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- PDB-7m2k: CDC34A-Ubiquitin-2ab inhibitor complex -

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基本情報

登録情報
データベース: PDB / ID: 7m2k
タイトルCDC34A-Ubiquitin-2ab inhibitor complex
要素
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 R1
キーワードTRANSFERASE / Ubiquitin / Ube2R1 / Ubiquitin conjugating enzyme / inhibitor
機能・相同性
機能・相同性情報


positive regulation of inclusion body assembly / (E3-independent) E2 ubiquitin-conjugating enzyme / response to growth factor / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / female gonad development ...positive regulation of inclusion body assembly / (E3-independent) E2 ubiquitin-conjugating enzyme / response to growth factor / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / DNA replication initiation / protein K48-linked ubiquitination / cellular response to interferon-beta / energy homeostasis / regulation of neuron apoptotic process / 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 / 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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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 / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex
類似検索 - 分子機能
: / 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 / : ...: / 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
Chem-GZM / Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 R1
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: 2.47 Å
データ登録者Ceccarelli, D.F. / St-Cyr, D. / Tyers, M. / Sicheri, F.
資金援助 カナダ, 2件
組織認可番号国
Canadian Institutes of Health Research (CIHR)FDN-167277 カナダ
Canadian Institutes of Health Research (CIHR)FDN-143277 カナダ
引用ジャーナル: Sci Adv / 年: 2021
タイトル: Identification and optimization of molecular glue compounds that inhibit a noncovalent E2 enzyme-ubiquitin complex.
著者: St-Cyr, D. / Ceccarelli, D.F. / Orlicky, S. / van der Sloot, A.M. / Tang, X. / Kelso, S. / Moore, S. / James, C. / Posternak, G. / Coulombe-Huntington, J. / Bertomeu, T. / Marinier, A. / Sicheri, F. / Tyers, M.
履歴
登録2021年3月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年11月3日Provider: repository / タイプ: Initial release
改定 1.12021年11月10日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22023年10月18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

ダウンロードとリンク

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集合体

登録構造単位
A: Ubiquitin-conjugating enzyme E2 R1
B: Ubiquitin
C: Ubiquitin-conjugating enzyme E2 R1
D: Ubiquitin
E: Ubiquitin-conjugating enzyme E2 R1
F: Ubiquitin
G: Ubiquitin-conjugating enzyme E2 R1
H: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)119,42712
ポリマ－117,5738
非ポリマー1,8544
水48627
1
A: Ubiquitin-conjugating enzyme E2 R1
B: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,8573
ポリマ－29,3932
非ポリマー4631
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Ubiquitin-conjugating enzyme E2 R1
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,8573
ポリマ－29,3932
非ポリマー4631
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Ubiquitin-conjugating enzyme E2 R1
F: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,8573
ポリマ－29,3932
非ポリマー4631
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Ubiquitin-conjugating enzyme E2 R1
H: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,8573
ポリマ－29,3932
非ポリマー4631
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)55.800, 72.000, 76.500
Angle α, β, γ (deg.)70.140, 79.120, 80.420
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Ubiquitin-conjugating enzyme E2 R1 / (E3-independent) E2 ubiquitin-conjugating enzyme R1 / E2 ubiquitin-conjugating enzyme R1 / ...(E3-independent) E2 ubiquitin-conjugating enzyme R1 / E2 ubiquitin-conjugating enzyme R1 / Ubiquitin-conjugating enzyme E2-32 kDa complementing / Ubiquitin-conjugating enzyme E2-CDC34 / Ubiquitin-protein ligase R1


分子量: 20500.164 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDC34, UBCH3, UBE2R1 / プラスミド: PROEX / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P49427, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: タンパク質
Ubiquitin


分子量: 8893.206 Da / 分子数: 4 / 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: PETM30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0CG47
#3: 化合物
ChemComp-GZM / 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide


分子量: 463.397 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C24H28Cl2N2O3 / タイプ: SUBJECT OF INVESTIGATION
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 27 / 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Y

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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: 2.4 Å3/Da / 溶媒含有率: 48.74 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT

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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: APS / ビームライン: 24-ID-C / 波長: 0.97919 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年7月16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: 0.97919 Å / 相対比: 1
反射解像度: 2.47→67.3 Å / Num. obs: 34543 / % possible obs: 88.1 % / 冗長度: 2.1 % / Biso Wilson estimate: 63.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.044 / Rrim(I) all: 0.066 / Net I/σ(I): 8.1 / Num. measured all: 72984
反射 シェル

Diffraction-ID: 1 / 冗長度: 2.1 %

解像度 (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.47-2.530.839553626060.5150.761.1351.189
11.05-67.30.0238093800.9970.0210.03122.486.6

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
xia20.5.436-g557f8872-dials-1.7データ削減
XSCALE20171111データスケーリング
PHASER2.8.2位相決定
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 2OB4

2ob4


解像度: 2.47→67.3 Å / SU ML: 0.44 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 35.69 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2758 1767 5.12 %
Rwork0.2187 32767 -
obs0.2216 34534 88.06 %
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: 155.72 Å2 / Biso mean: 80.2926 Å2 / Biso min: 43.19 Å2
精密化ステップサイクル: final / 解像度: 2.47→67.3 Å
タンパク質核酸リガンド溶媒全体
原子数7196 0 124 27 7347
Biso mean--66.53 62.01 -
残基数----950
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.47-2.540.41821580.38352555271389
2.54-2.610.41911470.362476262388
2.61-2.70.38561400.33532539267989
2.7-2.790.47581410.34352485262686
2.79-2.90.35781400.29532444258487
2.9-3.040.41141190.28772666278592
3.04-3.20.36011540.27072519267389
3.2-3.40.32231310.26052486261786
3.4-3.660.28211340.2222461259586
3.66-4.030.2521170.19682616273390
4.03-4.610.23041210.17032426254785
4.61-5.810.20061630.17692584274791
5.81-67.30.22911020.1862510261287
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)
10.4602-0.02850.12960.2085-0.0150.10420.5461-0.12711.87130.4298-0.9305-0.36720.17830.54370.00120.6744-0.04670.25370.76640.0171.0906-58.19069.805322.673
20.28160.25660.54640.53430.61991.01170.0418-1.34340.08761.80750.2106-0.5470.36740.60070.04220.7104-0.01010.0630.752-0.04110.9351-59.3944-1.186729.9298
32.2514-1.93740.74673.10450.81591.32620.1452-0.14850.3737-0.1441-0.1853-0.47070.07730.3644-0.00040.6239-0.0321-0.02330.73960.0140.5189-57.0293-7.031424.9159
40.26820.23870.05030.16450.10540.06070.69581.26860.2661-0.292-0.05950.2525-2.00840.50670.00680.91510.04890.1470.69460.19410.9244-62.16616.481912.1706
50.17480.04730.00790.2575-0.35060.20360.27660.694-0.0858-1.11890.0648-0.62290.33040.36440.0010.6123-0.06340.00070.72820.0080.4656-58.5016-13.265618.1471
60.061-0.008-0.01570.04910.00570.11920.16241.62770.5744-1.2213-0.14610.0019-0.0241-0.22420.00340.7863-0.00330.06440.89760.10130.641-65.218-11.343214.0622
70.9688-0.4772-0.57220.0033-0.05210.54660.61990.75720.8073-1.2158-0.21360.7245-0.0491-0.51120.00050.81120.0264-0.00890.79070.05630.7317-70.1345-1.09519.0261
80.6261-0.2502-0.45990.46420.01370.49151.541.84490.0652-0.5866-1.04940.02550.503-1.99120.02330.6481-0.0438-0.12411.0528-0.04690.7908-73.2309-16.005314.8174
92.6263-1.3679-0.54933.3756-1.74272.119-0.0258-0.4241-0.3976-0.1141-0.10810.2710.1637-0.2464-0.00030.65170.0133-0.00540.68050.0050.6492-63.1912-22.569725.2388
100.99190.20280.3040.02270.02930.08370.0945-3.05271.41341.3920.17260.0889-0.5796-0.0936-0.00751.73220.2280.36761.27180.06921.0584-80.12530.666940.9451
110.4768-0.36990.27330.1027-0.27550.12140.3485-1.11071.62810.60250.4348-0.1785-0.14970.3741-01.09280.1150.44540.9045-0.14721.7194-79.44644.293533.1988
120.1527-0.3425-0.37690.54990.79440.84780.0952-1.04650.27221.05060.23351.7417-0.2512-0.1612-0.00140.82010.09240.2391.29680.10781.2499-87.2787-3.730934.6747
130.59050.1856-0.57990.76850.35930.8599-0.3465-0.50931.3728-0.0395-0.23960.38270.172-0.8852-0.00120.6857-0.0420.17920.73440.02621.1421-79.4244-6.413228.2718
140.2614-0.18740.02390.34270.05290.11-1.2221-0.5715-1.68731.26480.63750.70073.2623-2.1940.00291.143-0.03590.31651.55630.34290.9524-80.3763-12.920837.0154
150.0097-0.0076-0.04040.0169-0.00330.0595-0.79920.66940.28950.3186-0.1819-0.1207-0.75811.24470.00051.3897-0.09670.1721.1074-0.10840.8526-75.8481-3.778143.257
161.5145-0.1489-1.12570.6331-0.2740.85710.56930.08431.2094-0.9726-0.4798-0.31-0.4452-0.8378-0.00040.80360.05790.13270.78130.01710.8913-77.6257-4.721625.4658
170.38850.2195-0.45120.6515-0.55960.5346-0.08131.68060.3463-0.71760.2574-1.2871-0.80931.1645-0.00370.926-0.16690.01830.9350.07491.3132-37.9269-2.65656.6985
183.2292-0.9174-0.42162.46330.34712.62980.1482-0.01970.0812-0.11540.0764-0.6914-0.33790.53660.00030.72220.0189-0.0750.734-0.07080.7661-51.23564.574662.1676
190.1909-0.0207-0.29520.0683-0.0340.3113-0.7827-1.1409-0.68070.44910.6807-0.0830.5196-2.0561-0.00011.053-0.02850.06251.15990.15121.3797-50.7489-6.436472.8547
200.66641.11270.27031.5721-0.05430.22660.0239-0.5608-0.98310.5198-0.0887-0.05780.05770.21560.00010.82420.0325-0.11550.77690.03750.8418-54.159-4.756268.4558
212.2705-1.52631.65713.0218-0.00423.1137-0.4556-0.3168-0.2849-0.08710.1303-0.48450.1411-0.3264-0.00020.75630.0188-0.10010.6401-0.09460.7095-68.18777.863164.2395
220.3843-0.0892-0.36710.7901-0.61840.6926-0.28040.3378-1.3253-1.32650.3758-0.66540.2403-0.02940.00231.0668-0.10910.0790.8009-0.13630.8644-56.4232-20.390854.5094
230.0737-0.0154-0.08120.00120.02340.0697-0.6615-0.72840.7288-0.66180.58430.7199-0.3152-0.9626-0.00051.2728-0.11710.22831.2958-0.22031.093-70.8343-22.236453.5504
240.57360.0813-0.23190.2189-0.0090.5691-0.4054-0.4737-0.7140.68680.5552-0.28180.3630.08020.00070.92170.042-0.01850.76820.09921.048-62.019-21.143363.8669
250.018-0.11780.16270.3853-0.05080.34080.4891-0.03740.25870.0007-0.07791.9541-0.3502-1.27450.00020.9017-0.0622-0.12390.8226-0.12161.1304-69.045-12.074157.2485
260.0548-0.02380.0010.0585-0.04750.0260.0558-0.80270.997-0.03390.35390.4537-0.9666-0.18260.00091.5814-0.094-0.00810.9695-0.04660.7207-64.3925-15.69748.0462
270.63080.2933-0.020.68140.28390.10920.0299-0.55570.1547-0.09170.1444-1.1909-0.11-1.05170.00050.9156-0.0525-0.18030.7428-0.10860.7905-58.4355-13.105363.4548
280.9062-0.1659-0.23650.4345-0.31920.2530.46330.0595-0.83890.2340.3179-0.9254-0.619-0.18060.0010.774-0.05890.01760.78930.07021.3905-93.519610.849622.5351
290.1555-0.5784-0.26740.99920.73470.4083-0.1076-0.6653-0.3040.9373-0.00680.35640.5389-0.5921-0.00020.878-0.05980.02680.75670.06360.9017-96.487521.236224.7243
303.816-0.16840.74343.1296-0.80621.6272-0.3154-0.0233-0.6996-0.07140.4004-0.141-0.0431-0.0593-0.00050.6097-0.00710.08410.6331-0.00770.7029-91.363629.623418.6489
310.10870.06450.13110.06010.10380.06781.02731.1938-0.68960.1247-0.6520.6891-2.3112.1473-0.00051.5231-0.04490.18181.566-0.03991.5512-83.374820.911513.6968
321.32370.21040.98260.64020.44180.914-0.27040.7223-0.4759-0.66880.3298-0.78-0.07960.2025-0.00020.5792-0.10140.06850.7554-0.02120.7775-81.782730.450318.4159
33-0.0706-0.1925-0.13740.3833-0.09250.2680.29970.12730.8349-0.77040.1252-1.574-0.9501-0.03210.00040.866-0.12240.20730.91550.01021.0846-79.366347.435218.7409
342.0038-0.65440.26831.16331.13221.6273-0.3326-0.1365-0.90880.71060.1579-0.7519-0.0619-0.32840.00020.6376-0.02520.04410.7080.01580.6491-95.13340.887427.9117
350.2864-0.1329-0.50760.01940.27591.1498-0.4551-1.7444-3.01190.76180.9145-0.50741.61461.7049-0.00330.96080.27370.0781.22270.41051.9961-72.302616.737631.0612
360.02640.0456-0.00490.9579-0.46120.23880.08110.3123-0.18250.5615-1.0927-0.1599-1.84020.4626-0.01321.39330.04710.35991.7479-0.61051.6239-64.43127.225539.2878
370.0377-0.06890.07750.05910.06330.2492-0.3599-1.08541.5823-0.38840.6857-0.0854-0.3739-0.1313-0.00051.02130.1086-0.22351.0804-0.09021.6784-63.601523.55429.0302
380.6308-0.33770.57240.8961-0.01480.4052-0.9563-0.25550.68060.60691.3674-0.70141.10080.23890.00090.81290.1389-0.02010.87740.01261.1475-71.533927.101725.7479
390.0934-0.2039-0.07330.35290.10350.05080.40890.24191.30520.5008-0.33120.576-1.5569-0.03030.00871.16140.1323-0.14771.7768-0.2591.4329-70.809633.472634.7934
400.49860.53470.16940.60120.48970.3952-0.526-0.6772-0.30660.9440.39060.6349-0.3319-0.64040.00110.98630.1675-0.00480.92940.07431.005-74.863424.199432.0532
412.709-2.51840.19692.87690.98290.67390.26880.2917-0.1753-0.0369-0.16440.5924-0.0505-0.3840.00020.77890.01950.02160.71210.01120.7516-86.628531.988166.1862
421.06110.606-0.55530.2645-0.03370.3467-0.073-0.21280.99011.05690.2684-0.2983-0.4596-0.12150.00110.93540.0843-0.06930.7167-0.03980.8843-74.97833.566569.8998
430.49820.2277-0.59951.3238-1.37141.20190.6163-0.28680.1425-0.1304-0.4859-0.887-0.44140.5920.00040.9603-0.0331-0.00290.7732-0.06730.8277-73.445438.635264.1373
441.1651-0.55320.05643.8095-0.51582.45870.1094-0.14150.1267-0.1713-0.2747-0.6434-0.10110.1758-0.00010.78720.0085-0.07870.6521-0.03470.8658-65.864325.659459.193
450.6847-0.14380.17730.262-0.0620.68770.65740.21890.2173-1.537-0.19751.04050.0376-1.69020.0091.4870.27490.11441.09580.07190.9357-85.337649.155951.016
460.6910.4194-0.33550.4157-0.44540.31160.97851.29330.967-1.7779-0.6172-0.8708-0.3415-0.1977-0.00021.49730.32880.29581.0960.12121.1371-78.20653.291146.6012
470.8738-0.6969-0.26690.7613-0.37890.77790.85180.22250.6115-0.8269-0.6288-0.9788-0.60530.2995-0.00060.98740.04570.02760.75690.06570.8163-74.407646.839654.5752
480.1297-0.1323-0.16630.09270.10180.15180.78742.0357-0.4004-1.4788-1.1605-0.29390.23721.41290.00021.91340.58070.47171.54580.29051.1533-72.00943.019844.3303
492.73113.29080.35133.97660.43740.0516-0.3969-0.51221.17750.2307-1.2675-0.1356-0.43551.4518-0.00522.46620.4425-0.50631.30590.13711.0141-83.671741.722741.9539
500.06070.07850.12010.5289-0.33370.13590.1508-0.7231-1.1316-0.13240.0751-0.45370.25920.0734-0.0050.97640.05560.01510.76270.01540.6978-77.855546.022856.855
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 22 )A7 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 32 )A23 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 63 )A33 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 73 )A64 - 73
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 82 )A74 - 82
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 97 )A83 - 97
7X-RAY DIFFRACTION7chain 'A' and (resid 98 through 132 )A98 - 132
8X-RAY DIFFRACTION8chain 'A' and (resid 133 through 141 )A133 - 141
9X-RAY DIFFRACTION9chain 'A' and (resid 142 through 184 )A142 - 184
10X-RAY DIFFRACTION10chain 'B' and (resid 0 through 6 )B0 - 6
11X-RAY DIFFRACTION11chain 'B' and (resid 7 through 17 )B7 - 17
12X-RAY DIFFRACTION12chain 'B' and (resid 18 through 34 )B18 - 34
13X-RAY DIFFRACTION13chain 'B' and (resid 35 through 49 )B35 - 49
14X-RAY DIFFRACTION14chain 'B' and (resid 50 through 59 )B50 - 59
15X-RAY DIFFRACTION15chain 'B' and (resid 60 through 65 )B60 - 65
16X-RAY DIFFRACTION16chain 'B' and (resid 66 through 74 )B66 - 74
17X-RAY DIFFRACTION17chain 'C' and (resid 7 through 22 )C7 - 22
18X-RAY DIFFRACTION18chain 'C' and (resid 23 through 92 )C23 - 92
19X-RAY DIFFRACTION19chain 'C' and (resid 93 through 112 )C93 - 112
20X-RAY DIFFRACTION20chain 'C' and (resid 113 through 141 )C113 - 141
21X-RAY DIFFRACTION21chain 'C' and (resid 142 through 184 )C142 - 184
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 16 )D1 - 16
23X-RAY DIFFRACTION23chain 'D' and (resid 17 through 22 )D17 - 22
24X-RAY DIFFRACTION24chain 'D' and (resid 23 through 44 )D23 - 44
25X-RAY DIFFRACTION25chain 'D' and (resid 45 through 59 )D45 - 59
26X-RAY DIFFRACTION26chain 'D' and (resid 60 through 65 )D60 - 65
27X-RAY DIFFRACTION27chain 'D' and (resid 66 through 74 )D66 - 74
28X-RAY DIFFRACTION28chain 'E' and (resid 7 through 22 )E7 - 22
29X-RAY DIFFRACTION29chain 'E' and (resid 23 through 46 )E23 - 46
30X-RAY DIFFRACTION30chain 'E' and (resid 47 through 92 )E47 - 92
31X-RAY DIFFRACTION31chain 'E' and (resid 93 through 119 )E93 - 119
32X-RAY DIFFRACTION32chain 'E' and (resid 120 through 141 )E120 - 141
33X-RAY DIFFRACTION33chain 'E' and (resid 142 through 159 )E142 - 159
34X-RAY DIFFRACTION34chain 'E' and (resid 160 through 184 )E160 - 184
35X-RAY DIFFRACTION35chain 'F' and (resid 2 through 15 )F2 - 15
36X-RAY DIFFRACTION36chain 'F' and (resid 16 through 22 )F16 - 22
37X-RAY DIFFRACTION37chain 'F' and (resid 23 through 34 )F23 - 34
38X-RAY DIFFRACTION38chain 'F' and (resid 35 through 49 )F35 - 49
39X-RAY DIFFRACTION39chain 'F' and (resid 50 through 59 )F50 - 59
40X-RAY DIFFRACTION40chain 'F' and (resid 60 through 72 )F60 - 72
41X-RAY DIFFRACTION41chain 'G' and (resid 7 through 73 )G7 - 73
42X-RAY DIFFRACTION42chain 'G' and (resid 74 through 119 )G74 - 119
43X-RAY DIFFRACTION43chain 'G' and (resid 120 through 141 )G120 - 141
44X-RAY DIFFRACTION44chain 'G' and (resid 142 through 184 )G142 - 184
45X-RAY DIFFRACTION45chain 'H' and (resid 1 through 11 )H1 - 11
46X-RAY DIFFRACTION46chain 'H' and (resid 12 through 34 )H12 - 34
47X-RAY DIFFRACTION47chain 'H' and (resid 35 through 49 )H35 - 49
48X-RAY DIFFRACTION48chain 'H' and (resid 50 through 59 )H50 - 59
49X-RAY DIFFRACTION49chain 'H' and (resid 60 through 65 )H60 - 65
50X-RAY DIFFRACTION50chain 'H' and (resid 66 through 73 )H66 - 73

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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