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- PDB-7m4m: Crystal structure of RBR E3 ligase RNF216 with ubiquitin -

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基本情報

登録情報
データベース: PDB / ID: 7m4m
タイトルCrystal structure of RBR E3 ligase RNF216 with ubiquitin
要素
  • E3 ubiquitin-protein ligase RNF216
  • Ubiquitin
キーワードLIGASE / E3 ligase / RBR / ubiquitin / Enzyme
機能・相同性
機能・相同性情報


regulation of interferon-beta production / regulation of defense response to virus by host / clathrin-coated vesicle / negative regulation of type I interferon production / protein K48-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex ...regulation of interferon-beta production / regulation of defense response to virus by host / clathrin-coated vesicle / negative regulation of type I interferon production / protein K48-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR2 signaling / Iron uptake and transport / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Recognition of DNA damage by PCNA-containing replication complex / Stabilization of p53 / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / EGFR downregulation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling
類似検索 - 分子機能
: / : / : / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / : / Ubiquitin domain signature. ...: / : / : / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
類似検索 - ドメイン・相同性
Polyubiquitin-C / E3 ubiquitin-protein ligase RNF216
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 / 単波長異常分散 / 解像度: 2.39 Å
データ登録者Cotton, T.R. / Lechtenberg, B.C.
資金援助 オーストラリア, 1件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)1182757 オーストラリア
引用ジャーナル: Mol.Cell / 年: 2022
タイトル: Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216.
著者: Cotton, T.R. / Cobbold, S.A. / Bernardini, J.P. / Richardson, L.W. / Wang, X.S. / Lechtenberg, B.C.
履歴
登録2021年3月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年1月5日Provider: repository / タイプ: Initial release
改定 1.12022年1月26日Group: Database references / カテゴリ: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22022年2月16日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.32024年4月3日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: E3 ubiquitin-protein ligase RNF216
B: E3 ubiquitin-protein ligase RNF216
C: Ubiquitin
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)81,25217
ポリマ－80,3224
非ポリマー93013
水39622
1
A: E3 ubiquitin-protein ligase RNF216
C: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,76410
ポリマ－40,1612
非ポリマー6038
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RNF216
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)40,4887
ポリマ－40,1612
非ポリマー3275
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)81.871, 81.871, 248.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 601 through 760 or resid 764 through 771 or resid 1005 through 1007))
d_2ens_1(chain "B" and resid 601 through 1005)
d_1ens_2(chain "C" and resid 1 through 76)
d_2ens_2chain "D"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUGLYA2 - 161
d_12ens_1PHELEUA165 - 172
d_13ens_1ZNZND
d_14ens_1ZNZNE
d_21ens_1GLULEUG1 - 168
d_22ens_1ZNZNH
d_23ens_1ZNZNI
d_11ens_2METGLYM1 - 76
d_21ens_2METGLYN1 - 76

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.118244247282, -0.985398285223, 0.122509254604), (-0.992966380325, 0.116592575913, -0.0205897738236), (0.00600545825147, -0.124082193408, -0.992253769834)30.2829272, 35.4178035584, 125.120647362
2given(-0.131616736724, -0.983983888024, 0.120219560482), (-0.991290276268, 0.13119947177, -0.0114143236255), (-0.00454123229142, -0.12067479735, -0.992681706537)30.3253996466, 34.1481918948, 125.47002035

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要素

#1: タンパク質 E3 ubiquitin-protein ligase RNF216 / RING finger protein 216 / RING-type E3 ubiquitin transferase RNF216 / Triad domain-containing ...RING finger protein 216 / RING-type E3 ubiquitin transferase RNF216 / Triad domain-containing protein 3 / Ubiquitin-conjugating enzyme 7-interacting protein 1 / Zinc finger protein inhibiting NF-kappa-B


分子量: 31584.145 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: RNF216, TRIAD3, UBCE7IP1, ZIN / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9NWF9, RING-type E3 ubiquitin transferase
#2: タンパク質 Ubiquitin


分子量: 8576.831 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: UBC / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0CG48
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 10 / 由来タイプ: 合成 / 式: Zn
#4: 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: 3 / 由来タイプ: 合成 / 式: C3H8O3
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 22 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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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: 2.59 Å3/Da / 溶媒含有率: 52.58 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 15% PEG 6000, 0.18 M NaCl, 0.09 M Na HEPES pH7.0, 0.1 M KCl

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.953724 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年7月8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: 0.953724 Å / 相対比: 1
反射解像度: 2.387→49.51 Å / Num. obs: 18242 / % possible obs: 52.6 % / 冗長度: 13 % / Biso Wilson estimate: 59.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.037 / Rrim(I) all: 0.132 / Net I/σ(I): 13.8
反射 シェル解像度: 2.387→2.732 Å / 冗長度: 12.1 % / Rmerge(I) obs: 2.276 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 913 / CC1/2: 0.47 / Rpim(I) all: 0.678 / Rrim(I) all: 2.378 / % possible all: 8.1

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_3965精密化
XDSデータ削減
XDSデータスケーリング
STARANISOデータスケーリング
Cootモデル構築
AutoSol位相決定
精密化構造決定の手法: 単波長異常分散
開始モデル: RNF216/ubiquitin

解像度: 2.39→47.46 Å / SU ML: 0.2567 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 30.7019
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2468 1825 10.01 %
Rwork0.2002 16406 -
obs0.2049 18231 52.56 %
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: 63.54 Å2
精密化ステップサイクル: LAST / 解像度: 2.39→47.46 Å
タンパク質核酸リガンド溶媒全体
原子数3909 0 28 22 3959
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0023985
X-RAY DIFFRACTIONf_angle_d0.48195340
X-RAY DIFFRACTIONf_chiral_restr0.0409574
X-RAY DIFFRACTIONf_plane_restr0.0042704
X-RAY DIFFRACTIONf_dihedral_angle_d12.31441587
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.26605567001
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.471329359864
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.291140.5636X-RAY DIFFRACTION1.53
2.45-2.520.7393120.440696X-RAY DIFFRACTION4.27
2.52-2.60.5245240.4356217X-RAY DIFFRACTION9.37
2.61-2.70.5718360.424331X-RAY DIFFRACTION14.12
2.7-2.810.4359520.3861453X-RAY DIFFRACTION19.38
2.81-2.930.3993690.3804628X-RAY DIFFRACTION26.53
2.93-3.090.3505990.3336890X-RAY DIFFRACTION37.62
3.09-3.280.36981680.30161503X-RAY DIFFRACTION62.65
3.28-3.540.32192590.25982325X-RAY DIFFRACTION97.73
3.54-3.890.26982690.20032417X-RAY DIFFRACTION99.96
3.89-4.450.20312690.15962422X-RAY DIFFRACTION99.93
4.45-5.610.21082740.17052460X-RAY DIFFRACTION100
5.61-47.460.20452900.17122628X-RAY DIFFRACTION99.73
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)
10.00699876094526-0.0002355180323550.02123664930540.02573715036850.05216311164920.1575431030920.0749393020802-0.05271749993130.05945291807030.0670566178953-0.05002988976470.0336561770080.00653795848043-0.00251506277481-0.2939940547460.2467423648230.06531908291220.1137662273980.3343090737170.001035113331460.0594964346064-2.89191136534.7530764435123.08678285
25.009726173971.480435534440.5755732210180.9831138517181.092257872151.630445369090.567437930716-0.899802969587-0.1914091096010.139785605422-0.0075114734357-0.2709306955510.182296147976-0.02958271097050.8667165702370.2821784884420.07344402745670.0148549415370.4350246747120.05167412762450.3004675150821.2795111724628.1284752115120.907591176
30.297057158371-0.00111598088376-0.3614879903070.29553342612-0.2311816653410.6788835187290.238041277068-0.008009046095-0.4289620221350.0330660139170.190780967373-0.165467682850.3478834990970.3590338358610.168253090070.6767433052880.24635893-0.03196113180890.520838496943-0.09501591953450.81295262939312.319134439723.7065662771120.16880353
40.1502894181020.0574212644719-0.05762717527390.636346749171-0.6614536133620.6877812330560.112259335409-0.3736421817750.3581624691070.416646446235-0.241105824430.144360701011-0.4621189473920.100797756703-0.2002493513710.5255412504510.1262311618770.04141596318240.519351564939-0.2516060248880.58017381468918.273183341728.1530072004113.467151427
50.0210253078445-0.043862802313-0.0320840174120.09091191418830.06490779826220.0695624206269-0.00385942499969-0.02079306570580.03708472842350.025668737453-0.0041977956570.0194176760538-0.00277291336562-0.0125952299697-0.4304079586710.06374223495960.09282560686030.1012888394740.2980210855720.005440953113830.28618462791720.618680829221.924666858898.2750773518
60.512653538858-0.0005651600196180.3322636364340.1205928488090.1400078423991.212484641210.1083994750560.0552345233863-0.1646219698360.06802809877480.06403717742090.01088752064430.274387016776-0.1401449033870.5171994431030.219763492188-0.0375859612086-0.1227135454950.2175256589010.04956061181520.14160053687327.2535538415.6154805516885.7343005779
70.3554318207990.151879538707-0.08017994298830.1902534920890.007321455466820.0315876433318-0.06302670474490.1830297169340.0574557907802-0.09319662782730.08774639189850.1500694814140.0568961267128-0.09348534581750.4792035398180.171462288123-0.211476465428-0.01941773345630.3649485857710.105565314880.25937502157320.12386588087.0273553110573.0828782976
80.164629176667-0.1250981906560.2494991270572.033803101860.3725384121280.797679902080.02287891824480.311043161966-0.218157663364-0.31535256723-0.108114166560.545609307115-0.0266049768098-0.0142646730484-0.00364675089680.192654712596-0.149466327091-0.1045707038260.602373884890.006336330770090.30280061960319.59971221387.8582556796870.2355504666
90.3888570257710.2105968824140.4226606648740.1156394453910.1963135889321.46250980860.308847116365-0.1201199106330.554117207764-0.6041532477160.1033258140790.421104364034-0.837048139814-0.233369551678-0.0318983152830.447995181938-0.004182633198970.1419107720180.3138351983150.09793754717840.5132769821221.073627737624.342920585185.0803009716
100.284423823773-0.2349591243240.1303638914860.516698463599-0.2407910569210.1147002631130.0731605569879-0.0551527333537-0.2401864582650.1327865780090.04755600742950.342561541812-0.0207578451626-0.02088594778520.1879028264960.7317786735460.3636001741760.2979881954340.91958779956-0.1116695341211.2359923291612.933360642834.217457755697.9766115538
110.118735726856-0.0740177902330.01668117726570.063866283361-0.02127149721040.0123449988155-0.0002410020327820.09559787007570.09117060007110.082131581829-0.05267921249870.0122179864837-0.397795572269-0.4373123498340.004103874917421.355569664980.1802548309710.1475514925740.636697276958-0.07138725068411.2658523868117.013650401239.495703524699.534182376
123.111729302650.7641138766350.3103624414210.278663596257-0.1806316424830.753949297310.02941616102420.4344696635280.0514028349337-0.7151202732560.303402947123-0.0498083744037-0.1308685546050.233082206193-0.1082319518690.659030405924-0.01047536584760.27412420550.378211021283-0.1607260842170.96882655371427.739670631230.597201586691.8644986862
130.0012015481665-0.00651898401141-0.01152754997740.05639540479070.04164724065190.0872754939841-0.0336268084539-0.07593829533180.02050696986480.01760048510520.01913437831430.007427444483140.0246867603764-0.0042137792907-0.6783821869970.3261462826110.310810157782-0.02761495729130.329131050907-0.1408181759360.12991139453512.117228425939.78760384890.390798621484
140.0721056015366-0.0865254608711-0.002842300477430.2077249376750.01049890347670.1528923176450.1524507462140.17958067521-0.111339996748-0.164136654376-0.09678316987070.05147873783380.1873346709860.05317064159230.5005028252230.413493021420.299419917334-0.0568145221230.38624055791-0.04704939592550.12958241726818.414953220937.4982986805-0.470069744299
150.0137656351826-0.0143380121302-0.007343620709420.0163675160180.01104698409920.00622143193781-0.0242856946445-0.0320313740002-0.01672537898930.01074225332530.007512849236160.002448356140780.03430555374460.0182450147483-1.72780566810.5497660827690.4918524101550.002936576908710.569641000482-0.0541385967410.23459929671816.820339746332.8445665614.21542183841
160.138605865288-0.2365337628440.05411348861610.402937322864-0.09187470712170.0208997402232-0.04149015616560.05870088264280.158249811659-0.0245968445053-0.0554932183639-0.157326897105-0.01405353306370.0600670312419-0.6578254123090.544561125020.4144627150040.1524815262060.858462459010.3283089768680.57240201701420.145966478223.79217426494.47125296228
170.150075568269-0.0230055461668-0.05969781847520.02281806924120.01095374172350.02426359415030.0623925415127-0.102358023939-0.0821006142799-0.276426979875-0.07431566942950.0503092654660.126232187664-0.140934772131-0.7338723415670.4694575720910.214439299347-0.00900503626810.5031499613620.08288621638630.18390809063115.412178399217.86445684515.4207355547
180.08695766872530.0402558223675-0.008562575604480.0964367490642-0.09038664364230.0926342906131-0.00197928211931-0.0668026350012-0.0481260149491-0.0705746742174-0.0492932128096-0.08057669464190.1192761291690.0858481138344-0.6333382572840.3544545785210.2038571173680.1274040519380.4907198641640.1774341250510.12363950394826.68800743459.9219441537734.3502135843
190.253029552117-0.04637393055550.261932679610.0697907259575-0.09091926881620.4713263516910.05450943378950.0527742615197-0.0123516772001-0.00792672168324-0.0583173165971-0.08742767143680.1224477217380.1111578036430.4018238825540.3386115651030.2088609220660.09880113494370.5023596624560.2673512979790.2779599640133.98186071425.0802966137243.3768023276
200.0160899832976-0.0270780915048-0.002938398622030.04007012863940.01204875199940.02131278842930.05405900140960.02838157018740.0266929873281-0.057936324865-0.0299977122269-0.01282126033590.01317107776330.06022710119320.8702114961510.280516449305-0.0210209063939-0.1265132675270.4308398597280.2870288079440.23253595075330.590653487214.391059052951.1436249595
210.5876775970670.189981035497-0.7430506611310.44325384375-0.1411913922581.2075878262-0.01795953315490.1497394617590.03369569014390.0196836421930.001261883320570.1070817284670.0340983133089-0.269715148986-1.651183081820.344110614699-0.05153580770050.1140764354220.5595486298020.1759528135970.16351519645923.54108097214.60506232850.7426709968
222.520398503332.377197578211.720059162062.442578534891.604833540671.22382367590.009860771599870.4890595446580.688675653524-0.2529177077240.05933652550270.770726084379-0.280113795769-1.16905443597-0.07737644890670.3714042484320.01949998878110.09646569168360.9237039497780.1076712994140.48323852279211.089303196418.805384797633.3269643791
230.0549984297122-0.001535730349-0.01443277442510.000826612790118-0.008260410701910.103392711918-0.328589046658-0.03183721905810.205168948284-0.1179052182030.1177094765830.0525876156089-0.2953357800780.002311598085758.21498164997E-51.678969580050.3914541928070.02394685384881.571715721940.03486340237461.228600451526.1722184259625.101895314723.7810567646
240.349885193395-0.5529248941190.2552018033812.272611156491.206362516922.037308884970.3484875100360.1019513797210.510332434819-0.2110261331560.3652539045660.359171877191-0.459933371052-0.367872503024-0.07151894198630.518026074041-0.1874569530430.2897307012841.3223334910.04530474364751.276332376316.543590504512.73967704827.5229149709
250.375660431836-0.0589257311366-0.1498189482831.985407342861.044922183190.663127969243-0.291507737075-0.5534960916680.3831809909820.380391795282-0.02761397689540.008045340693430.112477870446-0.201952593407-0.2185733450920.3551221743930.1734212902-0.02254687249220.425762813957-0.1015940152190.25518652993731.597659472313.3139402617105.054421434
260.4259813439780.2316558804810.2215066667420.1914482304940.08000908049170.2555192909780.00900346836863-0.1346939881650.07906369254730.03440684864950.0004829715756080.0113905908812-0.0248534136495-0.04553845963190.4355978522470.222392890074-0.0663228748731-0.1944949187570.516151524441-0.2038714244410.47160427818141.193900501120.125510916103.707024397
270.53574629597-0.4852522935780.1784537531270.461616309299-0.01989521179250.993205844585-0.0366783533871-0.0120317506891-0.225906728944-0.00664011938030.0550947751837-0.4064431333370.1909051355490.6963597904730.08868464256310.1170844569130.03583892313010.01537095722690.4815087969840.007208126431250.56695056508437.158218577813.887729109996.1353847131
280.447845726929-0.115755366930.3221290047610.0307364755077-0.08474015711040.2355935413550.006402304746780.207672744784-0.1086604312310.0856487462675-0.0726512240091-0.172274138721-0.09020372938590.301503969044-0.1479220339990.409243434095-0.195197545308-0.08664678538450.735194422026-0.1743839345391.1536471925238.968957161825.087215166595.0707808222
291.120859308630.583259149981-0.1996154818270.8093890462690.5701807176860.935634632426-0.0856242096928-0.02647843506060.52002755641-0.08036132461810.2408170579330.0301438786402-0.1584593317710.1761774672471.901448565460.137169279664-0.0647557770508-0.1293449386280.254067009544-0.07753848783080.41311582985430.603759825921.9062773265100.150173372
300.8819539859780.144782685997-0.08653174961830.7005885682760.7647614317170.946418346594-0.1176063210280.17074812993-0.321445550737-0.2735596115960.125813836286-0.3260728683630.0163323714482-0.0597733791351-0.2974295595570.432479790542-0.00827149901361-0.1002526341330.160014963574-0.1086845590750.34964029641334.31938967967.5912945711882.7901566205
311.5713403531-0.1556787855280.4396982581433.504938561540.1955472486670.1397417025240.018549385852-0.016619684197-0.212526277188-1.11809799843-0.2416655317090.09377002329390.1990358283180.310372282971-0.1679802002790.6938386564730.05703788119860.06581439658280.596110829911-0.009919212939590.24159465316124.80227426263.0604804852419.4154176706
320.123058749039-0.0888817724047-0.02432807481760.08345070019020.009467275743410.007785558773480.05720647264910.214718314913-0.736399709328-0.745752925427-0.0847850599367-0.585361888411.04111610003-0.8781236967670.002385502415611.21461842673-0.123116731264-0.02209156526020.869479080555-0.00142658485850.9184596759319.5932077158-5.5249919114620.9052296127
334.81114213657-1.949708299041.352931131494.42481129896-1.248429123140.5156158646620.5922573687930.112814946288-0.835759038514-0.434335007868-0.516111446909-0.5071898873410.951754092730.4348086663221.293278486430.9709381609930.1596892119330.04384537332190.4485669894020.2622079802210.69292308173223.0553309216-2.2354666342930.0238561938
340.129122698153-0.09274208170120.0143600943270.244725036410.1371479989580.13392342623-0.396248111034-0.300100159008-1.36988413524-0.134815226157-0.1143422554340.2300831691070.701622262415-0.288092310801-0.005621080228271.02308153531-0.2107526112380.1255697870530.7520515014410.2261490864340.87014081306413.4142488623-1.3832621230731.173747877
351.93155187788-0.503332814525-0.003794613977510.190620253737-0.05401892805950.0506847577520.550740829371-0.585156612794-0.557499403607-0.487806230384-0.04198235246030.5572746665111.2004370212-0.5795569616060.0564851401370.580208104925-0.0279773550868-0.2253336230630.5643105650770.05746327581290.37138587458216.05884050255.1064776530623.7344995295
360.2657705600560.193031502971-0.4373037634350.606939695220.08677521507641.071415633070.203099979752-0.202419762329-0.01429611311750.478705925666-0.239652042836-0.00590288945240.5492849063540.164841786167-0.449980728540.516416247320.07928785402070.1013980307920.7709060052880.2567407316650.35314103070129.11985099960.48114371487742.6557464748
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
11(chain A and resid 600:616)AA600 - 6161 - 17
22(chain A and resid 617:639)AA617 - 63918 - 40
33(chain A and resid 640:647)AA640 - 64741 - 48
44(chain A and resid 648:657)AA648 - 65749 - 58
55(chain A and resid 658:670)AA658 - 67059 - 71
66(chain A and resid 671:700)AA671 - 70072 - 101
77(chain A and resid 701:725)AA701 - 725102 - 126
88(chain A and resid 726:734)AA726 - 734127 - 135
99(chain A and resid 735:751)AA735 - 751136 - 152
1010(chain A and resid 752:759)AA752 - 759153 - 160
1111(chain A and resid 760:765)AA760 - 765161 - 166
1212(chain A and resid 766:772)AA766 - 772167 - 173
1313(chain B and resid 601:615)BG601 - 6151 - 15
1414(chain B and resid 616:627)BG616 - 62716 - 27
1515(chain B and resid 628:639)BG628 - 63928 - 39
1616(chain B and resid 640:648)BG640 - 64840 - 48
1717(chain B and resid 649:663)BG649 - 66349 - 63
1818(chain B and resid 664:685)BG664 - 68564 - 85
1919(chain B and resid 686:698)BG686 - 69886 - 98
2020(chain B and resid 699:724)BG699 - 72499 - 124
2121(chain B and resid 725:742)BG725 - 742125 - 142
2222(chain B and resid 743:752)BG743 - 752143 - 152
2323(chain B and resid 753:760)BG753 - 760153 - 160
2424(chain B and resid 764:771)BG764 - 771161 - 168
2525(chain C and resid 1:15)CM1 - 151 - 15
2626(chain C and resid 16:32)CM16 - 3216 - 32
2727(chain C and resid 33:49)CM33 - 4933 - 49
2828(chain C and resid 50:57)CM50 - 5750 - 57
2929(chain C and resid 58:70)CM58 - 7058 - 70
3030(chain C and resid 71:76)CM71 - 7671 - 76
3131(chain D and resid 1:17)DN1 - 171 - 17
3232(chain D and resid 18:35)DN18 - 3518 - 35
3333(chain D and resid 36:47)DN36 - 4736 - 47
3434(chain D and resid 48:55)DN48 - 5548 - 55
3535(chain D and resid 56:70)DN56 - 7056 - 70
3636(chain D and resid 71:76)DN71 - 7671 - 76

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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