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- PDB-7m4n: Crystal structure of RBR E3 ligase RNF216 in complex with K63-lin... -

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基本情報

登録情報
データベース: PDB / ID: 7m4n
タイトルCrystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-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 / protein linear polyubiquitination / LUBAC complex / 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) ...regulation of interferon-beta production / protein linear polyubiquitination / LUBAC complex / 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 / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / 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 / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR2 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation
類似検索 - 分子機能
: / : / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...: / : / : / 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 / 分子置換 / 解像度: 2.52 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
E: Ubiquitin
F: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,20022
ポリマ－65,8556
非ポリマー1,34516
水1,31573
1
A: E3 ubiquitin-protein ligase RNF216
C: Ubiquitin
E: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,60011
ポリマ－32,9283
非ポリマー6738
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RNF216
D: Ubiquitin
F: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,60011
ポリマ－32,9283
非ポリマー6738
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)41.791, 84.414, 96.418
Angle α, β, γ (deg.)90.000, 102.151, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
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 652 through 761 or resid 764...
d_2ens_1(chain "B" and (resid 652 through 1006 or resid 1008 through 1010))
d_1ens_2chain "C"
d_2ens_2chain "D"
d_3ens_2(chain "E" and (resid 1 through 75 or (resid 76 and (name N or name CA or name C or name O ))))
d_4ens_2(chain "F" and (resid 1 through 75 or (resid 76 and (name N or name CA or name C or name O ))))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAGLUA1 - 110
d_12ens_1PHELEUA112 - 119
d_13ens_1ZNZNC
d_14ens_1ZNZND
d_15ens_1SO4SO4F
d_16ens_1SO4SO4G
d_17ens_1GOLGOLH
d_21ens_1ALALEUJ1 - 118
d_22ens_1ZNZNK
d_23ens_1ZNZNL
d_24ens_1SO4SO4N
d_25ens_1SO4SO4O
d_26ens_1GOLGOLP
d_11ens_2METGLYR1 - 76
d_21ens_2METGLYT1 - 76
d_31ens_2METGLYV1 - 76
d_41ens_2METGLYY1 - 76

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.999985670129, -0.0015835732101, 0.00511388624793), (-0.0015529649827, -0.99998089133, -0.00598375085399), (0.00512326423592, 0.00597572342134, -0.999969020967)-10.8945712923, 4.77021722333, -47.0129132179
2given(0.999897760858, -0.00715776587609, 0.0123787809759), (-0.00726300084222, -0.999937690324, 0.00847728071345), (0.0123173312675, -0.00856632110019, -0.999887444412)-10.6082780156, 4.85215275408, -46.4714097639
3given(0.882464602601, 0.0635380923441, 0.466067737541), (-0.445013071792, 0.433756043929, 0.783466055608), (-0.152379759449, -0.89878729696, 0.411049636581)25.7170427136, -26.160613101, 12.6608659238
4given(0.890243992916, 0.0619354379953, 0.451253403972), (0.430017150679, -0.440914667415, -0.787832156097), (0.150169514878, 0.895409547402, -0.419154934627)15.0246223108, 30.7905968529, -60.0662583154

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要素

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タンパク質 , 2種, 6分子 ABCDEF

#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: 15773.959 Da / 分子数: 2 / 変異: C688A / 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: 4 / 由来タイプ: 組換発現
詳細: K63-linked di-ubiquitin: isopeptide bond between ubiquitin C-terminus and lysine 63 side-chain; chain C linked to chain E and chain D linked to chain F
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

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非ポリマー , 4種, 89分子

#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 8 / 由来タイプ: 合成 / 式: SO4
#5: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 73 / 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

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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: 2.52 Å3/Da / 溶媒含有率: 51.28 %
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: 7.9 / 詳細: 0.2M ammonium sulfate, 30% PEG 4000

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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9月17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: 2.52→47.13 Å / Num. obs: 22096 / % possible obs: 98.8 % / 冗長度: 3.5 % / Biso Wilson estimate: 34.5 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.146 / Rrim(I) all: 0.208 / Net I/σ(I): 5.6
反射 シェル解像度: 2.52→2.62 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2331 / CC1/2: 0.48 / Rpim(I) all: 0.882 / Rrim(I) all: 1.286 / % possible all: 91.7

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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
Cootモデル構築
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: RNF216/ubiquitin

解像度: 2.52→42.21 Å / SU ML: 0.4036 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 29.1167
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2732 1999 9.06 %
Rwork0.2163 20063 -
obs0.2214 22062 98.69 %
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: 46.24 Å2
精密化ステップサイクル: LAST / 解像度: 2.52→42.21 Å
タンパク質核酸リガンド溶媒全体
原子数4293 0 58 73 4424
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00314389
X-RAY DIFFRACTIONf_angle_d0.59825887
X-RAY DIFFRACTIONf_chiral_restr0.0459648
X-RAY DIFFRACTIONf_plane_restr0.0043766
X-RAY DIFFRACTIONf_dihedral_angle_d11.61461739
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS3.06712211498
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.509032001303
ens_2d_3EX-RAY DIFFRACTIONTorsion NCS3.01457224801
ens_2d_4FX-RAY DIFFRACTIONTorsion NCS3.03081044501
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.580.36651250.32291239X-RAY DIFFRACTION86.55
2.58-2.650.39011410.29651433X-RAY DIFFRACTION99.56
2.65-2.730.34041430.26951446X-RAY DIFFRACTION100
2.73-2.810.31651410.27071471X-RAY DIFFRACTION99.81
2.81-2.910.30321460.2621421X-RAY DIFFRACTION99.75
2.91-3.030.33981450.26751443X-RAY DIFFRACTION99.81
3.03-3.170.31661460.24781429X-RAY DIFFRACTION99.81
3.17-3.340.31061490.21821459X-RAY DIFFRACTION99.94
3.34-3.550.29351430.20731441X-RAY DIFFRACTION99.62
3.55-3.820.26041400.19561456X-RAY DIFFRACTION99.75
3.82-4.20.22391450.17681460X-RAY DIFFRACTION99.75
4.2-4.810.22841440.16611433X-RAY DIFFRACTION99.75
4.81-6.060.22191480.19351466X-RAY DIFFRACTION99.32
6.06-42.210.24351430.21521466X-RAY DIFFRACTION98.17
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)
10.4061200340680.005925211376970.1322176843010.09555217909690.0734007385480.095604064975-0.364677943875-1.458768481171.567146824820.959857170132-0.0826653277743-0.239427284737-0.984282669728-0.39661463798-0.003088785250121.09907317583-0.1166611557030.0769152426210.652664240626-0.1229466337360.522345874183-22.440163497640.2669130275-2.21758343021
29.9543133119-2.199330605574.598840699753.73508146187-3.877208141184.662679510520.2776741886290.364768144479-1.27413685738-0.90059782213-0.07730209684760.166012117288-0.1063609751350.7082060782770.5510205172250.38688457056-0.0161973061610.05750968095360.2086627261740.01057422063470.197837839222-17.502338962831.3157187653-3.48590840585
31.2260460847-0.2414618427260.1916851837391.68321698156-0.8049853216270.446364170359-0.03639488251140.7208710889430.374478411005-0.5715269533470.324126969240.157133688588-0.02324979902120.8062624223460.277732846750.292096220188-0.1080571772440.009301954232360.439528439884-0.04835797122640.193397314166-11.596169270619.9166780362-9.15840079461
40.4283121443520.7207774103891.868286697142.424655581061.993398864939.71896162846-0.6117870998510.3818459730630.545928167292-0.589565426065-0.543548185807-0.813114634052-1.019611327450.900070839681-0.3466376386080.315958786050.102240144577-0.02768961573330.5584933909660.1013280165090.569003281962-9.9005636361417.2083222729-19.270056421
53.43589934036-4.9290283253-4.976892938587.716963524478.33821137599.409561559380.4637186274210.513924646362-1.354163514550.0649752459981-1.027072900841.898050364060.273159905452-1.34246696787-0.6734444670750.4243072906080.0143072346605-0.1988459899860.410530651092-0.009062001056080.661432464593-10.01513972534.93928438818-10.4671426565
60.0898219123297-0.01756757000430.06895095847150.122675351702-0.08078880936140.08511920187320.4165180430790.165653788643-0.04935599304830.116164945551-0.2885674385730.871037144399-0.323483780051-0.9592604112480.0008132199458310.4987597246920.0630935419528-0.04669149676040.444242931184-0.05657956119480.473171073485-6.8923696374110.175056934-20.5194734816
70.4540242667220.08857599521841.340184102760.02674873086790.2657480141674.412266045480.3222043031860.05629381650180.516503248305-0.105663720556-0.1424203716380.2215629866290.08312319051141.009192454930.10879709410.409578707838-0.01954409918650.01796338846020.2740147588920.05329909293950.462666643708-2.0566476823813.6552547103-12.3531219553
85.39516619543-0.7940218710231.833983665523.800831937680.2700266957961.588440553440.806968922731.130553350270.157472974593-1.945105755650.05270928710650.0898369010210.0598450312450.4026977717760.4843478166480.5450919175880.0557847113383-0.04884178757720.41273371989-0.02723107501650.5094816046813.953824415655.05917651861-14.6825072941
95.78192405049-0.8781642056343.253030287387.39275223777-4.941813350294.547952856941.05425127014-1.12872707780.7242461689141.069282277380.817342554098-0.254617067771-0.993071884778-0.3161077930482.016120861440.521752270212-0.1331846135190.08761381866370.328049939358-0.02635681592110.4286340269815.875614796-1.48062923552-1.04308464773
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572.004371936714.41925242202-2.445142055745.044162924093.460085585376.34704120180.4966984866570.2196589050461.6032042602-1.90997525588-0.1829857802491.00773162678-1.26037885452-1.470666890391.540474021820.5028900127230.0826059187328-0.1224491374730.5314431993640.1336445996490.277875397991-7.97789916029-10.7030349973-13.4363284175
580.216050104401-0.125443506087-0.09584229489250.08516282969680.07905592685210.508731592006-0.103576253302-0.5260934089930.418064177837-0.1157504219370.2259330099820.675173762301-0.33733204452-0.40878643330.001316717205280.3281608969470.0711223626553-0.0392160593570.390309950385-0.002053775746370.44727472327-8.00120790148-13.3436568075-5.00530369621
593.90063390.765952700334-5.770745946625.47459970611-0.6952574959098.585603562930.5075347598121.238265502290.0512814738333-1.006198618410.486163621140.961890250469-0.187751303373-0.3533420258211.034422880610.269962429597-0.0520121692422-0.0389107915610.489634611523-0.1121313120780.421449769175-8.84717552694-24.0686141212-9.76181572982
606.185996688810.7578375928542.933907249050.9656388461140.06999059407311.539415143710.546684942781-0.636856487571-0.600181423833-0.325569795181-0.27306183245-0.8620511138890.1751571420.6380773451472.464906465630.327234087036-0.063131064740.04924969038630.420382772726-0.008062623567950.311770203227-2.17934205-22.9329603886-2.13146380465
613.933441872620.1009310920530.9655697101090.08710557502110.5584877650243.8970512322-0.748310606067-1.247545990120.001483296884650.5399366206291.03437325753-0.377537788729-0.09556446284240.403155210736-0.5615545310160.4329228137830.1653122482460.009507184518170.400343848742-0.06279251226190.3405258276526.63006129034-13.0796607496-3.40840201984
622.00370794831-0.478859729777-5.167235860018.138582094510.9781944328994.800754121460.605257647038-2.577881327330.1151589634261.113976762080.0449695128999-0.6439681354050.08371282610721.036602431290.789219986440.220772398789-0.1148402298870.01823632494860.5586765076330.07737730016490.464884637317-1.88416201054-12.08989465152.19060232163
631.307317646550.900683724939-0.2174965471340.742782263363-0.1012126919631.725589503570.215286660506-0.3628784998961.308141461410.2340595936360.4278936079760.614540375869-0.384020718067-0.2943698170.1694033696620.3655079582740.00689687760520.05389581831710.30052965733-0.02775055756650.39689028656-0.392928453169-4.93655511868-5.98813355385
642.586405564490.9191554289822.192116311910.3306445744090.8471220674742.72268571273-0.1034085799510.2517898924660.182478594132-0.452715969452-0.295185769549-0.00457896848296-0.3030201604651.2743811201-0.74737225290.3557881675270.04046274902590.07997830486960.360716172470.1270313843430.3012528781022.93499391704-14.9655030748-11.2631009151
650.01899724020690.0755300020850.1043080169510.761452591824-1.027802925564.119910386590.0071250883056-1.220070327120.1747771426260.102335421978-0.636454864315-0.07613752789120.646116451047-0.71506396135-4.78532215770.236130461894-0.0166337718007-0.3551240304240.9015422540840.460646725193-0.120660430733-0.422112629836-30.14061218530.531978271947
665.11742045474-0.4392149881060.567591940373.149365719410.3322134149350.1161029509170.296996138765-1.27180210130.1334486066680.138619013938-0.9387235591270.368795590569-0.1574975454550.345787907881-0.1198825631560.502170897963-0.133258711574-0.03248824558510.315304659076-0.04520577280420.327089567343-11.676799337518.6749205052-32.7155813172
671.97083287659-1.17460591795-0.07337151393691.608121383121.260821312416.64856630009-0.115087050165-0.3432994740321.201029895690.05837047221770.4693875191940.0608974724816-1.806763079912.00992754776-0.1327182331260.821777477476-0.141647218236-0.04750654100570.479174870428-0.1044774438370.376829974738-8.355598355927.8119478211-31.6809226022
681.349609504442.759875855811.919220072536.832335723554.46405356122.984897652380.120704694563-0.09855146850040.3923160666440.932144543994-1.097973164631.178982673260.976927095214-1.967052200540.2981916677280.510203868836-0.169523168394-0.001293488019810.448152369777-0.004437181885360.443863982862-18.892974961214.1740904247-35.6699502369
693.90477459286-0.272315563692-2.838001654510.619162334484-0.7345057129893.58779800466-0.02511912625610.5579556015840.7262507531990.2590608495390.76653365168-0.406376871707-0.313564236027-0.6086316086730.4170904321780.305586573629-0.0299402384755-0.03775991208870.361060504563-0.07152506346770.349915010295-18.878053706119.315927886-42.9391767382
705.804716926340.820979618559-1.49195571930.583082688176-0.568465025120.644840956880.272845809798-1.122615168720.2916840860780.742226822973-0.5468661375951.17037862452-0.652459976572-0.43780638053-0.08262289469530.5758269140450.1273753316840.06707654524530.441237231673-0.01134725051470.593333761763-19.793733084927.4149961222-36.0585254814
712.130239210961.064245742071.577554582782.54132680086-1.073125103494.84566260745-0.233877252402-0.3734159184370.9533444904190.0254227690593-0.609821203101-0.184701483641-0.8862525079470.00153649892798-1.715903221740.2913144282580.1250789941210.07170848654250.3689175416180.07513883755180.395720212896-16.547255585630.902703611-43.6809875901
722.94172753047-1.76526267256-0.4325872115231.627845490780.3595139101684.903482783740.76844329956-0.0112943394194-0.45427647412-0.191684761213-0.4726456844660.248288733997-0.210941548489-0.2050665502031.517452925220.2623620362790.0322772235999-0.03132781915730.335631240332-0.0691865679430.589662864156-8.2296377224222.57046203-43.1945578079
738.948373517893.189280468014.845923574445.34773526264-0.4541594854623.753798983890.1870710305870.956925320724-1.42693926056-0.953574071588-0.348060958567-1.46298311076-0.01500064863020.4221798420110.2959359209320.3208806612210.007188272269370.03969998675810.5151630184640.03098828054550.270008650087-6.0898759964717.9530997173-46.8266152835
740.425344852387-0.422739968469-1.304969331811.22130213512-0.8286703927639.338628641320.1878043944290.129443507039-0.00735493905555-0.0277245125091-0.2342728358490.4490596568330.9357033406330.872933826321-0.2277570109970.2686945976630.00838183677719-0.1197522514990.383966383674-0.03657848743630.54550172078-14.443043484813.5257489434-47.119274791
750.610957609544-0.2084090590110.2327514597610.7876213447890.04391181083720.107787383431-0.2765763007360.2661389576730.0812535388324-0.1683337573620.216962566151-0.153350594817-0.03973275153850.4541085649510.004838700708630.294450129938-0.000613519096119-0.0453730146340.4157515085030.006165372898920.341607528929-9.0014728904914.6980292217-38.3551786878
768.53584361613-4.70873547095-3.274502630824.594055575365.009402992226.33467896637-0.02758111834191.721794467270.16783567085-0.632066358626-0.822530233943-0.458823541368-0.841129349875-0.896540339843-3.876335695310.273010667842-0.07322925976190.1715727658280.4252641197370.1208863223390.643392436918-11.003790075635.0926883123-47.7047091875
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 652:657)AA652 - 6571 - 6
22(chain A and resid 658:665)AA658 - 6657 - 14
33(chain A and resid 666:675)AA666 - 67515 - 24
44(chain A and resid 676:683)AA676 - 68325 - 32
55(chain A and resid 684:689)AA684 - 68933 - 38
66(chain A and resid 690:699)AA690 - 69939 - 48
77(chain A and resid 700:707)AA700 - 70749 - 56
88(chain A and resid 708:715)AA708 - 71557 - 64
99(chain A and resid 716:723)AA716 - 72365 - 72
1010(chain A and resid 724:730)AA724 - 73073 - 79
1111(chain A and resid 731:737)AA731 - 73780 - 86
1212(chain A and resid 738:742)AA738 - 74287 - 91
1313(chain A and resid 743:751)AA743 - 75192 - 100
1414(chain A and resid 752:757)AA752 - 757101 - 106
1515(chain A and resid 758:766)AA758 - 766107 - 114
1616(chain A and resid 767:772)AA767 - 772115 - 120
1717(chain B and resid 652:657)BJ652 - 6571 - 6
1818(chain B and resid 658:671)BJ658 - 6717 - 20
1919(chain B and resid 672:676)BJ672 - 67621 - 25
2020(chain B and resid 677:684)BJ677 - 68426 - 33
2121(chain B and resid 685:690)BJ685 - 69034 - 39
2222(chain B and resid 691:696)BJ691 - 69640 - 45
2323(chain B and resid 697:704)BJ697 - 70446 - 53
2424(chain B and resid 705:710)BJ705 - 71054 - 59
2525(chain B and resid 711:716)BJ711 - 71660 - 65
2626(chain B and resid 717:724)BJ717 - 72466 - 73
2727(chain B and resid 725:732)BJ725 - 73274 - 81
2828(chain B and resid 733:742)BJ733 - 74282 - 91
2929(chain B and resid 743:751)BJ743 - 75192 - 100
3030(chain B and resid 752:758)BJ752 - 758101 - 107
3131(chain B and resid 759:765)BJ759 - 765108 - 112
3232(chain B and resid 766:771)BJ766 - 771113 - 118
3333(chain C and resid 1:6)CR1 - 61 - 6
3434(chain C and resid 7:12)CR7 - 127 - 12
3535(chain C and resid 13:18)CR13 - 1813 - 18
3636(chain C and resid 19:24)CR19 - 2419 - 24
3737(chain C and resid 25:30)CR25 - 3025 - 30
3838(chain C and resid 31:37)CR31 - 3731 - 37
3939(chain C and resid 38:47)CR38 - 4738 - 47
4040(chain C and resid 48:52)CR48 - 5248 - 52
4141(chain C and resid 53:63)CR53 - 6353 - 63
4242(chain C and resid 64:69)CR64 - 6964 - 69
4343(chain C and resid 70:76)CR70 - 7670 - 76
4444(chain D and resid 1:5)DT1 - 51 - 5
4545(chain D and resid 6:11)DT6 - 116 - 11
4646(chain D and resid 12:19)DT12 - 1912 - 19
4747(chain D and resid 20:25)DT20 - 2520 - 25
4848(chain D and resid 26:31)DT26 - 3126 - 31
4949(chain D and resid 32:37)DT32 - 3732 - 37
5050(chain D and resid 38:43)DT38 - 4338 - 43
5151(chain D and resid 44:55)DT44 - 5544 - 55
5252(chain D and resid 56:63)DT56 - 6356 - 63
5353(chain D and resid 64:68)DT64 - 6864 - 68
5454(chain D and resid 69:76)DT69 - 7669 - 76
5555(chain E and resid 1:7)EV1 - 71 - 7
5656(chain E and resid 8:13)EV8 - 138 - 13
5757(chain E and resid 14:18)EV14 - 1814 - 18
5858(chain E and resid 19:30)EV19 - 3019 - 30
5959(chain E and resid 31:37)EV31 - 3731 - 37
6060(chain E and resid 38:43)EV38 - 4338 - 43
6161(chain E and resid 44:49)EV44 - 4944 - 49
6262(chain E and resid 50:54)EV50 - 5450 - 54
6363(chain E and resid 55:63)EV55 - 6355 - 63
6464(chain E and resid 64:70)EV64 - 7064 - 70
6565(chain E and resid 71:76)EV71 - 7671 - 76
6666(chain F and resid 1:7)FY1 - 71 - 7
6767(chain F and resid 8:13)FY8 - 138 - 13
6868(chain F and resid 14:20)FY14 - 2014 - 20
6969(chain F and resid 21:29)FY21 - 2921 - 29
7070(chain F and resid 30:34)FY30 - 3430 - 34
7171(chain F and resid 35:40)FY35 - 4035 - 40
7272(chain F and resid 41:45)FY41 - 4541 - 45
7373(chain F and resid 46:51)FY46 - 5146 - 51
7474(chain F and resid 52:57)FY52 - 5752 - 57
7575(chain F and resid 58:70)FY58 - 7058 - 70
7676(chain F and resid 71:76)FY71 - 7671 - 76

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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://pdbjlvh1.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