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- PDB-5u2v: Structure of human MR1-HMB 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: 5u2v
タイトルStructure of human MR1-HMB in complex with human MAIT A-F7 TCR
要素
  • (MAIT T-cell receptor ...) x 2
  • Beta-2-microglobulinΒ2-ミクログロブリン
  • Major histocompatibility complex class I-related gene protein
キーワードIMMUNE SYSTEM (免疫系) / T-cell Receptor Complex (T細胞受容体)
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 ferrous iron binding / positive regulation of transferrin 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 ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / 免疫応答 / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / 小胞体 / ゴルジ体 / focal adhesion / 自然免疫系 / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / ゴルジ体 / 小胞体 / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / 生体膜 / identical protein binding / 細胞膜 / 細胞質基質
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 / Β2-ミクログロブリン / 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. ...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 / Β2-ミクログロブリン / 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 / 抗体 / Immunoglobulin-like fold / Immunoglobulin-like / サンドイッチ / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
2-ヒドロキシ-5-メトキシベンズアルデヒド / プロリン / Β2-ミクログロブリン / 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: 2.2 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: Drugs and drug-like molecules can modulate the function of mucosal-associated invariant T cells.
著者: Keller, A.N. / Eckle, S.B. / Xu, W. / Liu, L. / Hughes, V.A. / Mak, J.Y. / Meehan, B.S. / Pediongco, T. / Birkinshaw, R.W. / Chen, Z. / Wang, H. / D'Souza, C. / Kjer-Nielsen, L. / Gherardin, ...著者: Keller, A.N. / Eckle, S.B. / Xu, W. / Liu, L. / Hughes, V.A. / Mak, J.Y. / Meehan, B.S. / Pediongco, T. / Birkinshaw, R.W. / Chen, Z. / Wang, H. / D'Souza, C. / Kjer-Nielsen, L. / Gherardin, N.A. / Godfrey, D.I. / Kostenko, L. / Corbett, A.J. / Purcell, A.W. / Fairlie, D.P. / McCluskey, J. / Rossjohn, J.
履歴
登録2016年12月1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9月27日Group: Author supporting evidence / Refinement description / カテゴリ: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
改定 1.32018年4月18日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _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: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: MAIT T-cell receptor alpha chain
H: MAIT T-cell receptor beta chain
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: MAIT T-cell receptor alpha chain
F: 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)187,91713
ポリマ－187,3138
非ポリマー6045
水19,2401068
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: MAIT T-cell receptor alpha chain
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)94,0167
ポリマ－93,6564
非ポリマー3593
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: MAIT T-cell receptor alpha chain
F: 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)93,9016
ポリマ－93,6564
非ポリマー2442
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)216.232, 69.730, 142.400
Angle α, β, γ (deg.)90.000, 104.360, 90.000
Int Tables number5
Space group name H-MC121

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要素

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タンパク質 , 2種, 4分子 ACBD

#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
#2: タンパク質 Beta-2-microglobulin / Β2-ミクログロブリン


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 GEHF

#3: 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)
#4: 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 , 4種, 1073分子

#5: 化合物 ChemComp-PRO / PROLINE / プロリン / プロリン


タイプ: L-peptide linking / 分子量: 115.130 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C5H9NO2
#6: 化合物 ChemComp-7WQ / 2-hydroxy-5-methoxybenzaldehyde / 2-ヒドロキシ-5-メトキシベンズアルデヒド / 2-ヒドロキシ-5-メトキシベンズアルデヒド


分子量: 152.147 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H8O3
#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル / グリセリン


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#8: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 1068 / 由来タイプ: 天然 / 式: H2O

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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: 2.78 Å3/Da / 溶媒含有率: 55.69 % / Mosaicity: 0.7 °
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3月22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: 2.2→52.369 Å / Num. obs: 104386 / % possible obs: 99.7 % / 冗長度: 4.3 % / Biso Wilson estimate: 29.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.4
反射 シェル解像度: 2.2→2.24 Å / 冗長度: 3.9 % / Rmerge(I) obs: 0.508 / CC1/2: 0.86 / % 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
PHENIX1.11.1_2575精密化
MOSFLMデータ削減
Aimless0.3.6データスケーリング
PHASER位相決定
PDB_EXTRACT3.2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: 2.2→52.369 Å / SU ML: 0.25 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.83
Rfactor反射数%反射
Rfree0.2213 5207 4.99 %
Rwork0.1788 --
obs0.1809 104332 99.62 %
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: 122.16 Å2 / Biso mean: 37.4384 Å2 / Biso min: 12.53 Å2
精密化ステップサイクル: final / 解像度: 2.2→52.369 Å
タンパク質核酸リガンド溶媒全体
原子数12780 0 39 1068 13887
Biso mean--39.7 40.43 -
残基数----1598
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01113181
X-RAY DIFFRACTIONf_angle_d1.36417920
X-RAY DIFFRACTIONf_chiral_restr0.2171891
X-RAY DIFFRACTIONf_plane_restr0.0062336
X-RAY DIFFRACTIONf_dihedral_angle_d18.0354770
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.29631540.24573265341997
2.225-2.25120.29111810.24313204338598
2.2512-2.27860.28681720.23513251342398
2.2786-2.30750.28821830.22623213339699
2.3075-2.33780.29881850.22993262344799
2.3378-2.36990.28341870.219632863473100
2.3699-2.40370.2571610.213633333494100
2.4037-2.43960.26081920.20532053397100
2.4396-2.47770.25881550.214933323487100
2.4777-2.51830.29011660.213532903456100
2.5183-2.56180.27481630.214132913454100
2.5618-2.60840.27721550.209633053460100
2.6084-2.65850.29121690.206933073476100
2.6585-2.71280.2741670.204133023469100
2.7128-2.77180.23561740.206633363510100
2.7718-2.83620.28181800.207332943474100
2.8362-2.90720.25341690.209533083477100
2.9072-2.98580.26551590.195633103469100
2.9858-3.07360.22331660.186533443510100
3.0736-3.17280.21351900.177332953485100
3.1728-3.28620.20041860.180332603446100
3.2862-3.41770.2321820.181333103492100
3.4177-3.57320.20571920.163733043496100
3.5732-3.76160.2021600.157633493509100
3.7616-3.99720.19121720.159533103482100
3.9972-4.30570.17981680.142533643532100
4.3057-4.73870.15291920.12733373529100
4.7387-5.42380.18371900.139933343524100
5.4238-6.8310.20311690.17733853554100
6.831-52.38390.18851680.16853439360799
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)
11.10440.17360.00711.6793-0.34371.75050.06540.2496-0.0204-0.1301-0.08440.1144-0.0257-0.04540.0230.17330.0091-0.00280.2377-0.0350.2127-4.491262.2967159.3002
21.3742-0.110.06431.5779-0.54940.86970.05420.0217-0.05880.0858-0.0893-0.03920.02230.09520.03120.2182-0.02390.00270.2588-0.02050.19673.3254.5399169.6611
31.38290.1432-0.0661.05260.25460.9420.0027-0.1151-0.14520.0219-0.08-0.0007-0.0091-0.04870.08930.2610.00990.00990.1633-0.00650.254-19.977471.4203189.6192
42-8.36162222-0.3298-0.4774-0.02040.8193-2.2683-5.128-0.82121.68632.62940.7915-0.2890.24430.6325-0.04550.9387-29.226176.8497202.7776
51.5367-0.2854-0.19962.0826-0.12731.4717-0.0860.1309-0.09430.1245-0.1080.0854-0.01720.05220.20640.1445-0.0002-0.00890.1758-0.00490.1829-23.5657.9721173.344
62.349-0.49750.58860.3002-0.45721.0061-0.1038-0.09850.72940.0388-0.24560.5216-0.8735-0.68630.40020.44170.1147-0.00860.3214-0.10350.5435-32.118679.4992177.6188
71.455-0.2323-0.3121.2262-0.06830.9628-0.07080.2710.0994-0.326-0.06390.1642-0.2044-0.15480.09860.26110.0273-0.04950.2028-0.0210.2065-25.701963.9387167.6642
83.690.9155-2.78115.73531.02875.8737-0.040.6093-0.0866-0.9883-0.24120.20690.1027-0.41110.21870.38930.0464-0.11140.42260.02020.3386-37.924967.7428162.5761
93.2177-3.96221.55685.0072-2.39652.5106-0.13960.96190.1111-0.1946-0.14860.1135-0.7476-0.56660.29650.4474-0.0002-0.09210.4916-0.03370.4299-26.823971.2682160.7763
101.7905-1.54360.54821.6547-0.38290.21120.13470.0430.1655-0.32-0.1111-0.032-0.0620.1063-0.01470.28910.00780.02750.2282-0.05080.2549-12.35859.4645168.4159
113.1562-2.25810.22913.34140.26521.39530.04590.1260.2011-0.41350.08750.0312-0.3935-0.1266-0.0870.31360.0094-0.00690.24150.01320.1873-24.5969.5877167.9729
122.511-0.6491-0.4472.9131.14222.98570.0994-0.24450.25930.3658-0.64240.9460.3249-0.38370.47870.4290.0697-0.05820.4864-0.05670.6891-42.118473.4413173.5686
131.7527-0.8591-0.49191.76260.41721.1108-0.00880.3777-0.1677-0.3544-0.2510.5117-0.1223-0.18810.24410.2469-0.0117-0.06920.3197-0.07990.3488-30.796156.3877166.3864
141.77230.04920.26793.84831.78863.84820.2349-0.37130.4280.7110.05370.2766-0.1043-0.2204-0.26830.32520.02320.05910.3228-0.05830.4034-34.923765.6598176.5588
151.94490.4982-0.34861.1283-0.01781.38060.0010.0997-0.00490.0621-0.0205-0.03930.05330.15650.01520.199-0.0138-0.01170.24650.03540.180929.122461.0196159.8395
161.7781-0.1467-1.46740.45730.20181.14930.05980.0322-0.0556-0.1114-0.0135-0.10560.06230.1413-0.05410.2197-0.0066-0.00990.3730.00910.216241.532759.2073146.9367
172.7266-0.34080.59041.64-0.31643.49120.012-0.33160.09530.12420.0996-0.1687-0.10120.2164-0.06350.38560.01630.02770.4817-0.02350.444651.947960.2304141.2656
182.7138-0.0540.04051.11830.90990.92130.1413-0.10530.421-0.15450.1331-0.4672-0.2310.628-0.27940.4801-0.07860.05280.55540.00950.530259.338563.9112136.8045
192.22060.1781-0.77221.1673-0.01691.5608-0.07630.27750.0136-0.251-0.0190.11810.0758-0.24290.08920.2813-0.0347-0.03360.36570.0270.213114.239960.1006139.1444
201.72660.0515-0.47782.2937-1.10622.39250.00990.01420.05680.09850.13590.1975-0.134-0.498-0.15850.2895-0.0516-0.02020.36810.03670.242916.369459.7697142.0161
212.4410.3352-1.63550.8566-0.33682.66570.31010.33910.4251-0.12640.0710.10130.0451-0.096-0.27660.41690.00780.02090.40660.04850.285728.956365.6405123.8
222.96970.24281.06721.0551-0.47392.20540.41990.1224-0.6007-0.1814-0.0169-0.05080.45740.3261-0.34190.43320.0661-0.04450.3243-0.05590.313147.420353.3539130.5736
231.73120.6416-1.38492.9375-0.00312.04450.6340.4687-0.1026-0.83850.11660.22830.53610.0591-0.75480.61260.0278-0.02550.5075-0.11950.285435.89855.3895118.0673
241.4643-0.23060.31251.5530.20991.32030.02910.12920.1089-0.11590.024-0.0646-0.01220.1167-0.05310.1808-0.03140.01750.23210.01040.216950.372376.0912222.7376
250.9876-0.0833-0.10992.14080.06810.3694-0.0056-0.08690.10070.03580.01610.1102-0.0224-0.0252-0.00690.1945-0.01030.00750.20320.00070.222237.866979.8343233.5919
261.1774-0.11090.35690.82490.11821.09750.09340.0147-0.17350.13090.1216-0.2890.15730.2528-0.21190.22480.0239-0.04440.3042-0.0230.29362.218868.3121241.3008
271.11310.61750.7081.1703-0.16441.5698-0.0251-0.25770.38220.2748-0.00550.0242-0.3197-0.30930.03250.33140.1078-0.03740.4468-0.12150.397566.88578.7442254.9732
283.3059-1.39950.86212.6458-0.67831.6684-0.3924-0.0090.46840.48870.0929-0.2742-0.32860.20770.23770.3025-0.0272-0.00610.3336-0.08270.427362.85290.61237.5229
290.77571.15140.42981.95021.38682.5787-0.6782-0.56990.13710.1868-0.0518-1.4184-0.1761.12340.63140.31310.034-0.15980.67560.05410.750383.056278.4947240.1263
302.8074-0.17490.6890.23530.19160.89180.03570.17220.5049-0.22650.0511-0.3784-0.24540.4251-0.03930.2576-0.07450.02110.44210.01540.493968.134787.8501231.5178
312.582-0.96120.68695.2550.19574.07650.43050.09520.2077-0.44380.33110.2151-0.48390.322-0.63240.404-0.21250.02170.91070.21220.987279.900793.175227.2314
326.9185-0.51180.83934.3461.9212.7471-0.04130.72780.0737-0.90340.2195-0.0501-0.09570.2265-0.24010.4657-0.10320.06970.6895-0.07350.670673.361283.7939223.8928
333.79960.1166-0.55441.0235-0.44761.14240.17820.26260.191-0.1201-0.0495-0.0812-0.16370.2775-0.06890.1753-0.001-0.01730.20870.00180.271455.05182.7301232.088
343.01680.1162-0.18050.4518-0.53760.6163-0.4085-0.04040.13590.03820.1941-0.529-0.17220.67410.12610.2457-0.04460.0210.6463-0.01720.560776.042585.0125233.2152
352.8396-0.43330.69311.3188-0.3061.29840.02430.00621.36210.0255-0.0995-0.5268-0.56010.57360.12170.4452-0.0918-0.00640.46220.08560.742567.373197.0532231.4418
363.039-0.8396-1.45143.01671.23270.9497-0.45010.05970.80380.62750.06620.3014-0.1549-0.05880.33810.4669-0.1639-0.0850.5586-0.09840.777174.902493.3536238.545
370.54730.87450.39351.38810.69160.6435-0.00870.0565-0.2169-0.00840.0723-0.11830.11780.0623-0.0620.2218-0.0267-0.01220.20650.02590.246324.175653.7479220.9288
381.0112-0.1274-0.54171.29980.03250.30340.00860.16360.0225-0.08310.21120.2048-0.0081-0.1801-0.23070.1823-0.054-0.00540.16730.02940.234722.815563.0459218.965
394.57760.52562.92791.14620.66173.19480.1332-0.6514-0.0370.1807-0.11890.13250.0846-0.4323-0.06880.1981-0.0420.0430.1830.0320.257521.108458.1559228.7467
403.55071.1050.61991.03580.09240.8328-0.0491-0.1548-0.0175-0.0930.03910.2120.0678-0.09470.06010.2209-0.0153-0.01020.19710.01210.232216.024657.548217.9895
412.23671.20511.16830.74260.65010.70320.0251-0.2215-0.0587-0.0193-0.0293-0.0279-0.0324-0.042-0.01310.1829-0.0196-0.01730.17520.02790.167114.236251.6541212.7999
420.52310.3751-0.93050.3658-0.76955.14990.12670.15470.0546-0.36590.1320.30190.0194-0.162-0.23140.4239-0.031-0.01380.21170.00690.2952-1.177544.9273189.0613
431.8648-0.4075-1.17121.83061.43454.6767-0.0901-0.1404-0.2319-0.0292-0.0426-0.03970.43780.88770.1320.2630.05370.01070.29740.07210.32095.478838.7755203.2689
443.6275-1.3074-1.33833.19490.90363.53020.2488-0.31510.3939-0.1834-0.0395-0.2686-0.3441-0.035-0.20280.3033-0.0435-0.01950.2167-0.00680.24281.848650.9173203.7067
452.0479-0.04120.03620.2752-0.40461.1382-0.20880.0299-0.2514-0.34250.13340.14580.240.12390.02330.3742-0.04330.04680.16320.00390.33591.081140.8808195.6206
463.9622-1.08340.44592.3572-1.13411.6740.2712-0.1061-0.4539-0.3947-0.00380.2980.4482-0.196-0.23750.3946-0.0367-0.01750.25830.08790.3509-4.230135.2602202.0155
471.32510.47540.5531.56950.8171.0131-0.04010.27070.0731-0.17780.0039-0.0177-0.19610.16390.02370.2408-0.0506-0.00480.27440.03290.18534.296665.6146201.5946
481.10720.3815-1.10042.63090.69881.5595-0.10930.0210.2260.1846-0.07530.2025-0.20240.20490.20340.2331-0.0202-0.04270.18250.04220.224730.062870.7936214.667
492.1711.47671.80971.35630.73592.21640.16880.2764-0.29120.12790.1195-0.28680.34610.6-0.150.27470.0103-0.02250.3173-0.02440.282926.021852.8546187.4106
501.7452-0.4305-0.40640.9753-0.71651.51190.134-0.0669-0.0255-0.0582-0.0480.1121-0.1182-0.0019-0.08930.2622-0.023-0.01160.1612-0.00770.23651.997352.5907193.0189
512.25850.4856-1.03991.6088-0.2083.27350.0353-0.4349-0.29160.0084-0.0937-0.15140.0810.53320.06510.2869-0.0512-0.03640.25350.02420.253611.878951.3889195.2561
521.92120.6889-1.05620.6-0.07541.15550.13160.0580.3209-0.10630.02550.1429-0.223-0.0338-0.14540.2938-0.02770.00320.21460.02770.2464-1.17757.4755192.6232
531.8743-0.1682-0.69230.809-0.05521.95170.0555-0.0742-0.0357-0.034-0.0367-0.00730.01210.1555-0.0040.2587-0.02-0.04360.18780.0320.173315.150357.4972181.1291
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 'A' and (resid 301 through 301 )A301
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 11 )B1 - 11
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 19 )B12 - 19
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 41 )B20 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 46 )B42 - 46
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 51 )B47 - 51
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 61 )B52 - 61
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 71 )B62 - 71
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 77 )B72 - 77
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 90 )B78 - 90
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 99 )B91 - 99
15X-RAY DIFFRACTION15chain 'G' and (resid 1 through 75 )G1 - 75
16X-RAY DIFFRACTION16chain 'G' and (resid 76 through 135 )G76 - 135
17X-RAY DIFFRACTION17chain 'G' and (resid 136 through 165 )G136 - 165
18X-RAY DIFFRACTION18chain 'G' and (resid 166 through 199 )G166 - 199
19X-RAY DIFFRACTION19chain 'H' and (resid 3 through 73 )H3 - 73
20X-RAY DIFFRACTION20chain 'H' and (resid 74 through 109 )H74 - 109
21X-RAY DIFFRACTION21chain 'H' and (resid 110 through 124 )H110 - 124
22X-RAY DIFFRACTION22chain 'H' and (resid 125 through 215 )H125 - 215
23X-RAY DIFFRACTION23chain 'H' and (resid 216 through 244 )H216 - 244
24X-RAY DIFFRACTION24chain 'C' and (resid 0 through 83 )C0 - 83
25X-RAY DIFFRACTION25chain 'C' and (resid 84 through 158 )C84 - 158
26X-RAY DIFFRACTION26chain 'C' and (resid 159 through 203 )C159 - 203
27X-RAY DIFFRACTION27chain 'C' and (resid 204 through 269 )C204 - 269
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 11 )D1 - 11
29X-RAY DIFFRACTION29chain 'D' and (resid 12 through 19 )D12 - 19
30X-RAY DIFFRACTION30chain 'D' and (resid 20 through 41 )D20 - 41
31X-RAY DIFFRACTION31chain 'D' and (resid 42 through 46 )D42 - 46
32X-RAY DIFFRACTION32chain 'D' and (resid 47 through 51 )D47 - 51
33X-RAY DIFFRACTION33chain 'D' and (resid 52 through 61 )D52 - 61
34X-RAY DIFFRACTION34chain 'D' and (resid 62 through 77 )D62 - 77
35X-RAY DIFFRACTION35chain 'D' and (resid 78 through 90 )D78 - 90
36X-RAY DIFFRACTION36chain 'D' and (resid 91 through 96 )D91 - 96
37X-RAY DIFFRACTION37chain 'E' and (resid 1 through 37 )E1 - 37
38X-RAY DIFFRACTION38chain 'E' and (resid 38 through 52 )E38 - 52
39X-RAY DIFFRACTION39chain 'E' and (resid 53 through 75 )E53 - 75
40X-RAY DIFFRACTION40chain 'E' and (resid 76 through 91 )E76 - 91
41X-RAY DIFFRACTION41chain 'E' and (resid 92 through 120 )E92 - 120
42X-RAY DIFFRACTION42chain 'E' and (resid 121 through 135 )E121 - 135
43X-RAY DIFFRACTION43chain 'E' and (resid 136 through 150 )E136 - 150
44X-RAY DIFFRACTION44chain 'E' and (resid 151 through 165 )E151 - 165
45X-RAY DIFFRACTION45chain 'E' and (resid 166 through 185 )E166 - 185
46X-RAY DIFFRACTION46chain 'E' and (resid 186 through 200 )E186 - 200
47X-RAY DIFFRACTION47chain 'F' and (resid 3 through 94 )F3 - 94
48X-RAY DIFFRACTION48chain 'F' and (resid 95 through 109 )F95 - 109
49X-RAY DIFFRACTION49chain 'F' and (resid 110 through 124 )F110 - 124
50X-RAY DIFFRACTION50chain 'F' and (resid 125 through 162 )F125 - 162
51X-RAY DIFFRACTION51chain 'F' and (resid 163 through 188 )F163 - 188
52X-RAY DIFFRACTION52chain 'F' and (resid 189 through 215 )F189 - 215
53X-RAY DIFFRACTION53chain 'F' and (resid 216 through 244 )F216 - 244

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万見について

-
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