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- PDB-8tq7: Crystal structure of Fab.34.2.12 in complex with MHC-I (H2-Dd) -

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基本情報

登録情報
データベース: PDB / ID: 8tq7
タイトルCrystal structure of Fab.34.2.12 in complex with MHC-I (H2-Dd)
要素
  • Beta-2-microglobulin
  • Fab 34.2.12 Light Chain
  • Fab.34.2.12 Heavy Chain
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Transmembrane protein gp41
キーワードIMMUNE SYSTEM / histocompatibility complex class I / MHC-I / immune response / immune system Fab / antibody / anti-MHC antibody / cancer tumor
機能・相同性
機能・相同性情報


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / 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 ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / 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 / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Binding and entry of HIV virion / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / Neutrophil degranulation / host cell endosome membrane / actin filament organization / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / Assembly Of The HIV Virion / 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 / Budding and maturation of HIV virion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / viral protein processing / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
類似検索 - 分子機能
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
HIV-1 M:B_HXB2R (ヒト免疫不全ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Jiang, J. / Boyd, L.F. / Natarajan, K. / Margulies, D.H.
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) 米国
引用ジャーナル: J Immunol. / 年: 2024
タイトル: Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction.
著者: Boyd, L.F. / Jiang, J. / Ahmad, J. / Natarajan, K. / Margulies, D.H.
履歴
登録2023年8月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年3月20日Provider: repository / タイプ: Initial release
改定 1.12024年4月10日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22024年10月30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

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集合体

登録構造単位
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
E: Transmembrane protein gp41
F: Fab.34.2.12 Heavy Chain
G: Fab 34.2.12 Light Chain
H: Fab.34.2.12 Heavy Chain
L: Fab 34.2.12 Light Chain
P: Transmembrane protein gp41
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)182,19912
ポリマ－182,04510
非ポリマー1542
水2,342130
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)87.587, 113.326, 196.369
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 H-2 class I histocompatibility antigen, D-D alpha chain / MHC-I H2-Dd A chain


分子量: 31819.361 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: H2-D1 / プラスミド: pET21b / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P01900
#2: タンパク質 Beta-2-microglobulin


分子量: 11660.350 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 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P01887

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タンパク質・ペプチド , 1種, 2分子 EP

#3: タンパク質・ペプチド Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


分子量: 1075.265 Da / 分子数: 2 / Fragment: HV1: HIV-1 P18-I10 (UNP residues 311-320) / 由来タイプ: 合成
由来: (合成) HIV-1 M:B_HXB2R (ヒト免疫不全ウイルス)
参照: UniProt: P04578

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抗体 , 2種, 4分子 FHGL

#4: 抗体 Fab.34.2.12 Heavy Chain


分子量: 22982.766 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) / 細胞株 (発現宿主): 34.2.12 / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 Fab 34.2.12 Light Chain


分子量: 23484.734 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) / 細胞株 (発現宿主): 34.2.12 / 発現宿主: Homo sapiens (ヒト)

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非ポリマー , 3種, 132分子

#6: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 天然 / 式: C2H6O2
#7: 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
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 130 / 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: 2.68 Å3/Da / 溶媒含有率: 54.05 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: 12% PEG8000, 0.1 M MES, pH 6.5

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データ収集

回折平均測定温度: 273 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年9月23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: 1 Å / 相対比: 1
反射解像度: 2.8→56.62 Å / Num. obs: 48825 / % possible obs: 96.9 % / 冗長度: 6.7 % / Biso Wilson estimate: 55.21 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Net I/σ(I): 12.9
反射 シェル解像度: 2.8→2.9 Å / 冗長度: 6.7 % / Rmerge(I) obs: 1.32 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4505 / CC1/2: 0.528 / CC star: 0.831 / Rpim(I) all: 0.547 / % possible all: 93.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
PHENIX1.20.1_4487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: PDB entry 5WEU

5weu


解像度: 2.8→56.62 Å / SU ML: 0.3875 / 交差検証法: FREE R-VALUE / σ(F): 2 / 位相誤差: 27.0602
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2706 2374 5.01 %
Rwork0.2249 45031 -
obs0.2272 47405 96.95 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 72.22 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→56.62 Å
タンパク質核酸リガンド溶媒全体
原子数12390 0 10 130 12530
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003612736
X-RAY DIFFRACTIONf_angle_d0.679617356
X-RAY DIFFRACTIONf_chiral_restr0.04781876
X-RAY DIFFRACTIONf_plane_restr0.00472245
X-RAY DIFFRACTIONf_dihedral_angle_d17.90794498
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.37191360.34692494X-RAY DIFFRACTION92.74
2.86-2.920.32791390.30422558X-RAY DIFFRACTION94.43
2.92-2.990.34011270.28432539X-RAY DIFFRACTION94.84
2.99-3.060.35191370.27452571X-RAY DIFFRACTION95.12
3.06-3.150.30941340.27312569X-RAY DIFFRACTION95.89
3.15-3.240.32581410.26982630X-RAY DIFFRACTION96.82
3.24-3.340.37761380.28722624X-RAY DIFFRACTION97.29
3.34-3.460.27631320.24892602X-RAY DIFFRACTION96.71
3.46-3.60.2711400.22392656X-RAY DIFFRACTION97.86
3.6-3.760.22871400.21582690X-RAY DIFFRACTION97.99
3.76-3.960.27071390.21842636X-RAY DIFFRACTION97.75
3.96-4.210.24981420.20642700X-RAY DIFFRACTION98.41
4.21-4.540.2331440.17582691X-RAY DIFFRACTION98.54
4.54-4.990.23931430.1792703X-RAY DIFFRACTION98.65
4.99-5.710.26541440.19872736X-RAY DIFFRACTION98.6
5.71-7.20.24921460.242756X-RAY DIFFRACTION98.21
7.2-56.620.24771520.21042876X-RAY DIFFRACTION98.12
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)
16.126652646481.32744193114-1.712265060744.53884839265-0.4849547883084.091933317450.2558737476090.3853555662880.400875579032-0.05814755079760.008353394858590.35168096789-0.310001926312-0.327658912973-0.257779227280.319890852738-0.1256005707830.02483989639630.663136457457-0.02857144377610.629379306133-66.04992147550.41817709450123.7993222832
27.29908529529-0.813006658224-4.892472531552.223304719370.5153392642525.704951857380.0599063164974-0.260988966049-0.02703088246710.0256556958441-0.04102863039710.00528209965861-0.130641532490.0202728343724-0.001486702477410.256957564212-0.014764197458-0.03913097074480.2468035934680.04454636495690.204260585166-36.995554842221.333118169322.0048653316
34.206536635990.07954965741720.3720623123589.157369811574.799846956446.04647588291-0.2773641474820.68288988347-0.676497181972-0.5474044576490.07637847915730.424801876195-0.087567608084-0.269358689608-0.05307384061360.207774272748-0.03321803362270.06034241029620.4878293668780.004532883771110.358098062656-40.93054539340.29511041144723.4284498667
48.82453484342-5.208466819944.20425720736.69434532328-0.8291830667552.75931690597-0.351412035331-1.054241849621.22425641650.1855083920990.221357451311-0.460651901916-0.5414435090880.2775764918820.03795817048130.269368564708-0.06924672788850.01464089980010.569292260346-0.06957863141430.456885264451-33.188729503414.402699474640.0666742279
55.867680112021.913863257773.218923344775.422350542424.356976242695.10419254562-0.02442782670440.3121496546640.1141472140810.192339548172-0.01094097670160.3636861652260.0311245786549-0.359198430852-0.1493673197090.330905070167-0.001230354742360.09297096975740.3816338556690.1864372553710.488019330419-41.25498706114.5537451217831.3311915633
69.427343473583.459785399753.042159122024.948795325973.711366404563.307406875680.117394154285-0.284208007045-0.9146352626830.4235647151470.0946403626940.2290759708721.04048368699-0.660499719041-0.1918024230730.354303853637-0.09075373255370.05258011663810.5123431729520.1500434472270.486906317478-42.0237878762-6.1606316499430.9518586774
74.828236433843.608692619073.217051376593.878910772471.840032927412.41398507868-0.0176658986357-0.0998723714491-0.482294992218-0.23563397965-0.0571371291693-0.3585217431620.5833126066990.57933138819-0.06911116176940.4216561221620.19050902-0.02416443637570.8507493938850.1187061131080.486437287193-31.226740521-4.9329434138640.320574147
82.53519736747-1.425045574882.025155496271.79990397404-0.9772764931062.36450689492-0.181500341449-0.244199533176-0.22997972110.1301427730090.05995623550680.06127694350920.256851166419-0.0108701870406-0.162266261250.952413307433-0.01651702832220.3490003908230.548156346250.201581022320.609339028566-42.5433015105-1.8764777863741.1617441446
94.23961415660.8825879380055.081011719343.835546458611.474545249266.14079417664-0.460171879782-0.7478201653990.393680780430.03194474383050.350983906676-0.08510381660110.00027603567278-0.3085757250730.1372496614730.3072777868580.006290726539390.06589106798591.00832229054-0.01427916009980.73020687132-53.35787333370.97568152443123.9281045499
105.818126449172.297552293324.838577439546.118370910164.720549824638.5905731647-0.267206836729-0.1511829087670.3298049235750.7883149629320.08947206838590.1979670926590.239473566213-0.307045493090.1061214372670.29415014820.05133440882530.04493043609590.3444565752860.14408298220.422491816668-36.46781146444.3285809304837.079257392
117.730134180094.57801689154.213502857312.788592664892.610717179742.659326556190.06386354505990.810657089374-0.8662529658860.7585689942790.461174571445-0.3601624417321.107491820090.356561514522-0.5536804418760.3954225453150.02228177233580.0416866833280.3689776758990.006157641936360.474958101341-36.789487998-7.4747175465827.428930918
126.053972722541.701854581062.31533505124.73023288663.937495292137.88406610243-0.03782499221380.4435528794170.764719209292-0.262594692660.235708056446-0.042898748248-0.7215968805560.484173440506-0.5725608388840.230925631040.06623508612440.1602603588680.4628349354980.08130516827220.609878408864-30.27340837464.9512276363229.7227727809
134.582880588680.607382767431-0.02041825835454.09838119715-0.216144194244.009113942360.060189702972-0.478860492119-0.6568776955960.1824735882690.205367274046-0.1183580069720.727477410181-0.0424551503276-0.1854862087520.423101768526-0.0306524054972-0.08111583356440.3868676076720.05278428236720.6425006716467.4521021276441.989025143265.4817944082
140.7357477354430.371056981391-0.3341500697641.04334995414-0.7023838101024.640649642770.268388154225-0.116409606335-0.004013676364320.895362521929-0.402981870134-0.3530915108461.10333993914-0.321304997422-0.06111146743791.32981679974-0.277370456498-0.02384677294640.477641883876-0.05324662228820.454587868093-5.7581101193526.991438928334.7356053758
152.61970907954-1.272450298720.9951510557576.458980672383.641385526236.76807900080.3368704738190.443353935595-0.04388366576310.0629769705305-0.508581017870.5183388173780.230739815523-0.3103360657680.3698930381510.472999042331-0.100632391967-0.06379527819590.704630598163-0.05984594428260.2971601996-9.814192329643.414421683147.4612182283
162.035411441850.01105612379640.110130690941.02503985829-0.3472125377870.915892567095-0.1737289863960.376819205567-0.09327700416350.145864834973-0.4344389971770.9058110806780.87431659729-1.096938641410.4673864993710.677518714068-0.4013101315260.05914089545381.11807747216-0.2075435142440.788417263166-18.084262010637.184577382651.0427155148
176.227540573813.755626581331.573730969737.512792696112.051708696323.1818172318-0.02601503773780.0820721622962-0.2400386416790.445527469053-0.422945727930.7355427317720.683712238305-1.427739486420.5178512324180.632665190608-0.2275065498130.05154280668191.18756982766-0.1557835117160.54812118031-14.805530641540.481435190152.6858091139
182.604118850652.32934090093-0.1087717324053.11052122995-2.687161721016.52980874527-0.9720537290040.3950974498340.191941234237-0.642262619949-0.4087714404170.759899454987-0.116261091908-1.579988388691.339010271160.663240366832-0.12863888891-0.01914254429141.43854299945-0.3487576568030.802898750104-19.815344011238.469288007141.7317918811
195.84244346802-5.2493800741.623320603547.77453270842-2.508113113313.75419083989-0.30753155905-0.773094461334-0.7787418890080.6581266774820.703491883506-0.3488414045980.129295903036-0.185582020883-0.3296526725070.283086782212-0.121492235166-0.07044676521330.7040191601170.05162413595590.6352693985711.362142725444.875744343771.4098405971
202.531943617591.48521873438-0.9547116824652.75879357675-1.173959353715.50826575038-0.0540258219062-0.02396834151240.2754027563940.223625018023-0.0257056663436-0.0335570658036-0.281366208091-0.6214395362640.03359023850880.2627866329490.0273232810904-0.003804492924750.313799187427-0.0862441440790.356598907801-2.7093096999343.55288605245.08150197854
211.796624160191.41290161065-0.2256184357783.888507230350.7049953756520.364577928754-0.176877920655-0.666800367170.6122911101940.6304447800630.279788073059-0.930639259061-1.04153668120.3429844874440.06461434652471.44628407860.0583692384746-0.2276989423580.531093061332-0.2426143820880.9293212275188.8353959728973.01625310224.46628311689
221.870917324-0.6433851942420.3561356275151.32554407083-1.118962785513.22469553030.08186740414870.1775708065850.8180168950150.244361886462-0.2106776223830.362942353664-1.05400779624-1.59083552602-0.5642781068120.5655503995870.4635259229660.2409561466691.26573231243-0.1846161163170.691075836035-19.886532995555.830700992114.1060149381
231.22387756284-1.462882953960.5884579928135.9575084385-0.1452999447471.46867168973-0.206966547729-0.01321562978390.209970471653-0.1282073312620.0967051482353-0.30107839813-1.05746557814-0.3192778264630.01405966014161.595918254060.27442453516-0.05138142286350.53289164002-0.1094034399540.825742295618-1.7679849688582.0428441115-3.62202002549
242.7546835049-0.62487343015-1.284238611842.133496818720.2006671762646.93473693815-0.05464913442180.0405647165752-0.0253934367427-0.0850924472915-0.00979941733850.05795287630710.130603396090.4040570778650.05085503168260.166258230696-0.02211063034770.0246378111350.154237470880.04403268232040.260202459097-17.551804975420.9473215387-6.86731499758
252.967306330581.746259507250.4569440402263.1136169735-0.4205262296921.827447727020.4012582708340.177281410281-0.8816240914810.50416124932-0.4247221337280.2370218283931.65952500054-0.7740451062470.08183937943461.2662851581-0.279138518170.1011031387630.773605817742-0.1445352508510.883757452771-20.7285027002-1.46193263527-25.5118685557
263.098353258460.01592272839891.064930258321.080597773930.9578030427881.20167644263-0.1253947483630.43361653191-1.220947025090.9407491211010.283195999399-0.6533047522540.817249616767-0.684466504219-0.1547283247361.54707887166-0.2596960657710.1510132974210.738315679453-0.1570729843540.765167450382-17.1746015198-3.7887859624-24.9265030406
276.290004762991.412291965540.4099662437411.889942707940.1304981345843.31526489282-0.2699615812050.766204402352-0.4432518887230.4639572524890.09178288492321.011343213961.37269634875-1.07573499490.1569121080631.14797550824-0.3221114651390.1135542833031.19428426079-0.025675804170.945015696051-26.5401718182.22887465545-27.8375521081
282.666804005-0.128717404091-0.5729791227033.36968527189-0.2922225113681.32935431920.113387947416-0.0568566062207-0.622591171036-0.414061303871-0.206298917423-0.3719572048781.133314428820.7296564813270.06181606741210.8780185378320.298214944616-0.006949617475430.5977169784270.1841781724110.531067723705-6.571600570674.005091606433.573597125
297.27703237934-2.146201803135.239783985435.90312347869-4.501017661855.487814603770.7184344119030.928687796019-0.984032157497-1.13054692734-0.0342525326637-0.109602322132.63287980010.18919112836-0.7224348232121.949411938670.18577353795-0.1658666393880.879948113498-0.2453408515510.797887525691-11.3841717052-8.03155407761-29.733946803
301.141610240241.010110866520.327724884994.596374972560.2864490861170.1550309830290.1190833761360.564402732223-0.4750157108140.672940960183-0.334289736982-0.53145985950.225052571914-0.305654888094-0.00673964994131.358551368650.2133943171430.09865724970331.05651530409-0.2903346023850.836227637303-6.18860598031-5.93875106776-29.5627869932
310.876151060205-0.720751132680.6497778547530.59920605918-0.6850011734273.72584192966-0.001491610078320.0933342198522-0.4490370147550.1147857078750.04670994995930.09166422258381.846153314390.235244518398-0.1166300362452.090404034660.199231948176-0.08851127535981.42679770556-0.4209089053611.1348798411-5.4807503712-14.5255960581-35.329334374
326.743443192731.64459811075-1.428076647811.94924213784-0.9930142933873.10916353156-0.2480336765480.9719526610150.295937112481-0.01634337577790.07994056787670.56321190042-0.0373878757902-0.1717873495260.09662472192170.268888586734-0.209930687203-0.06188493739070.687126024926-0.01091839925770.705356043085-72.4298897384-3.5024249534323.0685056725
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 2 through 174 )AA2 - 1741 - 173
22chain 'A' and (resid 175 through 274 )AA175 - 274174 - 273
33chain 'B' and (resid 1 through 11 )BB1 - 111 - 11
44chain 'B' and (resid 12 through 19 )BB12 - 1912 - 19
55chain 'B' and (resid 20 through 30 )BB20 - 3020 - 30
66chain 'B' and (resid 31 through 41 )BB31 - 4131 - 41
77chain 'B' and (resid 42 through 46 )BB42 - 4642 - 46
88chain 'B' and (resid 47 through 51 )BB47 - 5147 - 51
99chain 'B' and (resid 52 through 61 )BB52 - 6152 - 61
1010chain 'B' and (resid 62 through 77 )BB62 - 7762 - 77
1111chain 'B' and (resid 78 through 90 )BB78 - 9078 - 90
1212chain 'B' and (resid 91 through 99 )BB91 - 9991 - 99
1313chain 'C' and (resid 2 through 174 )CC2 - 1741 - 173
1414chain 'C' and (resid 175 through 274 )CC175 - 274174 - 273
1515chain 'D' and (resid 1 through 11 )DD1 - 111 - 11
1616chain 'D' and (resid 12 through 46 )DD12 - 4612 - 46
1717chain 'D' and (resid 47 through 90 )DD47 - 9047 - 90
1818chain 'D' and (resid 91 through 99 )DD91 - 9991 - 99
1919chain 'E' and (resid 1 through 10 )EE1 - 101 - 10
2020chain 'F' and (resid 1 through 123 )FF1 - 1231 - 123
2121chain 'F' and (resid 124 through 215 )FF124 - 215124 - 211
2222chain 'G' and (resid 2 through 113 )GG2 - 1131 - 112
2323chain 'G' and (resid 114 through 214 )GG114 - 214113 - 213
2424chain 'H' and (resid 1 through 123 )HH1 - 1231 - 123
2525chain 'H' and (resid 124 through 166 )HH124 - 166124 - 157
2626chain 'H' and (resid 167 through 197 )HH167 - 197158 - 188
2727chain 'H' and (resid 198 through 215 )HH198 - 215189 - 206
2828chain 'L' and (resid 2 through 113 )LI2 - 1131 - 112
2929chain 'L' and (resid 114 through 144 )LI114 - 144113 - 143
3030chain 'L' and (resid 145 through 187 )LI145 - 187144 - 186
3131chain 'L' and (resid 188 through 213 )LI188 - 213187 - 209
3232chain 'P' and (resid 1 through 10 )PJ1 - 101 - 10

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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