880.0607322729671-0.1804788191160.0136188545315-1.55545568729E-50.3043003498310.00645395161209-0.03926120818040.3167092118420.009882741662180.4255256708310.43134400664.7344268905689.2280565258
210.0237869259845-0.00395836554479-0.0312521886466-0.001603018949770.006698212341120.0416235162443-0.1549948001930.133671374660.336154246326-0.104416255848-0.0433285308584-0.249909390339-0.07664903269990.007708364831971.34257803126E-60.769689259732-0.119979371428-0.2959370616230.4868604419170.05565258461571.03231985705-16.075116376110.110370118662.4413343739
220.00417638221546-0.017857917033-0.0217762450270.04917373893810.06047444626890.0756754250461-0.349234507046-0.1729055975440.453754016599-0.115457216676-0.0633880233660.0666439898606-0.0830418422364-0.160234435604-4.32694643476E-50.674320108189-0.0903694584127-0.214901227830.548050350914-0.01790561284020.730542299788-17.04551581429.983419781368.8783533341
230.1673418593450.0812674211910.169525806050.372874972348-0.1960880121690.174299505307-0.00109172788679-0.102533386742-0.25014718917-0.09291047950050.00189606853452-0.111792274812-0.0221880861568-0.049259046211-1.71695211636E-50.329860581751-0.00949935510755-0.002908456239950.319427238696-0.03683006823640.4383519834511.7929620032-16.388883589679.5085648808
240.112791423879-0.1237634240640.007632019205470.2539789994740.09438552637540.158972931599-0.008789159983020.06326421826850.0219930598613-0.8021357874610.1250543640450.3734201592240.1137326294150.02013550149930.02016838874970.998024853176-0.147755962769-0.2321938538270.5098822334260.03098776805660.672860308528-7.38198402297-2.6174518662859.8221864486
250.149395858507-0.1172287226210.1897060911850.11369492901-0.07759092886130.1982895816660.0210110441477-0.0394566872963-0.0716437993558-0.0293304358774-0.02023494786730.057409939197-0.0213407023777-0.1853362752381.50314726021E-60.318294706164-0.03298332908270.001708091552120.4148908281370.04276143869340.38336985050735.7489201926-9.13352890104105.124237696
26-0.00411355912670.07122914173570.004726285989270.09380954828770.03233032753820.0455829725858-0.02441630661110.1446637490330.1587368192510.0751362565255-0.00579467499199-0.136251878961-0.165921444215-0.219675824923-2.14516980243E-60.4048350943480.02024033819930.01399414854070.3613696684460.05655784999460.36764080860138.85305538313.434762577593.5494001463
270.2705717316910.251793055114-0.06057136594160.4536784974520.001844258917820.1345282496180.03285712084950.1471631457580.222890500738-0.00623351532361-0.01263121617310.2102314488840.02254670415860.2399781092780.04052364646760.4201944846910.0031610067013-0.03118296635550.605747750625-0.1275664885330.30731408294555.5837334158.43092522899123.523412417
28-0.006124460671210.03301731576020.003522915578710.04248852674560.0132040428320.0121858034864-0.224795285491-0.0654075095467-0.2614682450220.424790914920.065597844671-0.107009514848-0.09312461966590.09687352428930.00020066543310.487865990892-0.0193192584813-0.06968245248010.878214193399-0.09947708410480.44474142869557.1068756962-8.86789677899113.378319029
290.0236014969112-0.009771828849370.01158402749120.01496412739110.01839377778330.0191565069703-0.2388122016360.0935195274152-0.125577381180.09880627894690.0498863317954-0.2562180358280.153661512522-0.133086273519-0.002755122570840.5825990983150.120868740601-0.2323574654780.5356555108430.02366777831150.4578623649851.5989892856-8.27147133716128.205687308
300.09020161185410.02354778788870.05113500507370.01134454918740.01257794168920.0371253257947-0.198885237630.0530647345783-0.2330344102520.4149361924320.383714185622-0.02650371868340.2586921746910.0286405352682-0.00322741894940.8317366640790.13207944035-0.1267695066220.4372157180770.08432731517050.56694923103353.0986575611-17.7607658028114.911654758
310.00454897986602-0.003755693661830.004495128621420.002809416543970.0001542387822930.00871608861316-0.0171322443905-0.0176973909509-0.07690242176340.0274976412921-0.0551775772966-0.1154476439270.0272968088027-0.041046188453-1.97162608662E-51.506586202960.321669357649-0.3051538543080.836009479937-0.194164656370.55256716044555.5115501096-23.8568149353127.021442723
326.34746344045E-6-0.004483027811130.0002965127741280.00804310807096-0.00304971453293-0.0003431077886580.01665108881360.0480308814909-0.07975498410380.04091291729730.02595744095320.00973960485479-0.0327833375763-0.01379157760397.13065507907E-60.719605854055-0.0510378958563-0.01252368164180.6744996711260.1029224375950.83541337059245.1556408105-19.3262996613123.542036318
330.100268126651-0.132779758503-0.06621319610340.1721642404520.0650030625270.0355519431870.4138183486250.0249337669331-0.0238007990074-0.1974571006040.136339966412-0.2297582951940.08402029185820.04211968755330.01893614782870.404489712515-0.041443093169-0.1519845498260.411249110974-0.006629148790820.52049304014347.6206926277-8.80895870626115.443026069
340.0017424737078-0.006364969653720.003029765122780.001686397438590.001880260835250.00427730097027-0.0378238509213-0.00990380408062-0.0759679710349-0.00526972380084-0.101674037061-0.0910062375398-0.05927860988390.01685939906-8.90937932747E-51.354202485430.1958065161540.06172322073541.086945135020.3129904941280.6161773049359.3931374739-16.7499404705137.15643605
350.0105573311723-0.003801173706560.0101753316445-0.000410977113471-0.00607427518150.02257108280180.003030974307970.0120717847539-0.033771457963-0.00521419885581-0.03845184351360.0875828065995-0.01062290526130.0630585812397-0.004853672511940.8740041412430.173144029566-0.3717543521050.748621055268-0.1335136921210.70563720231857.6115187517-17.760000953119.030645705
360.0074169829417-0.007008722490130.01564109216020.02732586864210.01902425247530.007478011149120.0996505256364-0.1430309335230.00748291043083-0.181472250034-0.337842523829-0.2682254771820.01404079137450.143225948114.07040545232E-50.5763211031330.160952248077-0.1840985232080.735482555659-0.0391910038690.57312966880262.3532157713-13.3616342291120.565286652
370.00228837415122-0.00099917949849-0.001631593959410.01263236810030.007828544101570.00434605211533-0.185355137093-0.1913796584020.1361733490990.01433892935550.0007663288260070.02522954021390.0236193485414-0.155710278049-1.6197142067E-50.576633324636-0.0361584838963-0.02550635479230.457649456157-0.03853096100810.48500563332930.7829681387-4.2005730977897.372209471
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 2 through 110 )DA2 - 1101 - 109
22chain 'D' and (resid 111 through 152 )DA111 - 152110 - 151
33chain 'D' and (resid 153 through 202 )DA153 - 202152 - 201
44chain 'F' and (resid 4 through 108 )FD4 - 1081 - 105
55chain 'F' and (resid 109 through 128 )FD109 - 128106 - 125
66chain 'F' and (resid 129 through 172 )FD129 - 172126 - 169
77chain 'F' and (resid 173 through 187 )FD173 - 187170 - 184
88chain 'F' and (resid 188 through 241 )FD188 - 241185 - 238
99chain 'A' and (resid 1 through 118 )AF1 - 1181 - 118
1010chain 'A' and (resid 119 through 197 )AF119 - 197119 - 197
1111chain 'A' and (resid 198 through 276 )AF198 - 276198 - 276
1212chain 'B' and (resid 0 through 11 )BG0 - 111 - 12
1313chain 'B' and (resid 12 through 30 )BG12 - 3013 - 31
1414chain 'B' and (resid 31 through 41 )BG31 - 4132 - 42
1515chain 'B' and (resid 42 through 51 )BG42 - 5143 - 52
1616chain 'B' and (resid 52 through 61 )BG52 - 6153 - 62
1717chain 'B' and (resid 62 through 90 )BG62 - 9063 - 91
1818chain 'B' and (resid 91 through 99 )BG91 - 9992 - 100
1919chain 'C' and (resid 1 through 9 )CH1 - 91 - 9
2020chain 'E' and (resid 2 through 110 )EI2 - 1101 - 109
2121chain 'E' and (resid 111 through 137 )EI111 - 137110 - 136
2222chain 'E' and (resid 138 through 202 )EI138 - 202137 - 201
2323chain 'G' and (resid 4 through 123 )GM4 - 1231 - 120
2424chain 'G' and (resid 124 through 243 )GM124 - 243121 - 240
2525chain 'H' and (resid 1 through 103 )HQ1 - 1031 - 103
2626chain 'H' and (resid 104 through 162 )HQ104 - 162104 - 162
2727chain 'H' and (resid 163 through 276 )HQ163 - 276163 - 276
2828chain 'I' and (resid 1 through 11 )IR1 - 111 - 11
2929chain 'I' and (resid 12 through 30 )IR12 - 3012 - 30
3030chain 'I' and (resid 31 through 41 )IR31 - 4131 - 41
3131chain 'I' and (resid 42 through 46 )IR42 - 4642 - 46
3232chain 'I' and (resid 47 through 51 )IR47 - 5147 - 51
3333chain 'I' and (resid 52 through 71 )IR52 - 7152 - 71
3434chain 'I' and (resid 72 through 77 )IR72 - 7772 - 77
3535chain 'I' and (resid 78 through 84 )IR78 - 8478 - 84
3636chain 'I' and (resid 85 through 99 )IR85 - 9985 - 99
3737chain 'J' and (resid 1 through 9 )JS1 - 91 - 9

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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