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- PDB-7ojx: E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING ... -

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基本情報

登録情報
データベース: PDB / ID: 7ojx
タイトルE2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis
要素
  • (Polyubiquitin- ...) x 3
  • E3 ubiquitin-protein ligase RNF38
  • Ubiquitin-conjugating enzyme E2 K
キーワードLIGASE / UBIQUITIN / RING E3 / E2
機能・相同性
機能・相同性情報


free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein monoubiquitination / fat pad development ...free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / ubiquitin conjugating enzyme activity / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / sperm flagellum / protein K48-linked ubiquitination / energy homeostasis / cellular response to interferon-beta / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / positive regulation of protein ubiquitination / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4
類似検索 - 分子機能
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ring finger domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ring finger domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) / Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 K / E3 ubiquitin-protein ligase RNF38
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: 2.4 Å
データ登録者Majorek, K.A. / Nakasone, M.A. / Huang, D.T.
資金援助European Union, 英国, 2件
組織認可番号国
European Research Council (ERC)647849European Union
Cancer Research UKA23278/A29256 英国
引用ジャーナル: Nat.Chem.Biol. / 年: 2022
タイトル: Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension.
著者: Nakasone, M.A. / Majorek, K.A. / Gabrielsen, M. / Sibbet, G.J. / Smith, B.O. / Huang, D.T.
履歴
登録2021年5月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年1月12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 / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.22022年2月23日Group: Author supporting evidence / カテゴリ: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.grant_number
改定 1.32022年4月13日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.42024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.52024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: E3 ubiquitin-protein ligase RNF38
B: Ubiquitin-conjugating enzyme E2 K
C: Polyubiquitin-B
D: Polyubiquitin-B
E: Polyubiquitin-B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)57,9938
ポリマ－57,6425
非ポリマー3513
水90150
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-25 kcal/mol
Surface area23260 Å2
単位格子
Length a, b, c (Å)85.835, 85.835, 167.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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要素

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タンパク質 , 2種, 2分子 AB

#1: タンパク質 E3 ubiquitin-protein ligase RNF38 / RING finger protein 38 / RING-type E3 ubiquitin transferase RNF38


分子量: 9135.328 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RNF38 / プラスミド: pRSF-DUET1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q9H0F5, RING-type E3 ubiquitin transferase
#2: タンパク質 Ubiquitin-conjugating enzyme E2 K / E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier ...E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier protein / Ubiquitin-conjugating enzyme E2-25 kDa / Ubiquitin-conjugating enzyme E2(25K) / Ubiquitin-conjugating enzyme E2-25K / Ubiquitin-protein ligase


分子量: 22600.762 Da / 分子数: 1 / Mutation: C92K, K97R, D124C, C170S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2K, HIP2, LIG / プラスミド: pRSF-DUET1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61086, E2 ubiquitin-conjugating enzyme

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Polyubiquitin- ... , 3種, 3分子 CDE

#3: タンパク質 Polyubiquitin-B


分子量: 8778.012 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / プラスミド: pRSF-DUET1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0CG47
#4: タンパク質 Polyubiquitin-B


分子量: 8550.794 Da / 分子数: 1 / Mutation: K48C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / プラスミド: pRSF-DUET1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0CG47
#5: タンパク質 Polyubiquitin-B


分子量: 8576.831 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / プラスミド: pRSF-DUET1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0CG47

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非ポリマー , 3種, 53分子

#6: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#7: 化合物 ChemComp-ME7 / 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)


分子量: 220.182 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H8N2O4
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 50 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.1 Å3/Da / 溶媒含有率: 60.35 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: Crystals were grown in: 0.2 M sodium citrate, 0.1 M Bis Tris propane 7.5 and 20 % (w/v) PEG 3350. The crystallization drops were set as a 1:1 mixture of the protein complex solution and the precipitant solution.

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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: Diamond / ビームライン: I04-1 / 波長: 0.9119 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2020年2月9日
放射モノクロメーター: M / 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: 0.9119 Å / 相対比: 1
反射解像度: 2.4→74.34 Å / Num. obs: 28670 / % possible obs: 100 % / 冗長度: 8.6 % / Biso Wilson estimate: 62.67 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Net I/σ(I): 19.1 / Num. measured all: 246998
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
2.4-2.448.80.714190.371.10299.9
6.51-74.377.974.415870.0120.034100

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解析

ソフトウェア
名称バージョン分類
xia2データスケーリング
PHENIX1.17.1_3660精密化
PDB_EXTRACT3.27データ抽出
DIALSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1YLA, 1UBQ, 4V3L

1yla

1ubq

4v3l


解像度: 2.4→74.34 Å / SU ML: 0.37 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 26 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.236 1412 4.93 %
Rwork0.1878 27214 -
obs0.1902 28626 99.96 %
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 max: 237.02 Å2 / Biso mean: 94.6641 Å2 / Biso min: 42.81 Å2
精密化ステップサイクル: final / 解像度: 2.4→74.34 Å
タンパク質核酸リガンド溶媒全体
原子数3663 0 18 50 3731
Biso mean--112.88 75.34 -
残基数----488
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.490.3491590.297326322791
2.49-2.590.36041250.317427132838
2.59-2.70.35271490.285426662815
2.7-2.850.26851270.257927032830
2.85-3.020.32791360.266226862822
3.02-3.260.29211180.254427092827
3.26-3.590.2841600.214127212881
3.59-4.10.23251510.174827202871
4.1-5.170.19351440.141827492893
5.17-74.340.18531430.154629153058
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)
10.5691-1.5826-0.78184.44432.25491.15820.0595-0.414-1.29951.328-2.1989-4.05290.41663.52581.98820.99520.0165-0.44811.35690.31551.3276-28.98442.88275.2108
23.98813.79915.24334.40865.22696.89430.1529-0.9906-1.41250.1093-0.5412-1.41071.3031-0.84540.37681.21040.1488-0.16970.60310.03220.8694-41.0668-11.53244.1523
3-0.0040.0278-0.04751.2417-2.40474.67541.7485-0.98422.2382-1.3057-0.5265-1.55081.6306-1.0605-0.83261.5603-0.1812-0.25310.57350.11681.4072-47.2277-5.92247.0561
44.59343.0787-3.90397.6339-0.10417.92270.0842-0.173-0.5847-0.36520.33230.89230.4839-0.2201-0.49450.82510.1019-0.0870.8090.10860.6751-46.5274-1.5579-3.8999
52.423-0.0382-0.5945.03025.08415.25320.56180.5387-0.6772-0.9522-0.2542-0.62211.1711-0.7213-0.64890.99230.0833-0.11770.5561-0.07370.8234-38.8953-6.78480.0751
65.8259-4.4223.43863.418-2.97442.421-0.36920.47850.5840.9822-0.2196-1.0624-0.1224-0.54030.70620.77290.0519-0.11330.5343-0.01750.7288-37.98593.73780.783
79.51283.6787-4.67638.08993.29548.9026-0.6063-0.47050.67150.52870.4424-0.7091-0.21140.0860.28010.95190.1042-0.15150.54550.04120.8144-38.733211.1774.2704
82.7121.93083.46123.5117-0.46428.49671.03910.7066-0.4671-1.0347-0.80760.44530.8908-0.1722-0.32371.2871-0.0637-0.1290.6409-0.06440.7627-48.78572.9196-13.6469
93.1688-4.09910.18848.734.22098.85560.01330.0762-0.4764-0.8130.50780.3280.28570.3805-0.22651.003-0.1248-0.19060.78270.0270.7417-57.305212.6503-17.6248
102.75561.62562.63433.93564.02774.6719-0.3991-1.0760.03450.56260.10722.12870.9846-1.8540.23230.68340.02080.06760.80430.09670.8867-65.486227.7197-6.8556
117.5093-3.18036.05187.7205-5.45476.2459-0.12010.51830.1976-0.3807-0.3836-0.58060.69810.33990.41590.72320.09830.00730.4995-0.07540.4488-47.765215.1142-15.1373
123.0727-1.0346-1.62182.7279-0.85181.49050.0547-0.0597-0.2139-0.19830.28060.55260.15230.535-0.35080.5338-0.0051-0.02450.68010.05130.4082-52.441329.1032-15.1611
136.1902-5.29580.77046.9097-1.44678.52450.1531-0.3984-0.25530.6807-0.0218-0.05390.74470.1679-0.19520.68750.0057-0.0990.45510.04220.4662-49.532118.4169-6.376
143.4973.8926-0.6125.24191.64417.0358-0.0355-0.89830.48841.08220.55990.16390.21260.7319-0.58170.570.1282-0.00150.72510.07830.4674-49.630133.1516-4.4819
155.20884.167-5.17963.4602-4.02085.22720.6177-1.2194-0.04421.4659-0.5194-0.1551-1.1615-0.3483-0.09150.6492-0.02040.01980.67770.04230.5406-53.772141.3496-6.0783
168.48512.48814.33974.75296.24878.5691-0.031-0.3873-0.30830.34530.03781.02050.0759-0.7349-0.00060.59650.0578-0.02980.71990.16960.5717-63.356336.6514-12.5878
174.8896-3.90630.94633.1472-1.07052.0893-0.22530.4530.25910.13280.72670.3838-0.2068-0.6998-0.53640.58210.0394-0.06710.80810.04330.7529-68.041642.2909-19.3025
187.5334-1.9863.09138.6588-4.75373.10540.1860.69480.6032-0.4468-0.3671-0.36530.10560.79880.23680.64620.0831-0.02750.63190.13330.6169-57.236147.0394-22.3489
198.48353.9503-1.11886.0148-2.4547.5484-0.70080.7312-0.3313-0.13981.2582-0.3632.0537-2.6203-0.33111.0034-0.10040.2940.82480.38451.5482-65.46226.67815.7983
202.96361.54351.54531.20440.19611.6842-1.57741.8642-5.198-3.18481.6722-3.37921.8130.63390.3611.044-0.13140.50151.2784-0.69232.5763-54.75114.63660.5438
215.2597-6.53530.07878.38460.7942.83130.1175-1.7399-0.67791.06840.80113.2299-1.9853-0.8024-0.73531.69650.31210.61381.0940.15941.2879-65.60769.688712.1871
227.4262-4.19054.74682.4391-2.69453.25960.2802-1.3907-1.38153.57170.84011.2645-1.03390.1579-1.18821.65060.2460.15940.76070.13070.8441-57.572711.355512.8569
234.6344-4.3195-2.54236.5428-0.2534.1861-1.28-0.5954-0.21361.73851.4019-0.7566-2.3517-0.2435-0.29811.80870.2789-0.2090.8266-0.20781.0516-50.553111.05359.0497
244.6855-4.9473-4.37445.12714.58174.3589-0.25-0.60570.6177-0.49121.31780.7107-2.14760.7368-0.98751.15210.09240.06850.77810.09311.176-60.745819.47544.632
259.2643.5124-2.81173.53571.373.6950.7183-0.4693-1.2021-0.16190.20163.0604-0.1778-0.8784-0.7721.01160.1780.04131.13220.46221.9091-69.886315.67467.1441
265.50865.2478-6.10685.111-5.64058.434-0.46791.06191.3613-0.01260.97351.5181-0.20850.2808-0.3640.7573-0.06480.04360.66860.07040.9997-53.70617.72270.4106
277.15025.0972-3.96829.6066-1.1727.6566-0.51190.13870.6846-0.79520.3933-0.4478-0.51570.20380.11780.59820.02380.01160.77120.22570.7598-34.401244.8589-22.2035
287.6778-2.78292.88047.27090.74128.6070.09490.854-0.3927-1.0259-0.2261-0.27110.08640.98870.090.62250.03640.03620.90030.22450.6615-30.236135.6255-22.5965
299.57815.29522.60498.0845.26143.80440.1991-0.9338-0.42630.1627-0.2679-0.24360.6509-0.18550.0150.70060.0057-0.02960.83280.1050.7288-38.184236.4744-12.9932
305.76735.6134-5.01215.4242-4.86784.35320.06270.5531.3588-0.29840.10181.6074-0.6825-0.4208-0.16630.59940.0335-0.0750.57360.08030.7977-43.054644.2609-16.1953
315.3131-1.097-5.02885.12865.45338.7452-0.4672-3.23630.6193-0.620.8892-1.2612-0.17941.707-0.42640.51470.0301-0.0160.96550.39710.8283-28.94942.1363-15.486
325.0545-4.4142-5.08955.15951.6112.00251.87631.4228-5.52923.37820.991-6.82741.16011.0749-1.87991.8598-0.0705-0.06751.1951-0.40222.4346-19.464329.7078-15.8416
334.5636-4.01315.13623.7527-5.06947.5146-0.67610.434-0.30381.46791.48080.7486-0.2567-2.1247-0.72581.4868-0.21270.0581.25180.17090.9499-28.104316.1478-18.7744
342.00119.121-2.93831.9989-5.0693.0416-0.0465-1.0012-2.0465-0.8031-0.5683-0.75091.3135-5.10910.70511.9831-0.4338-0.19482.54080.56451.0827-27.356915.994-31.703
351.89732.6336-1.66039.648-0.20495.49440.5102-0.01340.8981.14450.33721.5335-1.1235-0.9241-0.52291.3289-0.36230.03381.55940.4911.578-26.081511.7367-15.6276
365.1913.21470.72953.68552.13393.2081-0.4151.3167-2.0143-1.85881.69262.16652.9924-2.22960.13772.8625-1.52460.42360.75360.6811.9665-22.03326.149-20.8553
373.47093.76884.06794.46974.3774.64750.9264-0.4118-1.87650.6383-1.0803-1.49663.63930.3107-0.21381.7971-0.02440.13980.90750.19291.3019-16.506514.2486-24.3736
386.8257.02283.79129.23062.31793.46110.6617-1.11421.3072-0.1259-0.8493-3.57571.6892-1.63190.26721.34080.13280.09111.1470.31081.1445-18.612717.0214-13.7596
393.9878-3.51090.19216.41413.36164.0703-0.17280.28481.9568-1.10961.2672-1.12791.4711-0.4333-1.24071.2044-0.26610.25931.11320.19971.1418-18.960216.5613-26.4376
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 392 through 397 )A392 - 397
2X-RAY DIFFRACTION2chain 'A' and (resid 398 through 405 )A398 - 405
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 410 )A406 - 410
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 420 )A411 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 428 )A421 - 428
6X-RAY DIFFRACTION6chain 'A' and (resid 429 through 446 )A429 - 446
7X-RAY DIFFRACTION7chain 'A' and (resid 447 through 459 )A447 - 459
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 18 )B1 - 18
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 44 )B19 - 44
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 54 )B45 - 54
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 71 )B55 - 71
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 90 )B72 - 90
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 117 )B91 - 117
14X-RAY DIFFRACTION14chain 'B' and (resid 118 through 127 )B118 - 127
15X-RAY DIFFRACTION15chain 'B' and (resid 128 through 137 )B128 - 137
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 153 )B138 - 153
17X-RAY DIFFRACTION17chain 'B' and (resid 154 through 171 )B154 - 171
18X-RAY DIFFRACTION18chain 'B' and (resid 172 through 200 )B172 - 200
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 6 )C1 - 6
20X-RAY DIFFRACTION20chain 'C' and (resid 7 through 12 )C7 - 12
21X-RAY DIFFRACTION21chain 'C' and (resid 13 through 22 )C13 - 22
22X-RAY DIFFRACTION22chain 'C' and (resid 23 through 32 )C23 - 32
23X-RAY DIFFRACTION23chain 'C' and (resid 33 through 40 )C33 - 40
24X-RAY DIFFRACTION24chain 'C' and (resid 41 through 54 )C41 - 54
25X-RAY DIFFRACTION25chain 'C' and (resid 55 through 65 )C55 - 65
26X-RAY DIFFRACTION26chain 'C' and (resid 66 through 76 )C66 - 76
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 22 )D1 - 22
28X-RAY DIFFRACTION28chain 'D' and (resid 23 through 44 )D23 - 44
29X-RAY DIFFRACTION29chain 'D' and (resid 45 through 56 )D45 - 56
30X-RAY DIFFRACTION30chain 'D' and (resid 57 through 65 )D57 - 65
31X-RAY DIFFRACTION31chain 'D' and (resid 66 through 71 )D66 - 71
32X-RAY DIFFRACTION32chain 'D' and (resid 72 through 76 )D72 - 76
33X-RAY DIFFRACTION33chain 'E' and (resid 1 through 6 )E1 - 6
34X-RAY DIFFRACTION34chain 'E' and (resid 7 through 11 )E7 - 11
35X-RAY DIFFRACTION35chain 'E' and (resid 12 through 22 )E12 - 22
36X-RAY DIFFRACTION36chain 'E' and (resid 23 through 34 )E23 - 34
37X-RAY DIFFRACTION37chain 'E' and (resid 35 through 49 )E35 - 49
38X-RAY DIFFRACTION38chain 'E' and (resid 50 through 65 )E50 - 65
39X-RAY DIFFRACTION39chain 'E' and (resid 66 through 72 )E66 - 72

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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