[日本語] English
万見
- PDB-8shi: Valpha3S1 Vbeta13S1 HLA C 0602 VRSRRCLRL -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 8shi
タイトルValpha3S1 Vbeta13S1 HLA C 0602 VRSRRCLRL
要素
  • (T cell receptor ...) x 2
  • Beta-2-microglobulin
  • MHC class I antigen (Fragment)
  • VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
キーワードIMMUNE SYSTEM / COMPLEX / T cell receptor / psoriasis / TCR HLA-C / HLA-C6:02 / ADAMSTL5
機能・相同性
機能・相同性情報


antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / : / : / 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 ...antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
MHC class I antigen / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.90001719663 Å
データ登録者Littler, D.R. / Anand, S. / Vivian, J.P. / Rossjohn, J.
資金援助1件
組織認可番号国
Other private
引用ジャーナル: J.Biol.Chem. / 年: 2023
タイトル: Complimentary electrostatics dominate T-cell receptor binding to a psoriasis-associated peptide antigen presented by human leukocyte antigen C∗06:02.
著者: Anand, S. / Littler, D.R. / Mobbs, J.I. / Braun, A. / Baker, D.G. / Tennant, L. / Purcell, A.W. / Vivian, J.P. / Rossjohn, J.
履歴
登録2023年4月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年6月28日Provider: repository / タイプ: Initial release
改定 1.12023年7月26日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.title

-
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

-
集合体

登録構造単位
A: MHC class I antigen (Fragment)
B: Beta-2-microglobulin
C: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
D: MHC class I antigen (Fragment)
E: Beta-2-microglobulin
F: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
G: T cell receptor alpha
H: T cell receptor beta
I: T cell receptor alpha
J: T cell receptor beta


分子量 (理論値)分子数
合計 (水以外)188,02610
ポリマ－188,02610
非ポリマー00
水181
1
A: MHC class I antigen (Fragment)
B: Beta-2-microglobulin
C: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
G: T cell receptor alpha
H: T cell receptor beta


分子量 (理論値)分子数
合計 (水以外)94,0135
ポリマ－94,0135
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: MHC class I antigen (Fragment)
E: Beta-2-microglobulin
F: VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU
I: T cell receptor alpha
J: T cell receptor beta


分子量 (理論値)分子数
合計 (水以外)94,0135
ポリマ－94,0135
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)106.001, 192.963, 211.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
要素

-
タンパク質 , 2種, 4分子 ADBE

#1: タンパク質 MHC class I antigen (Fragment)


分子量: 32202.309 Da / 分子数: 2 / 変異: C2S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-C / Variant: 06:02 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: F6IQM2
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 2 / Fragment: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61769

-
T cell receptor ... , 2種, 4分子 GIHJ

#4: タンパク質 T cell receptor alpha


分子量: 21604.844 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: TCRAV / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: タンパク質 T cell receptor beta


分子量: 27182.135 Da / 分子数: 2 / 変異: S169C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRBV / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

-
タンパク質・ペプチド / 非ポリマー , 2種, 3分子 CF

#3: タンパク質・ペプチド VAL-ARG-SER-ARG-ARG-ABA-LEU-ARG-LEU


分子量: 1144.419 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: ADAMTSL5 / 由来: (合成) Homo sapiens (ヒト)
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.94 Å3/Da / 溶媒含有率: 58.13 %
結晶化温度: 297 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 20% w/v polyethylene glycol 3350, 0.2M NaSO4.

-
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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.953728 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年1月1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: 0.953728 Å / 相対比: 1
反射解像度: 2.9→48.2 Å / Num. obs: 48398 / % possible obs: 100 % / 冗長度: 6.9 % / Biso Wilson estimate: 66.046152005 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.083 / Net I/σ(I): 8.4
反射 シェル解像度: 2.9→3.06 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7008 / CC1/2: 0.44 / Rpim(I) all: 0.705 / % possible all: 100

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
XDSデータ削減
SCALA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 / 解像度: 2.90001719663→48.2 Å / SU ML: 0.51380713506 / 交差検証法: FREE R-VALUE / σ(F): 1.35179031073 / 位相誤差: 31.8727937447
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.290914703424 2419 4.99876012564 %random selection
Rwork0.234571561804 45973 --
obs0.237350055406 48392 99.9876027935 %-
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: 80.8752400949 Å2
精密化ステップサイクル: LAST / 解像度: 2.90001719663→48.2 Å
タンパク質核酸リガンド溶媒全体
原子数12829 0 0 1 12830
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.011992119733113169
X-RAY DIFFRACTIONf_angle_d1.6445762997717908
X-RAY DIFFRACTIONf_chiral_restr0.07892555587171887
X-RAY DIFFRACTIONf_plane_restr0.01076141560052359
X-RAY DIFFRACTIONf_dihedral_angle_d24.60824026814808
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-2.95920.4015236560861460.3403751678212660X-RAY DIFFRACTION100
2.9592-3.02350.4187053881161260.3345580398362688X-RAY DIFFRACTION100
3.0235-3.09390.3772407666671520.3338636712662661X-RAY DIFFRACTION100
3.0939-3.17120.4063297065091450.3263778403772670X-RAY DIFFRACTION100
3.1712-3.25690.4163533566221370.3312382632292697X-RAY DIFFRACTION99.9647266314
3.2569-3.35280.3915239671231340.3130224574192660X-RAY DIFFRACTION100
3.3528-3.46090.3592395864431360.2800881440742702X-RAY DIFFRACTION100
3.4609-3.58460.3525170192361570.2569358551652648X-RAY DIFFRACTION100
3.5846-3.72810.3245617470691380.2585565373282713X-RAY DIFFRACTION100
3.7281-3.89770.3106392933671520.2493961327592684X-RAY DIFFRACTION100
3.8977-4.10310.2606299000651250.2268719935232712X-RAY DIFFRACTION100
4.1031-4.360.2367733096651490.1946472293172688X-RAY DIFFRACTION100
4.36-4.69640.2483068682231380.1695382070832692X-RAY DIFFRACTION100
4.6964-5.16850.1983825774271450.1739192939672726X-RAY DIFFRACTION100
5.1685-5.91520.2660071708891490.2036686209282736X-RAY DIFFRACTION100
5.9152-7.44810.2684854418681420.235575228582752X-RAY DIFFRACTION100
7.4481-48.20.2505468115311480.2053346036632884X-RAY DIFFRACTION99.8353638459
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)
13.833240630630.5899995612230.9612670128323.663372856490.1171920883921.507779868910.0706338306267-0.0664186557089-0.1007008637980.279507866702-0.08134823322110.09033486167970.0657781654534-0.07720050540760.0225928308990.3648302291680.0596854209906-0.04566451175520.349823586374-0.05204462933830.424464004032-11.4166640603-17.6276314693-43.2896767615
29.87643399625-6.57242554511-1.665067782415.665369756241.843112778840.8504805003760.3504934111240.522222947467-1.385775147240.175246050857-0.7614035976731.452880296460.211124760597-0.5642495773840.2709664781820.40710575558-0.02015998058780.009076335532570.5439137472130.1250450874950.594542857893-19.369925241-38.5443709431-40.632479982
39.3462593258-2.382917009492.60966874234.92100251053-1.91648719985.033918760340.1014676212130.0346323562256-0.1922787631560.167367816503-0.151455504443-0.0139532424599-0.005592727851440.5618781973020.008055965706190.361468716632-0.0430219549267-0.0953502380630.317668085713-0.009178308587870.3990273582815.03269447805-50.7445272703-38.9267829704
46.824185057714.84589834683.917228937638.099132911714.816023058146.105213201480.133745308327-0.512365000287-0.6913439614860.304464251072-0.160900407096-0.5082807482730.568354698423-0.0143941089007-0.05328817959610.3039256147660.04865524663550.006114423444910.4352932925360.03551208163750.4866170423922.73601481437-40.1572272865-53.4298268401
51.325193678040.585719448256-1.340022116237.266839443485.067608985536.32819682329-0.1875407246390.22634326750.231941766231-0.293810016326-0.226277864970.870325706875-0.396333640799-0.3319397292920.4703323848840.2841367853130.0794914317977-0.01438231929060.3468724247240.03240796259590.533072237105-0.0316888651292-37.8733530387-55.0798193631
63.385346487740.4109254007630.1647716069082.435331902692.075169109832.432757932860.06605516813940.4907290763390.00654063661418-1.210384648010.0813972218285-0.302018003109-1.208813259920.18937324059-0.2071094569880.351409718340.02036594232960.06155710861910.4172653002660.04211903946210.4342220478914.38127544732-28.9888261669-59.0237472497
72.002416351772.001948802660.3791004652312.00131760463-5.712349784434.05081261492-0.7209409754940.4938390032841.990730472491.20630901265-0.120286150698-1.922531905850.144246075827-1.442330134550.7600031927230.449045972329-0.0517764267146-0.1032451591810.522176282142-0.02436373773820.4819858216715.62623753357-37.4389466468-69.1533126118
83.81706214539-6.06963456353-4.614647861729.729670557717.377759712275.60419183923-0.460155368241.0672296355-0.434455605242-1.88143178045-0.7208534007261.437860845-2.40188979973-1.175798993961.157761569210.8492911188040.0360005228506-0.2376473002090.812642354966-0.03034409941230.745257634478-4.12267268057-33.6302743637-64.8923423465
95.507105508996.718518797365.792729379318.346429514826.909937270946.226192507810.518520468374-0.4404732624650.1566557694270.893635402795-0.6515522287780.6534897134980.958386066278-0.471789127692-0.03794549491040.4051898530930.03167858909160.0302652173860.3795323377140.02187681230240.733083674799-3.13894620553-26.0482692594-45.2841323376
103.51776236232-3.77423071324-3.981418382448.202022953826.246962262197.70094590049-0.3248033290720.06437390325820.008390161526290.454590811939-0.03211976711380.02339230482140.483590782037-0.2844370644680.4330638555220.331216224253-0.0116824280261-0.05901079108360.3722839050030.05780429018140.451421479377-2.66272840085-36.2876530514-57.5637563924
112.890975561593.21117503008-4.156634153294.42208310206-3.258647738248.10884845456-0.005919922396770.736048110399-1.348068111620.2932923283280.527684450075-2.022056746390.3991647861780.480345667782-0.4808888151390.530858411754-0.2144123081950.02776292851880.569316079227-0.08883039491430.8045901063566.40989402592-49.6883998517-66.6868453518
122.541529534551.241040502821.91400519437.513241448985.59958659144.58419871016-0.176674205340.1762095542420.705082360678-0.8673159728120.0768930712281-1.6420453923-1.389250382490.533608246670.0127794810560.544418942037-0.0203813302339-0.02168015504190.4703349583580.1305548199670.7970596719477.77787316391-35.4247163811-61.5001615658
136.39368209321.597682903552.377564168073.948291722843.994945667544.156668426680.320914156899-0.7171666232290.597268665238-0.8750252270840.264247879467-1.07746939872-0.9249436484690.909468871569-0.4846138447090.4594631751470.0119574224586-0.02783103055240.519707202035-0.1940359920880.89089127091713.5075009743-25.5431333013-56.3933175082
143.817125756790.831103032450.74434748785.543180940946.040345202066.63788204066-0.210456394293-0.466245756439-0.8983973337981.174339904260.114267223725-0.00412932790991.072653139640.2629872191910.2257675454540.4951962546870.06381053266210.08976529721440.278282406945-0.00378303279420.8507239966168.6454490825-44.6737972547-56.3707645657
155.799408194236.074694308912.042856403746.94695107162.936277775156.250604933720.4869373843570.1164483262640.2084437229530.0986763240528-0.4672044197461.09730471583-0.5074800891-0.257611152168-0.123389760060.4454119737910.154306772082-0.1577658500960.480756548567-0.03670832740990.631702394607-16.6950358198-13.4075783104-41.822544342
162.38277767424-1.00182767413-0.1673555344813.55131857777-0.3255956688084.69766196990.1272716973120.3921905424790.419649372965-0.400750738241-0.232948758009-0.181489455281-0.4631334293420.2367680404840.077763820360.575530562129-0.02792699844850.130527487150.4891339609280.1061378866660.482378314841-23.0839194186-21.5985051705-86.928568476
173.926077736430.756779009581-0.158125936432.58076214826-0.3354620854942.946495542180.1143174609170.4086720699230.108456380571-0.183094981459-0.01020563528520.389346517764-0.349322960154-0.54042097113-0.03753930955740.8096680649310.2343950588610.06833181271310.6591410016940.01131398746310.502038504405-37.9597212647-22.3543354984-90.2860423357
183.1832035271-1.35233470054-0.137213567066.898020860550.1877385239743.788815492430.1883296508320.4395103669870.491748266513-0.718163170685-0.4235228561340.493360641961-1.16789682899-0.7603471082890.231068599410.8795073823860.25161980516-0.03046255655330.634623471063-0.02287672514410.570801840236-36.27418577187.80545821553-70.7335028641
192.896588883171.775340486960.2598809997012.9953710364.356536589859.118423979881.12252113524-1.25622538528-0.540124247801-0.1061456159250.699759015278-0.000434444019021-0.437279857152-0.56892656351-1.228497435020.9807485973630.308532568320.06312018228210.6600672418810.3710978859261.06696529322-26.22974862961.93254236415-88.2167560747
204.2875367634-1.1253658493-3.142309830823.46567753851-1.989526253374.886160971681.05427512499-0.9339484183730.3431503932070.418341842882-0.22474790428-0.676927283207-1.758242785190.958471031906-0.7793066683550.997208012344-0.210183099490.4129241842310.59786140883-0.1181871296990.784021584131-19.0426366282.5169551932-74.6505637471
212.707243831781.75072711732-0.7669685560463.569654553931.553742862592.178119883340.3567247828570.6873881051590.0950247154982-0.1905844952790.4383712530540.0272848354477-1.62574663104-0.539338406157-0.3151985336531.38939545112-0.1687671671170.4351034863630.4038743166150.341328741260.812343115041-17.0684904531-0.841086695089-89.9692067715
224.158714101563.18207436436-0.8439911194523.578690199-2.088710720951.993924239360.0380736824159-0.281985020473-0.251551896947-0.31164870378-0.194528154136-0.425409126568-0.3801802396640.30668024130.01633965901721.32212757033-0.6261524608820.8357715165890.726999336275-0.06750190301191.74627423256-7.306180171556.46626938672-84.0903803828
239.933322514995.64469174433-7.886611367712.00225296299-1.601972852779.8588536781.344029340330.677761775198-2.21801727669-1.18054029282-2.24892801963-1.70185724045-0.1488020935410.7562639012160.2833318333771.157880376590.1000770522150.2888095820640.3898530880460.08815226406771.23708057882-10.4841755993-4.64886217977-81.6875402165
245.599326690711.11166114143.390786601726.24825265275.02182411126.363413547370.426981607383-0.6711073880260.364377447585-1.12444171771-0.409323823158-0.922517927392-0.655684352054-0.5776167283650.07487281197250.7890362752790.0198551255820.236725004350.7463653721360.1951373314160.721740114209-23.2770701489-6.02851381326-83.4645457336
251.606175142940.666447393985-1.303951184561.64673080561.005046557842.78722814012-0.5603917801560.3887703122070.130370390451-1.59535407529-1.64292557535-0.572165453573-1.891750516650.4909214211841.997171122281.990053454890.120818796330.3712281449880.715819914260.1096514579161.4682421273-10.317626511513.5776937352-73.8280751612
269.403237066994.356167200677.668631019464.534613823154.261630883358.167711672430.2563763659870.5036483238440.672640423445-0.37481730853-0.0545447187338-0.198406338837-0.6113687932530.483612971729-0.1882855038611.50599132688-0.03829243749190.2466299081320.6177749447960.1207210471810.770536453256-17.63173761115.06059539826-92.5773290707
277.308921784912.609447832892.202703583762.83530405243.202795568773.75666982430.382043454704-0.4429331644961.715349791290.748107870285-0.3707550710270.3712595144750.807086261421-1.32771380604-0.5528488978771.350286341150.1984247790780.4318254284490.5700284970350.1044234239950.832649007966-20.149210397611.6285624636-79.5610653487
285.834229946682.33787329692.939474442614.22148352634-2.610595301525.840391695510.8310771252360.489658670682-0.226921158732-1.35925832711-0.101418055906-0.953426390946-0.2105700607770.206708865234-0.6888044130260.7550857998230.3038158844490.2785026986870.6963460062010.07902443502830.674183614915-31.2894499367-28.5689263239-90.7283137791
295.38391025127-2.77095231406-2.444462505926.14752473875-1.233224598747.73029515803-0.2346439644330.0611347065601-0.401860385417-0.261315126419-0.1976324824430.09525987456670.730362014928-0.6804220554640.07133134651360.312337173376-0.03070619635680.009297770895290.406946074665-0.1258077551161.00734926292-48.29113796931.30244033099-32.6368109623
305.50987619097-3.95242291518-1.551640666562.906853233551.056674631540.7796929261320.6494226109490.953815795809-0.365941796673-0.696987367061-1.165310958380.51692702435-0.152267532205-0.4216469055010.6378723341370.5330173403040.0470228705437-0.1299951997510.64077829502-0.04126292419550.701889602359-35.1160258888-4.97470963349-42.4743097773
317.71513067495-0.650796454605-1.050142832877.410070548443.64576647533.228546041660.00218539028438-0.483503513225-1.19229098781.04689309385-0.2613165453320.7615073710460.8932416999210.2775146883940.274907583850.577341984590.04717225416380.06819334029850.550763958710.1083915351850.808736215778-36.5173406273-6.81860145184-35.8048334548
322.26696413978-1.88437264569-0.9473149093985.341881619360.3222890680521.275433367310.3038430450460.501276932401-0.606004361307-0.279683868978-0.433267805360.119364376525-0.164135851524-0.101285988570.2028901117130.285104699564-0.0170066197057-0.09915343414130.570427030496-0.1322724215420.84270987458-36.6682559768-2.59113001104-39.6714905496
332.62818183169-2.45156988327-4.248312959985.773246839515.215170074498.422976300070.4528121417941.168155957750.0724337731571-0.721066080688-0.9721730877021.26850918525-0.914198650818-1.602823228990.3967833096230.3314177818960.0956258126639-0.06010244347610.5489923437730.08200928387360.900148724274-41.00157180444.06951881188-40.3459878104
344.55993398674-1.15946876094-1.115389539619.81156381992-2.923453055966.50115244314-0.02902620283580.0920756036452-0.3755457504420.858984701842-0.2265939092060.3934551303890.0745133541869-0.6815504826210.1679417686990.379743421621-0.02815168634050.1017509925640.549639235999-0.1037067228460.650958935862-54.037661201526.3149272967-27.658013944
355.118764825563.846214402160.4907258254325.455859384983.558703820043.97341346292-0.5100386935741.766660540530.57509534257-1.02616364591-1.056811401461.60567012630.246745815617-1.544916166781.532942838620.7147426328940.0960815990227-0.2218874402680.961415688846-0.224289454931.03718319354-54.370010345626.5888805843-42.5767610351
362.68991831938-0.5910001034353.370638104038.13893782172-2.904840007199.09534471193-0.3473102831190.0867778821537-0.5620426738610.494874374793-0.452795580021-0.3451135429430.7459667521160.4310749336160.755911222060.403002073657-0.02662490387680.2359433585240.538849981763-0.01677949626980.987716098767-46.756734691120.2269151169-22.8540339695
372.84873156638-0.778711430491-0.3822455738787.246372490273.630994981318.490458793050.8177536385931.026217146992.858690124-0.952617263967-0.617591910760.864301655312-1.0254147662-2.600437411030.08342570042240.7640361805350.318959101804-0.110582150520.841210918396-0.09046477508261.17151225832-57.974817852933.0324581977-38.4847556547
383.91023923525-0.47590873920.395091188122.63810792415-1.361204605323.68721300730.1992077306690.06388251804780.0210988367226-0.221299412723-0.0540720993332-0.0565423137217-0.0620909380009-0.0864486188692-0.1298730606130.4800046552390.02848086864920.04855476608340.346860557912-0.03509270486510.553820211469-23.74392046578.70706100187-49.4985896039
393.47637600764-0.908605040165-0.0003946100633920.244104074435-0.04699634621940.01727719219621.076984911081.0605441422-0.393159712727-2.91057882836-1.461886635640.763801227687-0.176399360172-0.042465612874-0.07438919429971.416228805270.375406635335-0.02599423626940.517332552029-0.03314661159730.578678307661-33.478468350328.0464013161-52.7117607425
401.9456454254-0.939611595101-0.5776291726463.429569102151.389862212048.79065530247-0.0492113616820.007651577558830.0091274447352-0.108467382209-0.2089699325580.4426151154530.415956230176-0.2904715130760.3301162860990.3547070073380.0009952137305720.03717176007880.3084036002310.05243178629180.634400314619-42.41403809829.1204668668-33.5538534593
411.135006628840.334788679663-0.8276203891113.046531570341.257689559224.96675768664-0.0307192302597-0.184456572279-0.25494466107-0.0249815153773-0.1915066567060.108672764714-0.1933740052850.2119886133210.179894837490.3019406613150.0640173262290.04582739312140.4561612284190.04496208335240.539524059293-35.430385315834.7704483587-34.4139793996
424.041215789263.242876439621.676652187354.754764060770.6904638989842.876240440070.4739111132350.0314732482124-0.1297700493450.241542785162-0.4430811990530.01883176650230.3488703953230.0191575959182-0.08844746931380.4533536203990.1240485929030.1446406703350.53052663468-0.06495131484690.662334735956-29.9889021879-56.6976795573-87.4260577032
434.990235556533.727524448181.720841481879.576534358462.940251094354.61059336880.08642754109810.5343739156220.1785345000620.05510552115380.02611894327670.49222994385-0.169955685538-0.396978584718-0.1310808426150.4141466083660.09584230921340.08994333881240.5759304582320.04378124942950.434323796155-31.8128865851-50.7680225251-87.3268757767
447.980622784175.18237397367-4.181737753084.62086568127-4.57749231786.839617740320.32332654805-0.101608934092-0.438515074892-0.525189180307-1.16559508342-0.3877054142851.193284368580.4450112130990.6105531553140.4965839645790.1683295591310.06522002145760.589603877904-0.05987265438310.519072587982-27.4322126419-58.3494576323-92.6227929361
453.42640064554-1.729955677141.200683769923.685377779322.645455595924.19022867436-0.5695793427580.831813925865-4.009883322770.67493208936-1.535222102920.2445161267342.29557815496-1.473523362051.676356617041.49041140278-0.5161154785430.2179485718291.19808454575-0.6473245409281.83550049842-40.7579811417-83.9730628888-97.9403039495
467.17701703233-1.145255119563.053000584951.64144651776-0.8129230932522.31646286168-0.02629713744321.33782385225-0.05299609284380.505501041473-1.025571570610.2816594403010.1927043470840.8916757706420.5294543239130.811615895777-1.46192378991.016224678191.52853230851-0.7540828184792.25900881027-31.3309308097-84.8344369549-111.804116558
471.89434696643-1.191410960641.205763125285.43736916721.944268642693.05892148469-1.125935311833.70315392849-4.428508839430.997129847543-1.00912368772-1.472344549260.689984446301-2.533894512292.179905578681.07926489084-0.0560825221762-0.1284168706661.52835968743-0.4499726393411.70185890675-25.1993945631-81.513527039-97.7711971988
481.2673941228-2.63006409787-0.7930416891518.91692886783-1.891024169933.776384572910.2933586835052.05697115746-2.04986635163-1.71494936619-0.5594538193790.2162590857390.821184577452-1.093540157660.384313448831.35957543908-0.0664982871979-0.267294866061.18536906971-0.6434596832051.88050938944-36.4018327935-77.0457887808-103.449364664
499.8567087031-3.44190865686-5.994260415862.041873743031.826807728044.8282687214-1.457824664960.465653583064-4.103598523290.1898053540230.0558012906029-2.321861304323.263283694360.4191265323971.775554467261.75541746420.04750036987120.4889865361320.9797420769330.06853790792922.8413351407-23.5946128113-89.4275256537-105.199490251
502.42951795539-0.455519413363-1.016718860263.610004474891.74389607543.344750580740.1440701000560.714351113398-0.328271335095-0.953842304342-0.220174793409-0.205339283765-0.7218546031920.02219600877230.1068085554460.7895817948350.09316204581360.1780242134580.768346165439-0.04117301731270.45247406482-21.2946426814-43.9879550836-107.15583189
516.93844716758-2.00916913633-4.12174188826.933330178110.6415474736656.06020026909-0.4238223518640.06687246209350.08563171753570.1483808876320.5548874532310.0494647107441-0.596742862273-0.437737612088-0.3308632315890.4789805284880.06545212003510.06321794085680.591754089639-0.02668888997350.341613333079-22.9689524193-45.8160829085-104.501814576
521.573406584380.09252760836131.466340112419.382314300791.964217132711.901468959330.2082129503631.266571379430.333725603392-0.304563137296-0.860738195347-1.209567608630.909319752471-1.80337253538-0.162355201531.27581353442-0.2009627753880.1161428025411.71397887867-0.953757889620.505474071455-21.9963256192-68.2717225113-117.968731945
535.34557478391.81978010204-1.32171930149.04508319397-2.926579644435.816853168180.0958894939890.284982512383-0.814574272792-0.617550297077-0.5527515154650.1096615547910.837513090354-0.9401278121860.3353143867210.840748832863-0.0520649878360.1333106260281.18114973141-0.4675288802790.869251176578-32.1473181726-73.0013086829-112.219922873
540.726197979771.618321752191.225230956867.95785133446-0.7576226842174.83967761093-0.4346059102432.65757917716-0.399259924022-0.5805292959570.4685699621381.474158519970.31139232506-2.5960588859-0.177383752561.09167388025-0.5260928025380.1808711479151.81199274485-0.6572586546791.40006944519-40.3242485203-77.5530543152-112.267302499
558.67263729941-0.300181900791-0.4195066630744.54125295913-3.349928512942.51554949877-1.474572402613.51660289478-1.19913430467-1.78516487451.995106639950.50296861329-0.417530065136-1.39598091146-0.6410864223041.09349784097-0.2501709888110.0515573418422.45922417844-0.35884145930.904037793068-40.6003022978-72.3801906622-121.065435855
563.22169542263.92918174696-2.890432841728.64705734136-1.839874830253.60066427691-1.39817230452-0.5774770809570.0819005756593-2.591767973550.601316268518-0.3390779449250.249594663821-0.5958459025970.6507669414971.51123559903-0.08942149515970.08251582927872.20243120394-0.4424731092960.839605379355-25.4221839801-66.3841586844-126.321130803
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 162 )
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 188 )
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 274 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 19 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 46 )
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 61 )
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 83 )
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 99 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 9 )
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 84 )
17X-RAY DIFFRACTION17chain 'D' and (resid 85 through 174 )
18X-RAY DIFFRACTION18chain 'D' and (resid 175 through 274 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 11 )
20X-RAY DIFFRACTION20chain 'E' and (resid 12 through 30 )
21X-RAY DIFFRACTION21chain 'E' and (resid 31 through 41 )
22X-RAY DIFFRACTION22chain 'E' and (resid 42 through 46 )
23X-RAY DIFFRACTION23chain 'E' and (resid 47 through 51 )
24X-RAY DIFFRACTION24chain 'E' and (resid 52 through 71 )
25X-RAY DIFFRACTION25chain 'E' and (resid 72 through 77 )
26X-RAY DIFFRACTION26chain 'E' and (resid 78 through 90 )
27X-RAY DIFFRACTION27chain 'E' and (resid 91 through 99 )
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 9 )
29X-RAY DIFFRACTION29chain 'G' and (resid 18 through 33 )
30X-RAY DIFFRACTION30chain 'G' and (resid 34 through 46 )
31X-RAY DIFFRACTION31chain 'G' and (resid 47 through 79 )
32X-RAY DIFFRACTION32chain 'G' and (resid 80 through 110 )
33X-RAY DIFFRACTION33chain 'G' and (resid 111 through 123 )
34X-RAY DIFFRACTION34chain 'G' and (resid 124 through 160 )
35X-RAY DIFFRACTION35chain 'G' and (resid 161 through 170 )
36X-RAY DIFFRACTION36chain 'G' and (resid 171 through 188 )
37X-RAY DIFFRACTION37chain 'G' and (resid 189 through 201 )
38X-RAY DIFFRACTION38chain 'H' and (resid 3 through 107 )
39X-RAY DIFFRACTION39chain 'H' and (resid 108 through 122 )
40X-RAY DIFFRACTION40chain 'H' and (resid 123 through 186 )
41X-RAY DIFFRACTION41chain 'H' and (resid 187 through 242 )
42X-RAY DIFFRACTION42chain 'I' and (resid 18 through 46 )
43X-RAY DIFFRACTION43chain 'I' and (resid 47 through 110 )
44X-RAY DIFFRACTION44chain 'I' and (resid 111 through 123 )
45X-RAY DIFFRACTION45chain 'I' and (resid 124 through 135 )
46X-RAY DIFFRACTION46chain 'I' and (resid 136 through 152 )
47X-RAY DIFFRACTION47chain 'I' and (resid 153 through 165 )
48X-RAY DIFFRACTION48chain 'I' and (resid 166 through 190 )
49X-RAY DIFFRACTION49chain 'I' and (resid 191 through 204 )
50X-RAY DIFFRACTION50chain 'J' and (resid 3 through 74 )
51X-RAY DIFFRACTION51chain 'J' and (resid 75 through 107 )
52X-RAY DIFFRACTION52chain 'J' and (resid 108 through 130 )
53X-RAY DIFFRACTION53chain 'J' and (resid 131 through 186 )
54X-RAY DIFFRACTION54chain 'J' and (resid 187 through 201 )
55X-RAY DIFFRACTION55chain 'J' and (resid 202 through 213 )
56X-RAY DIFFRACTION56chain 'J' and (resid 214 through 242 )

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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