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- PDB-5u72: Structure of human MR1-5OH-DCF in complex with human MAIT A-F7 TCR -

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基本情報

登録情報
データベース: PDB / ID: 5u72
タイトルStructure of human MR1-5OH-DCF in complex with human MAIT A-F7 TCR
要素
  • (MAIT T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
キーワードIMMUNE SYSTEM / T-cell receptor / immunology / MHC-like 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 / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi 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
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
5-hydroxydiclofenac / ACETATE ION / Beta-2-microglobulin / 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: 2.5 Å
データ登録者Keller, A.N. / Rossjohn, J.
資金援助 オーストラリア, 2件
組織認可番号国
Australian Research Council (ARC)CE140100011 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)AF50 オーストラリア
引用ジャーナル: NAT.IMMUNOL. / 年: 2017
タイトル: T-cell receptor complex
著者: Keller, A.N. / Rossjohn, J.
履歴
登録2016年12月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年2月8日Provider: repository / タイプ: Initial release
改定 1.12017年9月13日Group: Author supporting evidence / Data collection / カテゴリ: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
改定 1.22017年11月22日Group: Refinement description / カテゴリ: software
改定 1.32018年1月17日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年10月4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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.62024年11月20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: Major histocompatibility complex class I-related gene protein
B: MAIT T-cell receptor alpha chain
G: MAIT T-cell receptor beta chain
H: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: MAIT T-cell receptor alpha chain
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)187,97214
ポリマ－187,3138
非ポリマー6606
水7,873437
1
A: Major histocompatibility complex class I-related gene protein
B: MAIT T-cell receptor alpha chain
G: MAIT T-cell receptor beta chain
H: Beta-2-microglobulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)93,8677
ポリマ－93,6564
非ポリマー2103
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-42 kcal/mol
Surface area36400 Å2
手法PISA
2
C: Major histocompatibility complex class I-related gene protein
D: MAIT T-cell receptor alpha chain
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)94,1067
ポリマ－93,6564
非ポリマー4493
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-37 kcal/mol
Surface area36450 Å2
手法PISA
単位格子
Length a, b, c (Å)213.090, 69.600, 142.370
Angle α, β, γ (deg.)90.000, 103.720, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21chain C
12chain B
22chain D
13chain E
23chain G
14chain F
24chain H

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALchain AAA0 - 2691 - 270
21METMETVALVALchain CCE0 - 2691 - 270
12GLYGLYPROPROchain BBB1 - 2001 - 200
22GLYGLYPROPROchain DDF1 - 2001 - 200
13ALAALAALAALAchain EEG2 - 2442 - 244
23ALAALAALAALAchain GGC2 - 2442 - 244
14ILEILEARGARGchain FFH1 - 971 - 97
24ILEILEARGARGchain HHD1 - 971 - 97

NCSアンサンブル:
ID
1
2
3
4

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要素

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タンパク質 , 2種, 4分子 ACHF

#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 / 断片: UNP residues 23-292 / 由来タイプ: 組換発現 / 詳細: Fragment: extracellular domain, residues 23-292 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MR1 / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q95460
#4: タンパク質 Beta-2-microglobulin


分子量: 11748.160 Da / 分子数: 2 / 断片: 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 / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P61769

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MAIT T-cell receptor ... , 2種, 4分子 BDGE

#2: タンパク質 MAIT T-cell receptor alpha chain


分子量: 22650.072 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: TRAV/TRAC / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
#3: タンパク質 MAIT T-cell receptor beta chain


分子量: 27546.562 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: TRBV/TRBC / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)

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非ポリマー , 5種, 443分子

#5: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H3O2
#6: 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: 1 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物 ChemComp-7ZV / 5-hydroxydiclofenac / 2-[2-[[2,6-bis(chloranyl)phenyl]amino]-5-oxidanyl-phenyl]ethanoic acid / 5-ヒドロキシジクロフェナク


分子量: 312.148 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C14H11Cl2NO3
#8: 化合物 ChemComp-DMS / DIMETHYL SULFOXIDE / 2-チアプロパン2-オキシド


分子量: 78.133 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6OS / コメント: DMSO, 沈殿剤*YM
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 437 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.74 Å3/Da / 溶媒含有率: 55.07 % / Mosaicity: 0.77 °
結晶化温度: 294 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: BTP, PEG 3350, NaAc

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データ収集

回折平均測定温度: 100 K
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: 0.953 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2015年6月27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: 0.953 Å / 相対比: 1
反射解像度: 2.5→36.815 Å / Num. obs: 69625 / % possible obs: 98.9 % / 冗長度: 3.9 % / Biso Wilson estimate: 39.07 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.044 / Rrim(I) all: 0.088 / Net I/σ(I): 12.3 / Num. measured all: 273724 / Scaling rejects: 46
反射 シェル解像度: 2.5→2.56 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.462 / Num. unique all: 4403 / CC1/2: 0.874 / % possible all: 97.8

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
MOSFLMデータ削減
Aimless0.5.9データスケーリング
PHASER位相決定
PHENIX1.9_1692精密化
PDB_EXTRACT3.22データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 4L4T

4l4t


解像度: 2.5→36.815 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.57
Rfactor反射数%反射
Rfree0.2305 3455 4.96 %
Rwork0.1731 --
obs0.176 69597 98.65 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 143.85 Å2 / Biso mean: 45.675 Å2 / Biso min: 18.27 Å2
精密化ステップサイクル: final / 解像度: 2.5→36.815 Å
タンパク質核酸リガンド溶媒全体
原子数12750 0 42 437 13229
Biso mean--55.65 38.16 -
残基数----1600
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00613158
X-RAY DIFFRACTIONf_angle_d0.97117856
X-RAY DIFFRACTIONf_chiral_restr0.041891
X-RAY DIFFRACTIONf_plane_restr0.0042334
X-RAY DIFFRACTIONf_dihedral_angle_d13.9944703
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2345X-RAY DIFFRACTION7.724TORSIONAL
12C2345X-RAY DIFFRACTION7.724TORSIONAL
21B1790X-RAY DIFFRACTION7.724TORSIONAL
22D1790X-RAY DIFFRACTION7.724TORSIONAL
31E2224X-RAY DIFFRACTION7.724TORSIONAL
32G2224X-RAY DIFFRACTION7.724TORSIONAL
41F903X-RAY DIFFRACTION7.724TORSIONAL
42H903X-RAY DIFFRACTION7.724TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.53430.35661350.25642567270297
2.5343-2.57050.30081310.23932618274998
2.5705-2.60890.31591490.23612617276698
2.6089-2.64960.30141320.24512570270298
2.6496-2.69310.36251280.2452640276898
2.6931-2.73950.34131260.22912660278698
2.7395-2.78930.32071320.23842639277199
2.7893-2.84290.30791400.22472588272898
2.8429-2.90090.30561420.21682645278799
2.9009-2.9640.31171180.20872646276499
2.964-3.03290.27511520.20872639279199
3.0329-3.10870.28091300.20552616274699
3.1087-3.19270.26051330.20282641277499
3.1927-3.28660.2991470.19522644279199
3.2866-3.39260.23941520.18052627277999
3.3926-3.51380.21721340.17242641277599
3.5138-3.65430.241430.1612662280599
3.6543-3.82050.21761380.15932641277999
3.8205-4.02170.19961290.15242670279999
4.0217-4.27330.17571640.13612651281599
4.2733-4.60270.14651380.11892656279499
4.6027-5.06480.18151390.12512683282299
5.0648-5.79520.19121570.14812673283099
5.7952-7.2920.2231370.16842717285499
7.292-36.81870.17321290.15722791292099
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)
11.6961-0.0146-0.38271.8134-0.71871.4798-0.0206-0.16950.34050.2377-0.00670.2174-0.1129-0.19130.02330.38180.1012-0.05750.4014-0.03730.4173-46.982338.8212191.6751
22.3920.54470.13063.2327-0.33751.111-0.02130.03860.1984-0.1435-0.0086-0.2966-0.17560.08750.0280.29190.0429-0.03020.28270.03540.3429-36.04640.351181.343
31.24550.079-0.05161.67320.17611.7478-0.09290.24930.3725-0.21780.01030.0705-0.3060.08930.010.3047-0.101-0.10870.47780.1450.4546-63.794440.047161.9077
41.4508-0.4605-0.12994.0949-0.47714.10310.0728-0.7009-0.7576-0.03360.11850.20060.6387-0.3426-0.09010.3986-0.0050.01360.18350.00990.2334-20.242112.0019196.3699
52.9877-1.66840.0161.9197-0.78641.34710.0553-0.0907-0.0375-0.09590.19230.045-0.05-0.0756-0.21140.33530.0196-0.08010.1561-0.00410.3341-20.289821.9927193.4681
63.8436-1.27640.67642.714-0.53152.06780.07570.09720.1995-0.0907-0.0261-0.1286-0.11680.0127-0.0360.29190.0347-0.02180.1915-0.02430.2593-17.985620.7495192.4516
71.693-0.1210.42781.82480.26810.98880.1368-0.0905-0.03710.5520.0975-0.2223-0.00230.2686-0.34370.49490.0427-0.03020.1523-0.0570.27426.58157.98216.9499
84.53120.9167-0.85562.8663-0.2295.28620.05940.5779-0.06460.18680.06930.120.2365-0.3465-0.14540.33780.06370.01020.1994-0.03710.29840.72828.7581211.3914
92.0604-1.0897-2.07770.62741.22632.3648-0.6329-0.3552-0.6741.21920.0393-0.51690.8808-0.16350.35460.98290.05170.06920.29320.02260.562.5623-2.6426224.7945
108.00371.19112.38514.73650.74956.17750.4080.3495-0.70160.6123-0.2296-0.26990.99470.29210.00220.56590.03170.02530.2704-0.01550.49367.6965-1.9232212.1162
113.25590.03430.05091.9942-1.75422.71450.0405-0.41790.34690.391-0.11040.077-0.3926-0.36350.07980.42220.1086-0.03670.4237-0.13920.3119-30.637229.8333212.1807
121.76380.6831-2.12733.5456-2.81263.6379-0.0015-0.13810.1588-0.00720.16230.1495-0.0265-0.5895-0.15920.37470.0539-0.08760.4733-0.06170.3176-28.717628.1327209.8648
132.6458-2.68271.88763.6665-3.67157.65530.0189-0.3344-0.1779-0.51010.35350.42861.1391-1.4732-0.4040.3569-0.0647-0.0320.4709-0.02970.2723-22.422315.8123227.5024
144.00760.1731-0.82052.12980.16512.63230.12810.3271-0.14290.1631-0.08240.0631-0.0624-0.2651-0.04750.30630.041-0.00540.1754-0.02350.209-1.123315.5991220.1365
153.914-0.1847-2.06070.2437-0.33062.73580.3055-0.00670.25780.1351-0.0851-0.0643-0.1864-0.1522-0.16370.39780.0058-0.04050.2713-0.09620.3187-6.206222.0597230.6919
161.045-0.9372-0.39090.9682-0.27742.9737-0.3560.02580.8782-0.6505-0.16690.7278-0.502-0.63390.40680.34160.1174-0.11080.50940.04530.9141-66.784249.4032175.8222
174.1981-0.94791.89340.4113-0.95712.253-0.5153-0.34641.02420.0372-0.03140.5052-0.7002-0.4680.45710.44720.1675-0.10120.6448-0.17260.7741-64.116651.23182.8449
182.5893-0.3140.29790.0467-0.07370.3452-0.0038-0.5965-0.22560.4373-0.35570.9549-0.3992-0.55850.43070.56180.24280.07331.1267-0.11641.1316-73.54351.4563188.751
194.68520.5423-1.43921.2432-0.17580.7931-0.15710.1183-0.3613-0.0348-0.0009-0.2533-0.3312-0.20530.18720.45750.0513-0.10450.4638-0.02510.4926-51.213145.9519182.0355
202.2202-1.87621.56031.5585-1.2942.5757-0.5166-0.9465-0.22030.57910.2550.6971-0.1972-0.60590.23130.36270.1737-0.03880.5932-0.09070.6394-67.126246.1143182.9966
210.0163-0.0856-0.1840.4370.97672.17240.67970.3461-0.815-0.38050.20020.0881-0.4357-1.3163-0.85580.48140.1372-0.11481.22280.28461.3774-82.9953.2182177.1502
221.62791.229-0.50592.5101-1.09530.6694-0.3081-0.31191.1754-0.09920.0330.6615-0.6528-0.6150.24070.67270.1766-0.21890.5579-0.10941.1342-67.055758.4173179.9557
231.6413-0.1238-0.17193.0478-0.08852.13510.0384-0.3360.04680.2424-0.2219-0.2917-0.15060.04520.15750.23780.0070.00480.3730.04090.2898.687425.4236255.0706
241.8629-0.42370.10362.59081.24361.7561-0.023-0.1164-0.1098-0.1792-0.21250.01820.0179-0.190.22350.26750.01970.04040.33220.03270.20570.837618.4123244.6836
253.0852-0.7018-0.71722.0279-0.37852.36480.29630.02490.1253-0.1253-0.1752-0.4618-0.25040.3241-0.06690.3585-0.06610.00820.21270.03380.356925.641937.8066227.7572
263.235-0.2349-0.55853.27081.13223.3705-0.02310.3065-0.1297-0.20150.17750.02150.1787-0.0282-0.07440.3525-0.00190.06660.24430.04920.382722.610534.2432224.9752
272.15850.7485-0.98353.68110.42324.2111-0.1330.097-0.09030.2650.1532-0.3680.40930.2520.03370.27620.03370.01370.22990.01620.363724.761130.751226.8929
284.5647-3.67240.29386.75990.41970.42940.20870.8681-0.255-0.5041-0.3656-0.38810.276-0.40310.14370.3475-0.05690.05570.21260.00880.258922.971536.3315216.4939
292.2965-0.169-0.67581.4940.12721.8119-0.07410.08860.0826-0.07940.09510.151-0.0412-0.3268-0.01990.23980.0237-0.00380.3852-0.07750.2702-24.374425.7784257.2194
306.26622.0657-2.5374.1096-1.20295.24550.26090.5440.10490.0632-0.00310.4820.1755-0.5127-0.23380.2621-0.0042-0.01460.4716-0.08470.2642-25.732322.3905249.0281
313.00050.6861-0.80261.0571-1.2571.9161-0.27570.01890.0305-0.15630.19790.30950.2889-0.40880.03970.352-0.01360.01050.5257-0.07620.3013-30.192820.2978259.7798
324.20420.2357-2.14320.9277-0.51121.7882-0.0095-0.14270.06760.10880.17610.27420.0989-0.2292-0.12630.28880.0156-0.03080.5257-0.04730.3025-39.885223.7161270.3307
337.64271.30751.90065.9652.61955.859-0.16571.04140.8532-0.30230.3563-0.5063-1.50820.0224-0.33610.4787-0.03980.02360.55370.07520.6393-49.012330.2782273.4842
344.29512.5281.10534.131.05425.4143-00.29090.0617-0.13390.02440.08440.2824-0.4184-0.08350.32820.03180.05770.44960.0220.3851-46.860619.4908274.5438
353.28471.93260.00384.02161.91814.5965-0.2939-0.17571.22830.0882-0.10580.6584-0.1252-0.99760.39850.39360.12250.08570.76210.03370.7812-57.494830.2011279.6763
363.63780.0654-1.35571.49070.3553.335-0.0663-0.4301-0.01330.23670.0058-0.06180.00720.45780.0820.30930.0449-0.04370.4442-0.03240.2241-10.429524.1103276.0098
372.5399-0.489-1.5020.94240.46783.34740.0654-0.27670.09950.09570.07590.0548-0.1570.1115-0.21740.29060.0010.02320.2973-0.01030.2987-17.979624.2376277.5385
383.8316-0.07141.29752.12740.27383.28490.1723-0.1139-0.71120.08910.26720.17670.4006-0.4862-0.37820.3472-0.05180.0280.38910.06840.3977-42.819518.1068283.1847
391.7062-0.8263-1.75912.6299-0.42472.59840.4013-0.875-0.8020.64670.41440.02940.5056-0.1606-0.11250.5494-0.0545-0.06810.59520.36630.4835-34.210115.2733293.8095
402.0411-0.7993-0.09611.9642-0.00561.73850.143-0.24290.14080.0925-0.3706-0.2707-0.37260.36850.27440.2827-0.0551-0.04060.2680.07120.368130.971929.5593239.2207
412.88941.3753-0.22131.7164-0.25331.429-0.1653-0.54250.12110.3255-0.0104-0.2965-0.29960.18790.20830.35210.02-0.09840.40140.05040.349629.986927.2337246.5338
423.70160.7250.23272.2403-0.01371.926-0.2779-1.11890.74711.4790.1814-0.8707-0.03010.452-0.00170.6615-0.0206-0.22690.57420.00090.61136.780833.3286252.589
432.52291.39550.12273.78791.2941.3395-0.2194-0.0946-0.1777-0.12770.4220.03720.1933-0.1438-0.10620.3866-0.00590.02820.34680.10620.287216.42522.9269245.6569
445.12791.4830.81052.41360.04121.7768-0.1743-0.49650.11140.14570.0451-0.5282-0.52180.31730.23220.4388-0.1085-0.150.48130.06860.571234.475334.1353244.3554
452.23381.3856-0.77765.05870.00810.64270.1628-0.5241-0.26630.7164-0.4829-1.3368-0.27710.40210.26530.2696-0.0315-0.07990.40640.18160.629836.177323.0298244.1924
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 83 )A0 - 83
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 171 )A84 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 269 )A172 - 269
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 13 )B1 - 13
5X-RAY DIFFRACTION5chain 'B' and (resid 14 through 52 )B14 - 52
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 108 )B53 - 108
7X-RAY DIFFRACTION7chain 'B' and (resid 109 through 135 )B109 - 135
8X-RAY DIFFRACTION8chain 'B' and (resid 136 through 175 )B136 - 175
9X-RAY DIFFRACTION9chain 'B' and (resid 176 through 185 )B176 - 185
10X-RAY DIFFRACTION10chain 'B' and (resid 186 through 200 )B186 - 200
11X-RAY DIFFRACTION11chain 'G' and (resid 2 through 73 )G2 - 73
12X-RAY DIFFRACTION12chain 'G' and (resid 74 through 109 )G74 - 109
13X-RAY DIFFRACTION13chain 'G' and (resid 110 through 124 )G110 - 124
14X-RAY DIFFRACTION14chain 'G' and (resid 125 through 202 )G125 - 202
15X-RAY DIFFRACTION15chain 'G' and (resid 203 through 244 )G203 - 244
16X-RAY DIFFRACTION16chain 'H' and (resid 1 through 19 )H1 - 19
17X-RAY DIFFRACTION17chain 'H' and (resid 20 through 41 )H20 - 41
18X-RAY DIFFRACTION18chain 'H' and (resid 42 through 51 )H42 - 51
19X-RAY DIFFRACTION19chain 'H' and (resid 52 through 61 )H52 - 61
20X-RAY DIFFRACTION20chain 'H' and (resid 62 through 71 )H62 - 71
21X-RAY DIFFRACTION21chain 'H' and (resid 72 through 77 )H72 - 77
22X-RAY DIFFRACTION22chain 'H' and (resid 78 through 97 )H78 - 97
23X-RAY DIFFRACTION23chain 'C' and (resid 0 through 84 )C0 - 84
24X-RAY DIFFRACTION24chain 'C' and (resid 85 through 171 )C85 - 171
25X-RAY DIFFRACTION25chain 'C' and (resid 172 through 195 )C172 - 195
26X-RAY DIFFRACTION26chain 'C' and (resid 196 through 216 )C196 - 216
27X-RAY DIFFRACTION27chain 'C' and (resid 217 through 245 )C217 - 245
28X-RAY DIFFRACTION28chain 'C' and (resid 246 through 269 )C246 - 269
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 52 )D1 - 52
30X-RAY DIFFRACTION30chain 'D' and (resid 53 through 75 )D53 - 75
31X-RAY DIFFRACTION31chain 'D' and (resid 76 through 91 )D76 - 91
32X-RAY DIFFRACTION32chain 'D' and (resid 92 through 135 )D92 - 135
33X-RAY DIFFRACTION33chain 'D' and (resid 136 through 150 )D136 - 150
34X-RAY DIFFRACTION34chain 'D' and (resid 151 through 175 )D151 - 175
35X-RAY DIFFRACTION35chain 'D' and (resid 176 through 200 )D176 - 200
36X-RAY DIFFRACTION36chain 'E' and (resid 2 through 94 )E2 - 94
37X-RAY DIFFRACTION37chain 'E' and (resid 95 through 124 )E95 - 124
38X-RAY DIFFRACTION38chain 'E' and (resid 125 through 203 )E125 - 203
39X-RAY DIFFRACTION39chain 'E' and (resid 204 through 244 )E204 - 244
40X-RAY DIFFRACTION40chain 'F' and (resid 1 through 19 )F1 - 19
41X-RAY DIFFRACTION41chain 'F' and (resid 20 through 41 )F20 - 41
42X-RAY DIFFRACTION42chain 'F' and (resid 42 through 51 )F42 - 51
43X-RAY DIFFRACTION43chain 'F' and (resid 52 through 61 )F52 - 61
44X-RAY DIFFRACTION44chain 'F' and (resid 62 through 77 )F62 - 77
45X-RAY DIFFRACTION45chain 'F' and (resid 78 through 97 )F78 - 97

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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