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- PDB-4mdk: Cdc34-ubiquitin-CC0651 complex -

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基本情報

登録情報
データベース: PDB / ID: 4mdk
タイトルCdc34-ubiquitin-CC0651 complex
要素
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 R1
キーワードLIGASE/LIGASE INHIBITOR / ubiquitin conjugating enzyme domain / E2 ligase inhibitor / LIGASE-LIGASE INHIBITOR complex
機能・相同性
機能・相同性情報


positive regulation of inclusion body assembly / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of cAMP-mediated signaling / response to growth factor / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / DNA replication initiation / cellular response to interferon-beta / protein K48-linked ubiquitination / Maturation of protein E ...positive regulation of inclusion body assembly / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of cAMP-mediated signaling / response to growth factor / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / DNA replication initiation / cellular response to interferon-beta / protein K48-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / 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 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Iron uptake and transport / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Peroxisomal protein import / Degradation of AXIN / Recognition of DNA damage by PCNA-containing replication complex / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Stabilization of p53 / Regulation of TNFR1 signaling
類似検索 - 分子機能
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 ...: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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-U94 / Polyubiquitin-C / 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: 2.6095 Å
データ登録者Ceccarelli, D.F. / Orlicky, S. / Tyers, M. / Sicheri, F.
引用ジャーナル: Nat.Chem.Biol. / 年: 2014
タイトル: E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin.
著者: Huang, H. / Ceccarelli, D.F. / Orlicky, S. / St-Cyr, D.J. / Ziemba, A. / Garg, P. / Plamondon, S. / Auer, M. / Sidhu, S. / Marinier, A. / Kleiger, G. / Tyers, M. / Sicheri, F.
履歴
登録2013年8月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年12月11日Provider: repository / タイプ: Initial release
改定 1.12014年1月15日Group: Database references
改定 1.22014年2月5日Group: Database references
改定 1.32023年9月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-conjugating enzyme E2 R1
C: Ubiquitin-conjugating enzyme E2 R1
D: Ubiquitin-conjugating enzyme E2 R1
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)119,34312
ポリマ－117,5738
非ポリマー1,7694
水82946
1
A: Ubiquitin-conjugating enzyme E2 R1
E: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,8363
ポリマ－29,3932
非ポリマー4421
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: 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)29,8363
ポリマ－29,3932
非ポリマー4421
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Ubiquitin-conjugating enzyme E2 R1
G: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,8363
ポリマ－29,3932
非ポリマー4421
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: 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)29,8363
ポリマ－29,3932
非ポリマー4421
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)55.403, 72.220, 75.912
Angle α, β, γ (deg.)71.89, 79.63, 81.61
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 / Ubiquitin-conjugating enzyme E2-32 kDa complementing / Ubiquitin-conjugating enzyme E2-CDC34 / ...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 / 断片: E2 domain (UNP residues 7-184) / 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 (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P49427, ubiquitin-protein ligase
#2: タンパク質
Ubiquitin


分子量: 8893.206 Da / 分子数: 4 / 断片: UNP residues 76-152 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBC / プラスミド: PetM30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0CG48
#3: 化合物
ChemComp-U94 / 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid / CC-0651


分子量: 442.290 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C20H21Cl2NO6
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 46 / 由来タイプ: 天然 / 式: H2O

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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: 48.84 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 28% PEG3350, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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データ収集

回折平均測定温度: 100 K
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: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2011年10月11日
放射モノクロメーター: Si(111) / 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: 2.6→50 Å / Num. all: 32770 / Num. obs: 31394 / % possible obs: 95.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / 冗長度: 2.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.7
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.6-2.641.70.4571.2185.5
2.64-2.6920.4991.4190.1
2.69-2.742.10.4331.7193.5
2.74-2.82.10.3971.8194.2
5.6-7.052.20.04824.7197.4
7.05-502.20.04434.3197.2

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解析

ソフトウェア
名称バージョン分類
ADSCQuantumデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.2_1309)精密化
HKL-2000データ削減
SCALEPACKデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRIES 2OB4 AND 3A33

2ob4

3a33


解像度: 2.6095→44.627 Å / SU ML: 0.46 / σ(F): 1.96 / 位相誤差: 31.74 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.259 1580 5.04 %RANDOM
Rwork0.2042 ---
obs0.2069 31377 94.24 %-
all-32752 --
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
精密化ステップサイクル: LAST / 解像度: 2.6095→44.627 Å
タンパク質核酸リガンド溶媒全体
原子数7539 0 116 46 7701
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0087836
X-RAY DIFFRACTIONf_angle_d1.26410653
X-RAY DIFFRACTIONf_dihedral_angle_d16.2492924
X-RAY DIFFRACTIONf_chiral_restr0.0861193
X-RAY DIFFRACTIONf_plane_restr0.0081367
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6095-2.69380.39271110.33842015X-RAY DIFFRACTION71
2.6938-2.790.34521440.29752697X-RAY DIFFRACTION93
2.79-2.90170.33371500.26892759X-RAY DIFFRACTION96
2.9017-3.03370.33121400.25942754X-RAY DIFFRACTION97
3.0337-3.19360.33851510.25762770X-RAY DIFFRACTION97
3.1936-3.39370.32191500.24072808X-RAY DIFFRACTION97
3.3937-3.65560.27471460.21232805X-RAY DIFFRACTION97
3.6556-4.02330.24361480.19272817X-RAY DIFFRACTION97
4.0233-4.60490.22221500.16452789X-RAY DIFFRACTION97
4.6049-5.79970.21071470.17172775X-RAY DIFFRACTION97
5.7997-44.6330.21571430.17792808X-RAY DIFFRACTION97
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)
15.60220.0174-0.36383.1138-0.60830.9204-0.04141.2366-0.6189-0.194-0.1034-0.4988-0.00780.1571-0.05870.63450.0320.09360.7494-0.03350.702861.98236.311-15.7037
23.9804-0.3363-0.46933.1518-0.20231.6549-0.104-0.22520.1192-0.0482-0.0142-0.3129-0.21490.1386-0.00660.46680.00310.00920.5356-0.03250.513953.628542.7948-6.6113
30.16740.1369-0.06180.0594-0.0130.04-0.3489-0.8498-0.04660.52030.1201-0.26481.1635-0.81190.00030.7562-0.0068-0.13120.94960.14771.179659.502529.3460.2922
42.3125-1.09260.16053.14060.57931.4312-0.1282-0.30250.12460.01640.06090.1838-0.1125-0.24940.07220.47690.0089-0.01160.572-0.04410.567939.914742.0034-5.1904
51.00880.17510.56943.29381.00461.94620.17780.0941-0.50610.29240.0236-0.26370.2925-0.1233-0.13460.51890.00090.00190.5695-0.02690.777515.605111.999923.0783
61.1346-0.3897-0.73833.3710.22950.91180.34950.9779-0.3135-1.0213-0.50390.8964-0.5203-0.2019-0.02310.54910.00450.00480.7194-0.11250.613715.0224.971517.9293
77.52812.42992.82842.39741.49941.8815-0.32971.03880.1514-0.7457-0.0969-0.96640.0786-0.5785-0.16760.6625-0.08920.11240.7413-0.040.591619.721125.980813.5752
8-0.01070.0067-0.01390.05670.0740.05880.52440.7145-0.85370.1022-0.7044-0.2547-0.45880.01250.00540.830.17820.09291.0135-0.22981.358626.336910.079813.1128
93.1735-1.21910.29314.0120.10271.5783-0.05360.1640.306-0.14650.0914-0.3683-0.26490.10530.00850.4177-0.07950.06140.5568-0.02170.450422.414430.198222.7441
103.1017-0.68430.25596.26841.18571.8809-0.0578-0.46580.65261.1713-0.0054-0.9595-0.10.3202-0.11990.60240.01140.12070.5849-0.060.635750.5446-4.011726.3845
111.98-0.30170.47785.72620.46331.810.10290.0290.2385-0.3767-0.0643-0.4227-0.14820.0793-0.01920.4467-0.03270.07230.51760.0130.44449.4551-16.552720.0871
120.78960.65570.8660.83850.36191.50370.31370.49150.5174-0.5677-1.43741.6823-0.2392-0.6017-0.0630.88510.25480.04550.98230.14990.95437.2979-7.145714.2401
131.9986-0.12960.28973.49181.13750.41470.06370.0108-0.2830.04490.15450.45860.1335-0.2935-0.07120.5333-0.05250.08480.63160.06550.418737.549-27.226421.1235
143.9178-0.01440.32235.61220.76061.83920.0717-0.29680.48660.83170.1376-0.17290.2788-0.0568-0.01020.58710.02930.03880.58380.05150.59553.5857-29.664529.1516
154.7981-1.4636-1.32313.97031.19573.62150.44720.82910.26910.2661-0.1760.41920.2279-0.8403-0.0320.71740.00910.02070.68490.02820.783-1.55343.374-3.3921
165.47190.4848-1.45373.576-0.81684.23550.46211.1859-0.09320.06960.8368-0.5582-0.681-0.2270.01750.79840.09840.08230.74590.01210.80327.1374-1.4251-11.6743
173.6519-0.829-1.93791.4310.18242.5403-0.1666-0.15180.15970.17160.20030.28490.8918-0.35370.09840.70840.0319-0.01930.6473-0.02670.70545.1129-5.6519-1.792
184.2982-0.945-1.65422.40591.21952.07120.33430.3437-0.0723-0.0868-0.26620.2292-0.2575-0.4098-0.05160.56010.1118-0.04780.52940.00930.590213.5775-1.1091-5.136
192.9449-0.7362-0.76780.25210.15070.2084-0.6518-0.0106-0.02571.14960.4835-0.58110.55740.18380.05540.6809-0.0323-0.03950.61670.01630.728920.6487-5.9001-2.1375
200.4754-0.0174-0.47410.81410.58660.7728-0.022-0.6771-0.11490.83040.256-0.18990.33630.30690.0290.64140.0072-0.02690.72280.0240.719419.26023.29190.078
211.9176-0.9495-0.58271.9956-0.5320.57750.5589-0.26940.5391-0.299-0.2705-0.33220.05080.2108-0.09590.71530.0469-0.05210.6593-0.04980.58321.15555.599-6.7827
223.7126-0.2508-0.22644.33290.27020.3853-0.2236-0.09280.5241-0.4486-0.1873-1.4066-0.1711-0.0164-0.02650.7924-0.0214-0.00350.60270.00750.873737.31140.2981-11.0882
236.36911.2873-0.30073.56391.11930.9690.2150.84310.05950.17630.06420.1404-0.0603-0.01450.14340.60410.0611-0.03620.5976-0.06470.622.3281-13.0403-12.2421
245.29626.42775.77558.84587.6236.7175-0.27211.45330.314-1.76250.7323-0.7121-0.350.9830.05061.19330.0685-0.08150.6385-0.06950.761944.783716.2901-20.8958
252.1565-0.12120.34125.86533.31044.3040.59160.3232-0.00880.01350.1858-1.06320.53930.6365-0.60960.6474-0.07580.15720.70220.10010.83756.007420.6397-10.5794
267.00892.5759-0.39467.53841.55011.96070.59890.3647-0.7266-0.65790.7627-0.1925-0.21040.437-0.35030.7571-0.05230.06030.7324-0.11441.101848.156713.9396-17.242
270.1575-0.9153-0.79346.03365.14734.39260.2592-0.00820.5011-0.5097-0.10071.15260.4155-0.80080.33840.6901-0.1405-0.02410.8672-0.06821.086935.078415.6342-17.3323
282.64660.42731.53748.04181.90293.253-0.3377-0.3506-0.74240.56930.31810.19381.1921-0.441-0.08360.764-0.09780.03270.57550.01450.859442.557313.9183-8.7933
293.5092-0.72470.75532.0592.13942.2074-0.0318-0.1424-0.42930.43750.2570.8481-0.1553-0.1656-0.11930.7425-0.0031-0.00680.57620.0470.65343.662123.5482-7.2231
304.1852.7299-1.1076.71514.75396.3540.4014-0.44440.37640.1889-0.3971.41170.5686-2.06230.34060.7112-0.03090.16980.9090.04251.241634.321924.7892-9.6114
312.70740.2241-1.39166.21123.27073.6870.34330.75440.417-2.2573-0.16860.6337-0.6846-1.53940.17371.1469-0.0899-0.28471.0070.18411.031737.561423.046-20.7691
320.26790.1449-0.34980.3299-0.22261.65180.42720.06810.4613-0.29270.7859-0.24420.44970.1652-0.24460.68350.01620.09550.52430.01220.572747.292224.8187-6.7256
332.88-0.36624.42980.2447-0.10388.18431.3629-0.0086-0.43340.0577-0.24831.56080.4406-0.68660.04470.88730.23060.00910.77660.09660.899338.68919.321439.207
343.4722-1.7381-0.35963.2071-0.41751.2570.24850.1641-1.55870.1807-0.0528-0.19910.52470.7721-0.20720.74450.1476-0.23170.8979-0.16261.221539.942710.612733.4459
354.249-2.6492-0.70822.70130.20512.3784-0.1840.26770.3330.0110.1145-0.9504-0.04760.767-0.19080.67140.06810.00020.9089-0.08680.996643.499415.244126.9557
364.0824-2.71290.21032.8364-0.49893.0252-0.10710.04120.40250.59870.3557-0.5176-0.25660.3291-0.30830.58850.0099-0.04180.7834-0.01830.761935.363422.860732.8775
372.0414-0.0777-2.09741.6321-0.40892.3684-0.0851-0.3299-0.32510.25550.09230.00080.34930.6516-0.13690.62720.06-0.00280.7307-0.09760.965334.684216.601432.4402
386.64045.5661-1.04415.4538-1.77861.17690.9784-0.9862.04770.35970.2005-0.6264-0.88961.1225-0.38091.19060.12850.48441.1377-0.32781.460930.9521-6.569539.002
390.07980.1843-0.04366.1516-0.99260.35331.2111-1.94951.32510.1912-0.27330.4719-0.7864-0.1193-0.36310.71020.95411.83721.4474-0.14521.262927.3429-8.657236.8958
408.46641.6125-2.47683.54793.40175.39810.92640.22771.6412-0.1281-0.88660.7299-0.7396-1.6481-1.49860.76420.21210.37471.37540.19180.812621.4936-11.583832.3325
415.3825-0.607-3.31486.08381.31748.20170.53770.1954-1.1592-0.190.15021.3833-0.0324-1.6077-0.0590.6110.11220.14031.05140.11570.696429.093-18.053930.0405
420.1097-0.25070.5320.5882-1.22632.5836-0.1317-3.9135-2.2091.0999-0.3075-0.35030.51840.09970.33651.47730.00390.112.14470.76340.988629.7609-21.910141.4201
433.69891.91721.81483.2182-0.42482.74230.1671-1.40630.34850.83910.5864-0.7722-1.6694-0.091-0.910.82030.30040.27051.0945-0.06160.851832.6222-13.577834.0545
440.3004-0.64410.87651.2545-1.9022.82790.2909-0.59790.0420.12040.43951.21070.1029-0.4522-0.42690.74260.1519-0.09150.91920.05260.74958.958316.3749-27.3453
454.3897-0.91561.68772.86440.09972.42910.49610.440.9151-0.1455-0.16390.4939-0.90240.0339-0.32180.8610.2096-0.03981.00730.08460.975811.89117.9706-23.3452
464.7206-1.91732.45145.36910.59374.16750.79730.8690.7839-0.1978-0.1924-0.664-0.83590.1954-0.20230.7690.0840.11350.82150.11840.789918.38322.2633-21.7946
475.6882-0.94141.39654.0628-0.5243.63650.21650.3854-0.15390.85850.6175-1.1280.040.9496-0.40080.62680.02330.05350.7059-0.02680.534819.959314.0467-16.3924
481.06040.2221-2.22521.7643-3.12938.71780.38631.4446-0.33540.056-0.3657-1.19641.03591.3537-0.47670.98630.1186-0.10251.151-0.1550.845325.034710.5085-23.8687
495.1125-0.58242.0232.8040.13323.78920.39010.6632-0.7793-0.52910.06240.32880.60080.0804-0.46440.73550.0791-0.06380.85330.06190.738714.945310.7291-23.2876
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 97 )
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 184 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 73 )
6X-RAY DIFFRACTION6chain 'B' and (resid 74 through 82 )
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 92 )
8X-RAY DIFFRACTION8chain 'B' and (resid 93 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 184 )
10X-RAY DIFFRACTION10chain 'C' and (resid 7 through 32 )
11X-RAY DIFFRACTION11chain 'C' and (resid 33 through 97 )
12X-RAY DIFFRACTION12chain 'C' and (resid 98 through 119 )
13X-RAY DIFFRACTION13chain 'C' and (resid 120 through 159 )
14X-RAY DIFFRACTION14chain 'C' and (resid 160 through 184 )
15X-RAY DIFFRACTION15chain 'D' and (resid 7 through 22 )
16X-RAY DIFFRACTION16chain 'D' and (resid 23 through 32 )
17X-RAY DIFFRACTION17chain 'D' and (resid 33 through 46 )
18X-RAY DIFFRACTION18chain 'D' and (resid 47 through 73 )
19X-RAY DIFFRACTION19chain 'D' and (resid 74 through 82 )
20X-RAY DIFFRACTION20chain 'D' and (resid 83 through 119 )
21X-RAY DIFFRACTION21chain 'D' and (resid 120 through 141 )
22X-RAY DIFFRACTION22chain 'D' and (resid 142 through 159 )
23X-RAY DIFFRACTION23chain 'D' and (resid 160 through 184 )
24X-RAY DIFFRACTION24chain 'E' and (resid -1 through 6 )
25X-RAY DIFFRACTION25chain 'E' and (resid 7 through 11 )
26X-RAY DIFFRACTION26chain 'E' and (resid 12 through 16 )
27X-RAY DIFFRACTION27chain 'E' and (resid 17 through 22 )
28X-RAY DIFFRACTION28chain 'E' and (resid 23 through 34 )
29X-RAY DIFFRACTION29chain 'E' and (resid 35 through 49 )
30X-RAY DIFFRACTION30chain 'E' and (resid 50 through 54 )
31X-RAY DIFFRACTION31chain 'E' and (resid 55 through 65 )
32X-RAY DIFFRACTION32chain 'E' and (resid 66 through 74 )
33X-RAY DIFFRACTION33chain 'F' and (resid -1 through 6 )
34X-RAY DIFFRACTION34chain 'F' and (resid 7 through 22 )
35X-RAY DIFFRACTION35chain 'F' and (resid 23 through 44 )
36X-RAY DIFFRACTION36chain 'F' and (resid 45 through 56 )
37X-RAY DIFFRACTION37chain 'F' and (resid 57 through 74 )
38X-RAY DIFFRACTION38chain 'G' and (resid 2 through 6 )
39X-RAY DIFFRACTION39chain 'G' and (resid 7 through 22 )
40X-RAY DIFFRACTION40chain 'G' and (resid 23 through 34 )
41X-RAY DIFFRACTION41chain 'G' and (resid 35 through 54 )
42X-RAY DIFFRACTION42chain 'G' and (resid 55 through 59 )
43X-RAY DIFFRACTION43chain 'G' and (resid 60 through 74 )
44X-RAY DIFFRACTION44chain 'H' and (resid -1 through 6 )
45X-RAY DIFFRACTION45chain 'H' and (resid 7 through 22 )
46X-RAY DIFFRACTION46chain 'H' and (resid 23 through 34 )
47X-RAY DIFFRACTION47chain 'H' and (resid 35 through 49 )
48X-RAY DIFFRACTION48chain 'H' and (resid 50 through 54 )
49X-RAY DIFFRACTION49chain 'H' and (resid 55 through 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