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- PDB-7lfk: MODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTID... -

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基本情報

登録情報
データベース: PDB / ID: 7lfk
タイトルMODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTIDE, THR MUTANT, REFINED AT 1.60 ANGSTROMS RESOLUTION
要素
  • Beta-2-microglobulin
  • Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
  • Histocompatibility 2, M region locus 3
キーワードIMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN/PEPTIDE / HISTOCOMPATIBILITY ANTIGEN-PEPTIDE COMPLEX
機能・相同性
機能・相同性情報


alpha-beta T cell activation involved in immune response / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / Complex I biogenesis / Respiratory electron transport / positive regulation of natural killer cell mediated cytotoxicity / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...alpha-beta T cell activation involved in immune response / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / Complex I biogenesis / Respiratory electron transport / positive regulation of natural killer cell mediated cytotoxicity / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to hydroperoxide / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / mitochondrial electron transport, NADH to ubiquinone / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / cellular defense response / nitric oxide biosynthetic process / Neutrophil degranulation / aerobic respiration / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / positive regulation of type II interferon production / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / positive regulation of nitric oxide biosynthetic process / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / response to hypoxia / mitochondrial inner membrane / defense response to bacterium / immune response / response to xenobiotic stimulus / signaling receptor binding / external side of plasma membrane / neuronal cell body / dendrite / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / cytosol
類似検索 - 分子機能
NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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 ...NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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
類似検索 - ドメイン・相同性
Beta-2-microglobulin / NADH-ubiquinone oxidoreductase chain 1 / Histocompatibility 2, M region locus 3
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / フーリエ合成 / 解像度: 1.6 Å
データ登録者Tomchick, D.R. / Deisenhofer, J. / Shen, S.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM079383 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-DA035778 米国
引用
ジャーナル: J.Biomol.Struct.Dyn. / 年: 2022
タイトル: Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides.
著者: Strand, A. / Shen, S.T. / Tomchick, D.R. / Wang, J. / Wang, C.R. / Deisenhofer, J.
#1: ジャーナル: Cell / 年: 1995
タイトル: Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3
著者: Wang, C.R. / Castano, A.R. / Peterson, P.A. / Slaughter, C. / Lindahl, K.F. / Deisenhofer, J.
#2: ジャーナル: Cell / 年: 1991
タイトル: H2-M3 encodes the MHC Class I molecule presenting the maternally transmitted antigen of the mouse
著者: Wang, C.R. / Loveland, B.E. / Lindahl, K.F.
履歴
登録2021年1月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年7月14日Provider: repository / タイプ: Initial release
改定 1.12022年12月28日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023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 1.32024年10月9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
A: Histocompatibility 2, M region locus 3
B: Beta-2-microglobulin
C: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
D: Histocompatibility 2, M region locus 3
E: Beta-2-microglobulin
F: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)90,89513
ポリマ－90,5366
非ポリマー3597
水8,305461
1
A: Histocompatibility 2, M region locus 3
B: Beta-2-microglobulin
C: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,5587
ポリマ－45,2683
非ポリマー2904
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-56 kcal/mol
Surface area19630 Å2
手法PISA
2
D: Histocompatibility 2, M region locus 3
E: Beta-2-microglobulin
F: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,3376
ポリマ－45,2683
非ポリマー693
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-46 kcal/mol
Surface area19620 Å2
手法PISA
単位格子
Length a, b, c (Å)63.430, 69.100, 54.800
Angle α, β, γ (deg.)102.537, 93.860, 114.100
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

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タンパク質 , 2種, 4分子 ADBE

#1: タンパク質 Histocompatibility 2, M region locus 3 / MHC Class Ib Antigen H2-M3 / MHC class I antigen H-2M3


分子量: 32650.650 Da / 分子数: 2 / 変異: G299 deletion / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: H2-M3, H-2M3 / プラスミド: pRMHa-3
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: Q31093
#2: タンパク質 Beta-2-microglobulin


分子量: 11704.359 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: B2m / プラスミド: pRMHa-3
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: P01887

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タンパク質・ペプチド / 糖 , 2種, 3分子 CF

#3: タンパク質・ペプチド Heptapeptide from NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


分子量: 913.091 Da / 分子数: 2 / Fragment: First seven amino-terminal residues / 変異: I6T / 由来タイプ: 合成 / 詳細: The N-terminal methionine is N-Formylmethionine / 由来: (合成) Mus musculus (ハツカネズミ)
参照: UniProt: P03888, NADH:ubiquinone reductase (H+-translocating)
#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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 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 , 2種, 467分子

#5: 化合物
ChemComp-NA / SODIUM ION


分子量: 22.990 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Na
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 461 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.33 Å3/Da / 溶媒含有率: 47.15 %
結晶化温度: 283 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 0.1 M Hepes, 20% (w/v) PEG 4000, 30% (v/v) ethylene glycol

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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: CHESS / ビームライン: A1 / 波長: 0.908 Å
検出器タイプ: ADSC QUANTUM 1 / 検出器: CCD / 日付: 1999年1月4日 / 詳細: monochromator
放射モノクロメーター: SAGITALLY FOCUSED Si(111) / 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: 0.908 Å / 相対比: 1
反射解像度: 1.6→31.7 Å / Num. obs: 93324 / % possible obs: 86.7 % / 冗長度: 3.5 % / Biso Wilson estimate: 19.13 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.6
反射 シェル解像度: 1.6→1.64 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5139 / % possible all: 68

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2-3874精密化
PDB_EXTRACT3.27データ抽出
DENZOデータ削減
SCALEPACKデータスケーリング
PHENIX位相決定
精密化構造決定の手法: フーリエ合成
開始モデル: 1MHC

1mhc


解像度: 1.6→31.62 Å / SU ML: 0.1955 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 27.252
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2445 2001 2.14 %
Rwork0.2082 91318 -
obs0.209 93319 86.6 %
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: 30.67 Å2
精密化ステップサイクル: LAST / 解像度: 1.6→31.62 Å
タンパク質核酸リガンド溶媒全体
原子数6236 0 20 461 6717
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01816446
X-RAY DIFFRACTIONf_angle_d1.43538749
X-RAY DIFFRACTIONf_chiral_restr0.0866915
X-RAY DIFFRACTIONf_plane_restr0.01151135
X-RAY DIFFRACTIONf_dihedral_angle_d18.53832416
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.27611170.23395139X-RAY DIFFRACTION68.1
1.64-1.680.29381360.24396218X-RAY DIFFRACTION82.59
1.68-1.730.30561440.2436363X-RAY DIFFRACTION84.73
1.73-1.790.29951360.24126341X-RAY DIFFRACTION84.39
1.79-1.850.29711450.23366198X-RAY DIFFRACTION82.06
1.85-1.930.25991380.23266335X-RAY DIFFRACTION84.35
1.93-2.020.26551340.21466579X-RAY DIFFRACTION86.89
2.02-2.120.26381400.2036645X-RAY DIFFRACTION88.06
2.12-2.250.23711460.20366737X-RAY DIFFRACTION89.67
2.25-2.430.26781570.20936878X-RAY DIFFRACTION91.46
2.43-2.670.28191490.21257043X-RAY DIFFRACTION93.57
2.67-3.060.22271500.20887121X-RAY DIFFRACTION94.54
3.06-3.850.22521560.20076852X-RAY DIFFRACTION90.91
3.85-31.620.2121530.19316869X-RAY DIFFRACTION91.24
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)
13.69567558043-1.20200648341-0.8125660223463.42703950318-0.1355038863543.22776681217-0.112814554991-0.2577589804960.1601559356960.208582443773-0.00758325557045-0.164053598343-0.1660900100590.3928735584930.06168685186760.17317805129-0.0263232976354-0.02220869646040.1903255593010.0112260487250.086555239265137.326491500321.971799541720.0039557787
27.77396069992-1.65899168368-2.092824772222.649621183980.5380959751991.658711852450.3117131197910.4196046903360.8939847139780.0148262479274-0.21377652764-0.149640889496-0.4892739078840.00937017180197-0.1086847057430.324946444169-0.0379194173685-0.04646077024390.1555091268290.04084417373890.1650542027931.119549411532.721218066716.6753235327
33.207148861110.297027238471-0.0011082933742.86355730568-0.5133635618982.85655659397-0.02053560802380.0800374697181-0.00817425800174-0.1188685682860.02051828036590.1241998710480.04956143589440.11808604053-0.005525529084260.09605139185750.012571240604-0.02249934949580.118913362281-0.007699489566080.088828555902424.878416949420.466558920612.9627491273
45.190750498481.06892137437-2.488770851760.699559609708-0.5540720021354.25285195807-0.007305808771910.4643607253480.198007254174-0.205534392020.05376209660610.189052630951-0.143261983631-0.0634600511231-0.03931225125380.1939612455040.00633605540481-0.04877023915140.138812052891-0.008997946749350.14934354698119.371452208424.37097454475.76250907896
50.8630649995520.675530854463-0.6637489791624.82877849508-2.963193867232.68420280922-0.140294065942-0.0555001815769-0.222184486045-0.484075823038-0.175711621243-0.2402642711220.5128218490480.3092830734420.285217880880.272426654620.09577724704870.04803048996830.245644818617-0.02551851980310.17677311052736.3382368341-2.1330265808619.7960632618
63.41811147211.28668147676-0.3932601708854.26192634257-1.704177929243.05925533360.03832190455620.0696176087542-0.143839592292-0.390301596821-0.03581832816580.421247767050.446246626257-0.169121701997-0.02316353996520.2212686773680.06448386976270.0022052801370.169400770339-0.05010606232190.20030017563727.3898735927-7.251172643125.7437937994
72.620287189920.294980253447-0.8408732545280.251463460033-0.3850621357872.29898314855-0.2436110105940.086157610749-0.802136566011-0.645030778768-0.0321334785049-0.2942477644110.9354989091970.001639382103290.2229232412860.6057418983410.05736722029220.08883892262590.222119569867-0.0478596835690.44127080550431.2383711566-17.170825650921.6105753404
88.3769588779-6.099159215913.665560843628.23729530638-3.062132382747.331687097510.2339977084980.242421943219-0.274086660206-0.219349019185-0.2194527921710.6148078264020.0521607702628-0.414473039162-0.0825549773910.130023392956-0.02929148815990.01181816999260.196813770257-0.03555136619280.14072625130625.61074352327.8978700598232.198443727
93.77442362383-0.01285530933531.07264383264.27375320186-1.92487403613.236388129560.1555857018220.225798819518-0.580669655902-0.0116621306725-0.420540761517-1.052183829470.8645130530971.201810846170.2686248691170.3749169741170.19603613040.005355385690470.439728918140.03367555217250.34756822297245.4452849213-4.0322094373835.2385297098
108.1002011286-6.889074810461.4099808857.88118831312-2.045096379252.422433190680.106869279792-0.0804719666276-0.0142969044672-0.200059474573-0.173185169867-0.1553045380090.1913587889990.2317485690770.04728796360490.1130374440110.003890282487110.03221501335880.1739383429320.00245315257770.09636760050534.49163554696.6015264689732.3308310983
119.41141307753-7.889267487048.625185652987.80234401881-7.235621705198.2847030326-0.358167732875-0.01684428752040.009070427109040.3798028102950.126737204878-0.110640823515-0.6506599685830.05052188863950.1926325331930.1641386448230.03414065261430.03057228743310.2758018384570.01515808530780.14464542718630.248299340514.980743555837.4951697415
122.119580963271.19739517648-1.930359131655.69913906675-5.277495834517.396737799860.06546356135340.01051697688680.1199328170460.375321536645-0.423430976048-0.705611265127-0.7446633560791.557842966290.3298846728870.295263485286-0.123980904334-0.05199695388610.4513246921920.04416341071960.28579367199840.802094133212.001380092542.6129607838
135.48449027471-3.551351602583.656990454093.99816799591-3.469068736884.657104726910.2529972662950.0472715136346-0.109349649433-0.211180440004-0.165151150974-0.01424251919070.2488172413440.357611774654-0.08267782734340.1644980559990.007939181021520.04265696869850.216641145189-0.008211441967720.09947081744832.826333988111.842711884527.7630314417
142.33435428338-0.4148304915550.4067293502270.7426150920350.7993477037132.0477421816-0.279867389751-0.672603952973-0.03878146645470.337030167540.2779246532680.04018577269490.207708535018-0.119294269987-0.0138174861240.2100690847610.04147191838260.059018591390.3028739623820.01088539070840.12211543707831.05040830157.3187319630842.9969962443
155.12035181308-4.38431967501-6.394641495618.148877024627.347525429729.21096639385-0.1171743479380.128939259438-0.3230654361620.51470716308-0.2149500921090.08447373673140.5973169961670.1508417947530.3328757541860.2370081567990.007938329668390.0067020370530.2396947666360.03643475918230.16270969222832.3626804942-1.1974587045440.4204235479
169.26297483907-7.49206009252-1.412001967168.936069661680.4617293253826.272229246320.5658700485570.1555978362411.17967720242-0.528212564383-0.03038540831591.48699265199-0.399408712434-0.0321423777336-0.2242741683110.386527139203-0.00189557748504-0.03078015615460.2627452473570.03860572251170.63935418954723.732138927630.106759292311.0130932458
173.33800402560.3960889778760.668185997363.433310941430.2588088031172.61402897941-0.1406553578010.376768180814-0.0821655469558-0.1194622271390.0495121689635-0.251851291593-0.003007529082950.3429373753820.0787195369580.192590661571-0.0407339781031-0.02504888519050.182628305870.0392401396160.1403726385947.17243455301-13.21266748932.57938013057
187.844759938251.678910372913.887451777222.426643600980.456991596013.567882406510.4432230865160.0726617919428-0.7135307875630.13842982769-0.13044792638-0.2115788306760.685572778005-0.017881586435-0.3083237420760.324887833673-0.02511646524170.0423110998290.128555018817-0.01218472815990.1615940401370.291363904418-23.61823101614.10664047792
192.42096414214-0.2423431933370.7558056178790.651618419898-0.6995967136481.55417646432-0.1296237815630.04114352705960.1380541770560.141083706045-0.04162864391770.00345792236462-0.236186368814-0.01688687567540.164691684280.202159980765-0.0366732224512-0.01788851706650.103763265461-0.007001444680810.149607411429-9.4122748022-11.1067355797.60930782178
207.251687124390.1610633757122.915111992372.53475605551-0.09335286044554.63397779169-0.0373439534535-0.313828187556-0.4305057207250.470221472265-0.02272300104320.149028811259-0.175164101677-0.2636923839560.05219762227410.242362074714-0.0241495061750.04709648512840.151391503766-0.01921573709360.145477799382-12.7466209228-17.969408544114.7267517125
211.334834404740.3492125011960.2547415441173.73088488393-1.056563648863.05222806742-0.1122922606540.1216589162850.281264223856-0.08147484103290.07298878049290.218844066565-0.315628190521-0.3498271169370.036487127660.22226470726-0.0479209445806-0.1062526892530.249440529890.008164078721480.2784991003813.2411779533712.74673723732.07301663167
225.44945421525-3.58207429592.870806863244.35519661284-4.790669903638.85470838431-0.07728837502940.2206855290330.608981280659-0.267451937711-0.1003516580130.515464603053-0.801377234481-0.3478371019120.0625732818520.393195746932-0.000165741401844-0.15655149470.2237280944790.000755183127780.4907508615820.61625071188526.13123090622.85872933527
236.823316725546.63716456158-0.6194464656518.926122046410.5014816843713.975678828080.1294398565450.0676136684372-0.04205247832-0.005381601343190.06978800340810.4507437333210.111584974863-0.696871680423-0.1703711222950.246499378865-0.0490667783612-0.112434008140.299652301820.1001768635110.282603584179-2.207972632841.96936251074-11.2549128345
246.370734140044.27148904074-2.062068684375.02656993857-2.189008736614.573139395190.355484246796-0.3539718471410.1927504577680.287425240705-0.340008846067-0.21990414231-0.401577727180.605705198894-0.003400924331820.212433910782-0.0560354632709-0.04541952677740.185053955090.01811958611360.22436849024311.41071665157.8851551056-9.86138062207
259.153418970357.85243347578-8.491063527897.08432575023-7.627216900468.5217431588-0.824230674030.342462599916-0.665822336461-0.957399163590.233778862302-0.719845155850.979652057693-0.1883954618410.5444485751010.502662916286-0.074975140622-0.02522873512410.2538647380640.02216436440660.2904106893713.33052931695-4.67392962179-15.7976909679
263.387635154212.78237579653-2.622659560839.607049778891.175567806973.54221441401-0.3267080366650.103873345631-0.247810792827-1.282464439880.484948954348-0.1918026608261.760127063170.364056443321-0.2536843659940.5514006101630.0106141001991-0.02088249125250.3272225139310.07305741722390.39971510819314.3670064601-1.31422767913-19.1643530276
276.023833094434.07896128513-3.982883406774.51065167161-3.475445925095.293442799890.507285166883-0.3237561921720.2171904329370.274780618848-0.323201959378-0.0269803493262-0.1267922714860.319214619064-0.1439227634910.23659293742-0.0556670538946-0.07637332471280.1528303663310.006836807874620.1559217500314.49035618047-2.32280548302-5.69845405375
284.352416664463.023750523831.47274078983.443213543282.391332412462.50690771815-0.8998158437170.896219045233-0.00719896603734-1.284040016250.682882996625-0.1421655739080.375538788882-0.176947445740.1596460434650.510563500264-0.128119074512-0.08037593765410.3948080592580.08361326723410.2456163779144.709187466123.29625364314-20.6684475875
293.86886297421-2.251208119522.367938435985.608096507584.002135595628.35508499320.07582611105450.3277152728310.451222200179-0.4062253146890.070293707187-0.0578890664884-0.4973764640090.134510380334-0.05597769419870.361846581822-0.0639165320948-0.03337711707910.245554036030.1139654026960.2816544828865.5322067751311.6596591166-17.0707915325
302.30211466866-3.41359363780.7479717323765.33814063087-2.494642762727.251948372840.182363924659-0.170910104383-1.594242260910.3779108962480.1105640865510.570287308540.732809803603-0.446107688466-0.1832974556940.319440652751-0.02306563045310.006263031866230.216687025894-0.03473339931790.353184079695-8.33176249943-20.76928089488.0691425567
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 'A' and (resid 1 through 56 )AA1 - 561 - 56
22chain 'A' and (resid 57 through 84 )AA57 - 8457 - 84
33chain 'A' and (resid 85 through 118 )AA85 - 11885 - 120
44chain 'A' and (resid 119 through 162 )AA119 - 162121 - 164
55chain 'A' and (resid 163 through 219 )AA163 - 219165 - 221
66chain 'A' and (resid 220 through 249 )AA220 - 249222 - 251
77chain 'A' and (resid 250 through 275 )AA250 - 275252 - 277
88chain 'B' and (resid 1 through 11 )BC1 - 111 - 11
99chain 'B' and (resid 12 through 19 )BC12 - 1912 - 19
1010chain 'B' and (resid 20 through 30 )BC20 - 3020 - 30
1111chain 'B' and (resid 31 through 41 )BC31 - 4131 - 41
1212chain 'B' and (resid 42 through 51 )BC42 - 5142 - 51
1313chain 'B' and (resid 52 through 71 )BC52 - 7152 - 71
1414chain 'B' and (resid 72 through 90 )BC72 - 9072 - 92
1515chain 'B' and (resid 91 through 99 )BC91 - 9993 - 101
1616chain 'C' and (resid 2 through 7 )CD2 - 72 - 7
1717chain 'D' and (resid 1 through 56 )DE1 - 561 - 56
1818chain 'D' and (resid 57 through 84 )DE57 - 8457 - 84
1919chain 'D' and (resid 85 through 137 )DE85 - 13785 - 139
2020chain 'D' and (resid 138 through 162 )DE138 - 162140 - 164
2121chain 'D' and (resid 163 through 249 )DE163 - 249165 - 251
2222chain 'D' and (resid 250 through 275 )DE250 - 275252 - 277
2323chain 'E' and (resid 1 through 11 )EF1 - 111 - 13
2424chain 'E' and (resid 12 through 30 )EF12 - 3014 - 32
2525chain 'E' and (resid 31 through 41 )EF31 - 4133 - 43
2626chain 'E' and (resid 42 through 51 )EF42 - 5144 - 53
2727chain 'E' and (resid 52 through 71 )EF52 - 7154 - 73
2828chain 'E' and (resid 72 through 90 )EF72 - 9074 - 92
2929chain 'E' and (resid 91 through 99 )EF91 - 9993 - 101
3030chain 'F' and (resid 2 through 7 )FG2 - 72 - 7

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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