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- PDB-8eaz: HOIL-1/E2-Ub/Ub transthiolation complex -

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基本情報

登録情報
データベース: PDB / ID: 8eaz
タイトルHOIL-1/E2-Ub/Ub transthiolation complex
要素
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 L3
キーワードLIGASE / LUBAC / ubiquitin / transthiolation / 2Zn-6Cys ZF / RBR
機能・相同性
機能・相同性情報


protein linear polyubiquitination / LUBAC complex / cell cycle phase transition / ubiquitin-protein transferase activator activity / cytoplasmic sequestering of protein / RBR-type E3 ubiquitin transferase / ubiquitin ligase activator activity / negative regulation of necroptotic process / protein K11-linked ubiquitination / positive regulation of extrinsic apoptotic signaling pathway ...protein linear polyubiquitination / LUBAC complex / cell cycle phase transition / ubiquitin-protein transferase activator activity / cytoplasmic sequestering of protein / RBR-type E3 ubiquitin transferase / ubiquitin ligase activator activity / negative regulation of necroptotic process / protein K11-linked ubiquitination / positive regulation of extrinsic apoptotic signaling pathway / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / negative regulation of NF-kappaB transcription factor activity / cellular response to steroid hormone stimulus / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / 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 / protein sequestering activity / 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) / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / 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
類似検索 - 分子機能
: / : / : / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / : ...: / : / : / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / : / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / 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 / Ubiquitin-conjugating enzyme E2 L3 / RanBP-type and C3HC4-type zinc finger-containing protein 1
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: 3.08 Å
データ登録者Wang, X.S. / 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)GNT1182757 オーストラリア
引用
ジャーナル: Nat Commun / 年: 2023
タイトル: The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family.
著者: Wang, X.S. / Cotton, T.R. / Trevelyan, S.J. / Richardson, L.W. / Lee, W.T. / Silke, J. / Lechtenberg, B.C.
#1: ジャーナル: Biorxiv / 年: 2022
タイトル: The unifying catalytic mechanism of the RING-between-RING E3 ligase family
著者: Wang, X.S. / Cotton, T.R. / Trevelyan, S.J. / Richardson, L.W. / Lee, W.T. / Silke, J. / Lechtenberg, B.C.
履歴
登録2022年8月30日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年1月18日Provider: repository / タイプ: Initial release
改定 1.12023年10月25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: RanBP-type and C3HC4-type zinc finger-containing protein 1
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
C: Ubiquitin-conjugating enzyme E2 L3
D: Ubiquitin-conjugating enzyme E2 L3
E: Ubiquitin
F: Ubiquitin
G: Ubiquitin
H: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,01722
ポリマ－134,1018
非ポリマー91614
水1448
1
A: RanBP-type and C3HC4-type zinc finger-containing protein 1
C: Ubiquitin-conjugating enzyme E2 L3
E: Ubiquitin
G: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,50811
ポリマ－67,0514
非ポリマー4587
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: RanBP-type and C3HC4-type zinc finger-containing protein 1
D: Ubiquitin-conjugating enzyme E2 L3
F: Ubiquitin
H: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,50811
ポリマ－67,0514
非ポリマー4587
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)83.953, 95.478, 115.006
Angle α, β, γ (deg.)90.000, 110.575, 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 266 through 510 or resid 1001 through 1007))
d_2ens_1chain "B"
d_1ens_2chain "C"
d_2ens_2chain "D"
d_1ens_3(chain "E" and resid 1 through 75)
d_2ens_3(chain "F" and resid 1 through 75)
d_3ens_3chain "G"
d_4ens_3(chain "H" and resid 1 through 75)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALHISA10 - 254
d_12ens_1ZNZNB
d_13ens_1ZNZNC
d_14ens_1ZNZND
d_15ens_1ZNZNE
d_16ens_1ZNZNF
d_17ens_1ZNZNG
d_21ens_1VALHISI1 - 245
d_22ens_1ZNZNJ
d_23ens_1ZNZNK
d_24ens_1ZNZNL
d_25ens_1ZNZNM
d_26ens_1ZNZNN
d_27ens_1ZNZNO
d_11ens_2ALAVALQ1 - 152
d_21ens_2ALAVALR1 - 152
d_11ens_3METGLYS1 - 75
d_21ens_3METGLYT1 - 75
d_31ens_3METGLYU1 - 75
d_41ens_3METGLYV1 - 75

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.70999148393, -0.0651406211065, -0.70119098128), (-0.0694122145536, -0.997337236382, 0.0223692064438), (-0.700781019447, 0.0327892727583, -0.712622499206)9.23543856975, -19.3324423388, 24.7845551981
2given(0.716871124806, -0.0786542741407, -0.692754859657), (-0.0843470293583, -0.996102049768, 0.0258124986568), (-0.692084799037, 0.0399275795395, -0.720711051209)9.42950167926, -19.5465832875, 25.0268212813
3given(0.7275051433, -0.0530115491658, -0.68405119847), (-0.0528974614976, -0.998376733975, 0.0211129255302), (-0.684060030289, 0.0208248100201, -0.729128385298)9.89893113292, -18.8373555733, 25.1243459151
4given(-0.682176786498, -0.458973966549, 0.569190416287), (0.505464347648, 0.266468073898, 0.820670798097), (-0.528337605343, 0.847548030275, 0.0502166422329)-78.1190103514, -26.0362299876, 0.214807062709
5given(-0.128691286039, -0.936958770175, 0.324879694486), (-0.445992721192, -0.23792099916, -0.86283491515), (0.885736442482, -0.255933313874, -0.387258432197)-44.3289734595, 12.2773856435, 78.9264618716

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要素

#1: タンパク質 RanBP-type and C3HC4-type zinc finger-containing protein 1 / HBV-associated factor 4 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / Hepatitis B virus X- ...HBV-associated factor 4 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / Hepatitis B virus X-associated protein 4 / RING finger protein 54 / RING-type E3 ubiquitin transferase HOIL-1 / Ubiquitin-conjugating enzyme 7-interacting protein 3


分子量: 31770.006 Da / 分子数: 2 / 変異: C460A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RBCK1, C20orf18, RNF54, UBCE7IP3, XAP3, XAP4 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q9BYM8
#2: タンパク質 Ubiquitin-conjugating enzyme E2 L3 / E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin- ...E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


分子量: 18126.848 Da / 分子数: 2 / 変異: C86K / 由来タイプ: 組換発現
詳細: The K86 residue forms an isopeptide bond with the C-terminus of ubiquitin.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2L3, UBCE7, UBCH7 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P68036
#3: 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: The C-terminus of ubiquitin in chains E and F is covalently linked to the UbcH7 K86 side-chains in chains C and D, respectively. Ubiquitin in chains G,H: SDS-PAGE analysis shows that the ...詳細: The C-terminus of ubiquitin in chains E and F is covalently linked to the UbcH7 K86 side-chains in chains C and D, respectively. Ubiquitin in chains G,H: SDS-PAGE analysis shows that the crystals contain a mixture of mono-ubiquitin and M1-linked di-ubiquitin. Clear density is visible for two mono-ubiquitin molecules only.
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
#4: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 14 / 由来タイプ: 合成 / 式: Zn
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 8 / 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: 3.22 Å3/Da / 溶媒含有率: 61.78 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.2
詳細: 28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2

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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: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年9月27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: 0.9537 Å / 相対比: 1
反射解像度: 3.08→47.74 Å / Num. obs: 31532 / % possible obs: 99.5 % / 冗長度: 3.5 % / Biso Wilson estimate: 86.12 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.23 / Χ2: 0.95 / Net I/σ(I): 4.3
反射 シェル解像度: 3.08→3.25 Å / 冗長度: 3.6 % / Rmerge(I) obs: 2.624 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4460 / CC1/2: 0.397 / Χ2: 0.97 / % possible all: 96.9

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解析

ソフトウェア
名称バージョン分類
XDSVERSION Feb 5, 2021データ削減
Aimless0.7.4データスケーリング
PHASER2.8.3位相決定
Coot0.9.6モデル構築
PHENIX1.19.2_4158精密化
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 4Q5E, AlphaFold

4q5e


解像度: 3.08→47.74 Å / SU ML: 0.5503 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 33.2876
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2664 1484 4.74 %
Rwork0.2316 29849 -
obs0.2333 31333 99.07 %
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: 110.79 Å2
精密化ステップサイクル: LAST / 解像度: 3.08→47.74 Å
タンパク質核酸リガンド溶媒全体
原子数8791 0 14 8 8813
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00178959
X-RAY DIFFRACTIONf_angle_d0.462512105
X-RAY DIFFRACTIONf_chiral_restr0.04131337
X-RAY DIFFRACTIONf_plane_restr0.00371592
X-RAY DIFFRACTIONf_dihedral_angle_d3.65771186
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.586153349169
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.680558210059
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.837091174092
ens_3d_3DX-RAY DIFFRACTIONTorsion NCS1.41107410184
ens_3d_4EX-RAY DIFFRACTIONTorsion NCS1.32995744219
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.180.45491260.42082552X-RAY DIFFRACTION93.15
3.18-3.290.39121260.36632686X-RAY DIFFRACTION99.26
3.3-3.430.35261230.32712734X-RAY DIFFRACTION99.44
3.43-3.580.35511570.30572680X-RAY DIFFRACTION99.54
3.58-3.770.30981540.25682691X-RAY DIFFRACTION99.72
3.77-4.010.29221080.23672769X-RAY DIFFRACTION99.83
4.01-4.320.27611090.21812730X-RAY DIFFRACTION99.61
4.32-4.750.22171270.19292738X-RAY DIFFRACTION99.86
4.75-5.440.24051330.19382742X-RAY DIFFRACTION99.79
5.44-6.850.25161570.21942746X-RAY DIFFRACTION99.9
6.85-47.740.20441640.18842781X-RAY DIFFRACTION99.66
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)
10.0850941503842-0.0007747795404410.02023895256440.2837917924650.1434411614950.0746410381846-1.025533973970.9871776036230.1496822259041.31545121635-0.0952006590832-2.44166932120.442020439244-0.1289709150770.00312421534392.153900727680.314150874548-0.186023943311.6049959495-0.1324819767581.3322167372-17.2843321486-26.7921640257-38.4110864326
20.7622365665811.076631648710.05004720047263.027250120660.9723531665770.9432260387040.5351269382130.720574975661-0.531546625962-1.32956701961-0.290125641561-0.384404187719-0.3478295768510.02691215362922.23623861040.6945297017880.3433078886290.3731465591651.58139505631-0.3817024413091.10624460382-7.82606829538-26.8683669557-20.553965783
31.12681540889-0.3568629995040.3553142862440.3011197344020.1908170990981.35167026060.2963682533910.598093170046-0.0349460970901-0.5723670209520.06873692075890.1551695524410.2332094433140.8081719357960.0002174509916161.163517869450.298004561201-0.07532493861581.35694017816-0.1636747115140.94671886999-14.4251913978-24.1813059507-14.175493108
41.937222268211.365551930281.765983566994.11988543619-1.824617382264.5698014877-0.0541519474927-0.464571322205-0.0883544804673-0.1078336135460.0960309265202-0.09131956918971.04299629657-0.0724893374090.002571960617351.60264296282-0.0221337748048-0.205025207330.552744557927-0.1345427680310.95130104797-37.1608152643-34.21769347021.80659675462
50.0278088911964-0.08338808710540.04493815052820.1622902588720.02563928228790.9523268470040.0249866200658-0.3413502728410.2471845035310.8103784455280.02635478458690.1788081818861.21369342427-1.3594762276-0.01215904445861.63088479394-0.129317244037-0.1732174549730.8770676995470.1122804905380.925780004965-45.7300382605-38.824130793220.9789660382
62.568746142741.537386454082.099334941574.161432542220.4906256754391.839463886490.0375235627085-0.217526798534-0.008487379201970.09489759783680.3078496511690.0211400643353-0.0037456892668-0.09945290579080.0008921269710380.8210187879390.01909789949340.01620003402480.5108547218790.002718746573680.76334376718-29.7784588006-16.954770089515.0485454148
71.03907376094-0.203827896331-0.2658014488321.40159657963-0.02856401044990.781679101718-0.1268211427420.5282022858750.506426605055-0.248354657948-0.4099743004980.117006739588-0.09719189531020.355808933068-0.0007603071740381.285600357030.176002669077-0.1785091485830.776292656169-0.00955715586750.934990030443-32.7101084856-2.367967413534.36966648032
80.615234305143-0.3683402840710.1399816629032.29138706419-0.8015695886651.07699667430.1515948241390.851438119040.08716913679020.732934319885-0.209655424317-0.440395736617-0.1106467898290.9435587208880.008191176820590.848318491154-0.312373948805-0.1358022078511.80179792029-0.2610253088781.3009807275719.19698965557.2409589880245.9010527702
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精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 257 through 268 )AA257 - 2681 - 12
22chain 'A' and (resid 269 through 288 )AA269 - 28813 - 32
33chain 'A' and (resid 289 through 346 )AA289 - 34633 - 90
44chain 'A' and (resid 347 through 399 )AA347 - 39991 - 143
55chain 'A' and (resid 400 through 425 )AA400 - 425144 - 169
66chain 'A' and (resid 426 through 478 )AA426 - 478170 - 222
77chain 'A' and (resid 479 through 510 )AA479 - 510223 - 254
88chain 'B' and (resid 266 through 305 )BI266 - 3051 - 40
99chain 'B' and (resid 306 through 346 )BI306 - 34641 - 81
1010chain 'B' and (resid 347 through 378 )BI347 - 37882 - 113
1111chain 'B' and (resid 379 through 440 )BI379 - 440114 - 175
1212chain 'B' and (resid 441 through 510 )BI441 - 510176 - 245
1313chain 'C' and (resid 2 through 17 )CQ2 - 171 - 16
1414chain 'C' and (resid 18 through 27 )CQ18 - 2717 - 26
1515chain 'C' and (resid 28 through 75 )CQ28 - 7527 - 74
1616chain 'C' and (resid 76 through 100 )CQ76 - 10075 - 99
1717chain 'C' and (resid 101 through 132 )CQ101 - 132100 - 131
1818chain 'C' and (resid 133 through 153 )CQ133 - 153132 - 152
1919chain 'D' and (resid 2 through 17 )DR2 - 171 - 16
2020chain 'D' and (resid 18 through 49 )DR18 - 4917 - 48
2121chain 'D' and (resid 50 through 66 )DR50 - 6649 - 65
2222chain 'D' and (resid 67 through 75 )DR67 - 7566 - 74
2323chain 'D' and (resid 76 through 100 )DR76 - 10075 - 99
2424chain 'D' and (resid 101 through 113 )DR101 - 113100 - 112
2525chain 'D' and (resid 114 through 132 )DR114 - 132113 - 131
2626chain 'D' and (resid 133 through 153 )DR133 - 153132 - 152
2727chain 'E' and (resid 1 through 22 )ES1 - 221 - 22
2828chain 'E' and (resid 23 through 45 )ES23 - 4523 - 45
2929chain 'E' and (resid 46 through 65 )ES46 - 6546 - 65
3030chain 'E' and (resid 66 through 76 )ES66 - 7666 - 76
3131chain 'F' and (resid 1 through 22 )FT1 - 221 - 22
3232chain 'F' and (resid 23 through 50 )FT23 - 5023 - 50
3333chain 'F' and (resid 51 through 71 )FT51 - 7151 - 71
3434chain 'F' and (resid 72 through 76 )FT72 - 7672 - 76
3535chain 'G' and (resid 1 through 7 )GU1 - 71 - 7
3636chain 'G' and (resid 8 through 16 )GU8 - 168 - 16
3737chain 'G' and (resid 17 through 34 )GU17 - 3417 - 34
3838chain 'G' and (resid 35 through 44 )GU35 - 4435 - 44
3939chain 'G' and (resid 45 through 54 )GU45 - 5445 - 54
4040chain 'G' and (resid 55 through 59 )GU55 - 5955 - 59
4141chain 'G' and (resid 60 through 75 )GU60 - 7560 - 75
4242chain 'H' and (resid 1 through 7 )HV1 - 71 - 7
4343chain 'H' and (resid 8 through 16 )HV8 - 168 - 16
4444chain 'H' and (resid 17 through 22 )HV17 - 2217 - 22
4545chain 'H' and (resid 23 through 34 )HV23 - 3423 - 34
4646chain 'H' and (resid 35 through 44 )HV35 - 4435 - 44
4747chain 'H' and (resid 45 through 49 )HV45 - 4945 - 49
4848chain 'H' and (resid 50 through 54 )HV50 - 5450 - 54
4949chain 'H' and (resid 55 through 71 )HV55 - 7155 - 71
5050chain 'H' and (resid 72 through 76 )HV72 - 7672 - 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