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- PDB-7bbf: Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in comple... -

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基本情報

登録情報
データベース: PDB / ID: 7bbf
タイトルCrystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2
要素
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-conjugating enzyme E2 variant 2
キーワードLIGASE / E2 conjugating enzyme / ubiquitin chain elongation
機能・相同性
機能・相同性情報


error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity ...error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / Maturation of protein E / protein monoubiquitination / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / ubiquitin ligase complex / 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 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / regulation of DNA repair / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / negative regulation of TORC1 signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / antiviral innate immune response / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / positive regulation of DNA repair / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling
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 domain ...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 / Ubiquitin domain signature. / Ubiquitin conserved site / 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
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 2
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: 2.54 Å
データ登録者Kiss, L. / Neuhaus, D. / James, L.C.
資金援助 英国, 3件
組織認可番号国
Medical Research Council (MRC, United Kingdom)U105181010 英国
Medical Research Council (MRC, United Kingdom)U105178934 英国
Wellcome Trust 英国
引用ジャーナル: Nat Commun / 年: 2021
タイトル: RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination.
著者: Kiss, L. / Clift, D. / Renner, N. / Neuhaus, D. / James, L.C.
履歴
登録2020年12月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年1月27日Provider: repository / タイプ: Initial release
改定 1.12021年3月10日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22024年5月15日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
H: Ubiquitin-conjugating enzyme E2 variant 2
B: Ubiquitin-conjugating enzyme E2 variant 2
E: Ubiquitin-conjugating enzyme E2 variant 2
G: Ubiquitin-conjugating enzyme E2 N
D: Ubiquitin-conjugating enzyme E2 N
A: Ubiquitin-conjugating enzyme E2 N
I: Polyubiquitin-C
C: Polyubiquitin-C
F: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)128,0679
ポリマ－128,0679
非ポリマー00
水72140
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: assay for oligomerization
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)145.840, 145.840, 49.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 4 through 9 or (resid 10...
21(chain D and (resid 4 through 23 or (resid 24...
31(chain G and (resid 4 through 9 or (resid 10...
12(chain B and ((resid 5 and (name N or name...
22(chain E and ((resid 5 and (name N or name...
32(chain H and (resid 5 through 71 or (resid 72...
13(chain C and (resid 1 through 59 or resid 61...
23(chain F and (resid 1 through 5 or (resid 6...
33(chain I and (resid 1 through 5 or (resid 6...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUILEILE(chain A and (resid 4 through 9 or (resid 10...AF4 - 95 - 10
121LYSLYSLYSLYS(chain A and (resid 4 through 9 or (resid 10...AF1011
131GLYGLYILEILE(chain A and (resid 4 through 9 or (resid 10...AF3 - 1524 - 153
141GLYGLYILEILE(chain A and (resid 4 through 9 or (resid 10...AF3 - 1524 - 153
151GLYGLYILEILE(chain A and (resid 4 through 9 or (resid 10...AF3 - 1524 - 153
211LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 235 - 24
221LYSLYSALAALA(chain D and (resid 4 through 23 or (resid 24...DE24 - 2525 - 26
231LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 1525 - 153
241LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 1525 - 153
251LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 1525 - 153
261LEULEUILEILE(chain D and (resid 4 through 23 or (resid 24...DE4 - 1525 - 153
311LEULEUILEILE(chain G and (resid 4 through 9 or (resid 10...GD4 - 95 - 10
321LYSLYSLYSLYS(chain G and (resid 4 through 9 or (resid 10...GD1011
331METMETILEILE(chain G and (resid 4 through 9 or (resid 10...GD1 - 1522 - 153
112THRTHRTHRTHR(chain B and ((resid 5 and (name N or name...BB510
122THRTHRASNASN(chain B and ((resid 5 and (name N or name...BB5 - 14510 - 150
132THRTHRASNASN(chain B and ((resid 5 and (name N or name...BB5 - 14510 - 150
142THRTHRASNASN(chain B and ((resid 5 and (name N or name...BB5 - 14510 - 150
152THRTHRASNASN(chain B and ((resid 5 and (name N or name...BB5 - 14510 - 150
212THRTHRTHRTHR(chain E and ((resid 5 and (name N or name...EC510
222THRTHRASNASN(chain E and ((resid 5 and (name N or name...EC5 - 14510 - 150
232THRTHRASNASN(chain E and ((resid 5 and (name N or name...EC5 - 14510 - 150
242THRTHRASNASN(chain E and ((resid 5 and (name N or name...EC5 - 14510 - 150
252THRTHRASNASN(chain E and ((resid 5 and (name N or name...EC5 - 14510 - 150
312THRTHRPROPRO(chain H and (resid 5 through 71 or (resid 72...HA5 - 7110 - 76
322LYSLYSLYSLYS(chain H and (resid 5 through 71 or (resid 72...HA7277
332SERSERASNASN(chain H and (resid 5 through 71 or (resid 72...HA4 - 1459 - 150
342SERSERASNASN(chain H and (resid 5 through 71 or (resid 72...HA4 - 1459 - 150
352SERSERASNASN(chain H and (resid 5 through 71 or (resid 72...HA4 - 1459 - 150
362SERSERASNASN(chain H and (resid 5 through 71 or (resid 72...HA4 - 1459 - 150
113METMETTYRTYR(chain C and (resid 1 through 59 or resid 61...CH1 - 591 - 59
123ILEILEARGARG(chain C and (resid 1 through 59 or resid 61...CH61 - 7261 - 72
133METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
143METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
153METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
163METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
173METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
183METMETGLYGLY(chain C and (resid 1 through 59 or resid 61...CH1 - 761 - 76
213METMETVALVAL(chain F and (resid 1 through 5 or (resid 6...FI1 - 51 - 5
223LYSLYSLYSLYS(chain F and (resid 1 through 5 or (resid 6...FI66
233METMETLEULEU(chain F and (resid 1 through 5 or (resid 6...FI1 - 731 - 73
313METMETVALVAL(chain I and (resid 1 through 5 or (resid 6...IG1 - 51 - 5
323LYSLYSLYSLYS(chain I and (resid 1 through 5 or (resid 6...IG66
333METMETARGARG(chain I and (resid 1 through 5 or (resid 6...IG1 - 741 - 74
343METMETARGARG(chain I and (resid 1 through 5 or (resid 6...IG1 - 741 - 74
353METMETARGARG(chain I and (resid 1 through 5 or (resid 6...IG1 - 741 - 74
363METMETARGARG(chain I and (resid 1 through 5 or (resid 6...IG1 - 741 - 74

NCSアンサンブル:
ID
1
2
3

NCS oper:
IDCodeMatrixベクター
1given(-0.467058080234, -0.883812248909, -0.0270676627517), (0.884188268324, -0.467104115031, -0.00498516586395), (-0.00823746600219, -0.0262612718541, 0.999621173122)70.2326561443, -42.0864235517, 3.04762290417
2given(-0.487293813855, 0.873237847136, 0.000633489190373), (-0.873237820982, -0.487294098228, 0.000412114445697), (0.000668569475094, -0.000352365900229, 0.999999714427)72.2002302673, 43.2891426453, 2.85990601349
3given(-0.434167973493, -0.900821357553, 0.00436492483613), (0.900821991596, -0.434135322012, 0.00680159082084), (-0.00423205022746, 0.00688505318727, 0.999967342363)67.9294463233, -42.1297834466, 3.89645183587
4given(-0.491834013038, 0.870685003853, 0.00263204946845), (-0.870654719988, -0.491839229354, 0.00738451287308), (0.00772412980154, 0.00134034830775, 0.99996927017)72.4517995597, 43.0178986667, 2.45730362017
5given(-0.522082918086, -0.852890303814, -0.00274887315107), (0.852858052369, -0.522087644106, 0.0075917310792), (-0.007910066534, 0.00161911451332, 0.999967404127)73.3613436463, -45.0544462733, -0.341718131093
6given(-0.472445986283, 0.881218286557, -0.0157835827244), (-0.881228272218, -0.47260899149, -0.00880189792165), (-0.0152158565184, 0.00975051798886, 0.999836689219)74.2060232575, 44.5388727484, -2.26592333698

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要素

#1: タンパク質 Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein


分子量: 16929.277 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2V2, MMS2, UEV2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q15819
#2: タンパク質 Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


分子量: 17182.756 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBE2N, BLU / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: タンパク質 Polyubiquitin-C


分子量: 8576.831 Da / 分子数: 3 / 由来タイプ: 組換発現 / 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: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 40 / 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: 2.36 Å3/Da / 溶媒含有率: 47.88 %
結晶化温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1 M bicine Trizma base pH 8.5, 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2 % of each Anesthetic alkaloids (lidocaine HCl H2O, procaine HCl, proparacaine HCl, tetracaine HCl)

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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: I03 / 波長: 0.9762 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年4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: 0.9762 Å / 相対比: 1
反射解像度: 2.54→47.74 Å / Num. obs: 38540 / % possible obs: 99.89 % / 冗長度: 5.3 % / Biso Wilson estimate: 79.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05449 / Net I/σ(I): 15.81
反射 シェル解像度: 2.54→2.63 Å / Rmerge(I) obs: 1.347 / Num. unique obs: 3845 / CC1/2: 0.497

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5S

解像度: 2.54→47.74 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 1.97 / 位相誤差: 35.11 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2534 2017 5.24 %
Rwork0.2056 36489 -
obs0.2081 38506 99.9 %
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: 241.52 Å2 / Biso mean: 109.3076 Å2 / Biso min: 30 Å2
精密化ステップサイクル: final / 解像度: 2.54→47.74 Å
タンパク質核酸リガンド溶媒全体
原子数8586 0 0 40 8626
Biso mean---85.41 -
残基数----1098
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A1961X-RAY DIFFRACTION13.874TORSIONAL
12D1961X-RAY DIFFRACTION13.874TORSIONAL
13G1961X-RAY DIFFRACTION13.874TORSIONAL
21B2033X-RAY DIFFRACTION13.874TORSIONAL
22E2033X-RAY DIFFRACTION13.874TORSIONAL
23H2033X-RAY DIFFRACTION13.874TORSIONAL
31C1002X-RAY DIFFRACTION13.874TORSIONAL
32F1002X-RAY DIFFRACTION13.874TORSIONAL
33I1002X-RAY DIFFRACTION13.874TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.54-2.610.40061470.353626212768100
2.61-2.680.35941440.321725752719100
2.68-2.750.34771460.315426532799100
2.75-2.840.35571400.316126062746100
2.84-2.950.34641400.332625902730100
2.95-3.060.34241500.302826142764100
3.06-3.20.31871400.274226072747100
3.2-3.370.36641480.278425822730100
3.37-3.580.27611460.257626232769100
3.58-3.860.24211380.213326182756100
3.86-4.240.26961330.187326012734100
4.25-4.860.20491640.170626202784100
4.86-6.120.21581400.174426012741100
6.12-47.740.20161410.13892578271999
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)
17.6926-0.4696-1.59316.69090.89986.01131.126-0.14940.410.6719-0.35460.2321-0.43570.0318-0.56120.6790.0036-0.00230.7366-0.2610.775424.6420.885618.8425
21.8621.42712.49743.41172.81813.15530.0810.2054-0.3388-0.02971.0386-0.7463-0.18651.3529-0.54320.7392-0.10210.05041.2018-0.26160.954435.205717.217615.8274
34.01091.92293.32791.2012.23365.4160.04840.10830.03250.56760.0656-0.9001-0.9821.5397-0.00950.9685-0.3490.06611.3048-0.22310.873241.613732.746224.1491
44.42740.8711.81035.51932.98782.54210.9066-0.5519-0.89460.8723-0.7858-0.63290.13480.5964-0.13310.8041-0.1651-0.10721.2247-0.22210.77835.937918.690527.1786
57.1916-0.89410.67375.1341-1.7412.96711.6664-1.1727-1.20720.91790.031-0.7374-0.23441.0917-0.61071.1421-0.2484-0.09351.7079-0.451.222846.039424.075932.5694
64.35073.3796-2.30039.54990.52732.1071.3875-1.36830.24922.1866-0.5268-1.0830.51821.4742-0.91780.8207-0.1258-0.07451.0218-0.25320.879835.216922.736836.3882
70.04030.00080.19896.89424.68328.16470.604-1.2270.53060.4663-0.659-0.067-0.53460.3307-0.16670.8897-0.22720.06431.1314-0.29330.86933.883630.132231.0577
85.35040.2243-0.01074.7173-1.76498.61030.9329-0.0159-0.4092-0.75130.0797-0.57511.23820.3433-0.17741.246-0.26090.01451.9998-0.49661.224951.823526.618123.1724
96.6095-2.63981.75912.101-0.18383.28130.0881-1.6127-0.276-0.27970.45630.15030.8384-0.3064-0.24440.82940.18020.11971.090.03590.683448.4799-31.400417.4347
105.0993-3.2629-3.21492.11141.93392.1314-0.8355-0.5484-0.44590.52680.810.38130.5614-0.53340.05030.96650.09310.10341.26880.14160.649832.7527-32.562612.2709
114.5790.4241-2.67453.42971.34643.8075-0.1162-0.48040.4251-0.076-0.00090.0293-0.4945-0.65330.07540.64260.30040.00491.08120.03580.529935.449-21.971718.5703
122.20072.7609-0.76632.4659-1.49995.40060.0384-0.64390.3630.4544-0.6043-0.1313-0.44770.17130.31870.71780.241-0.00731.10910.00260.582434.5651-20.303829.2098
133.78080.7844-1.51462.8644-0.09687.0745-0.6981-1.1792-1.32610.65990.21290.92130.7937-0.50530.37910.64970.23680.12911.07630.03110.714326.6704-26.826828.3708
144.032-0.53010.38794.9594-1.47969.159-0.5428-0.1621.4108-0.6943-1.0913-2-0.8756-1.30770.79621.34330.6662-0.05111.2957-0.04681.401223.283-10.917821.953
152.0499-1.5658-1.01587.91515.16267.5059-0.7928-0.38980.22440.09991.34420.2421-1.63191.2103-0.12381.14720.03520.06560.73170.081.336975.039715.42520.9164
160.3139-1.30410.88345.5335-3.68672.44110.40930.6340.9367-0.4335-0.1009-1.8349-0.04611.4114-0.85471.22260.0450.28131.0394-0.3431.621983.18431.613515.765
172.8103-0.0770.95864.8236-0.56124.8662-0.0624-0.0743-0.1082-0.43241.11970.35490.5366-0.9261-1.17871.1164-0.0218-0.04610.81310.07631.2868.365.243515.2379
182.07150.8251-1.79247.0818-2.08676.68811.27080.2096-1.27610.2613-0.18230.65531.68580.7818-0.61741.3510.1871-0.50540.4694-0.10751.497575.9853-8.099623.6507
193.06960.6764-1.14811.341-0.16152.68910.48830.18960.04011.82421.05560.55730.8435-0.2216-1.081.5502-0.0899-0.2210.70590.19731.346368.9631.52128.0372
204.38892.63112.64911.91430.58446.05050.7525-0.4809-1.26220.77791.0113-0.10410.7524-1.0341-0.99581.6180.0003-0.06060.93090.29621.536567.4313-9.24233.7982
211.2989-0.4895-0.93950.6936-0.50725.19840.8447-1.9685-0.21750.4141-0.33011.8634-0.0575-1.0542-0.74481.1118-0.05360.03730.82740.22861.218572.6870.499937.2934
221.7954-1.1671-0.42272.165-2.97088.55170.3894-0.36730.63391.53540.45590.339-1.03412.8321-0.58131.62790.13380.30220.61680.02231.118977.575410.098932.6208
234.2413-1.58120.18284.0813-1.42074.58981.4305-0.5237-0.77260.49030.0735-1.3940.2741.6552-1.10041.24840.0971-0.37930.5643-0.11871.372580.5366-2.321528.9866
248.42472.08981.99152.44310.22822.3037-1.3080.017-0.8226-0.91030.4819-2.1339-0.05320.1230.76341.8469-0.1251-0.13571.13070.14921.461478.8665-15.324635.5328
251.62281.5672-1.00552.37210.88494.5660.46890.3926-0.5783-0.732-0.09651.1029-0.4898-1.37980.11982.1948-0.1742-0.36731.3436-0.05141.593665.2905-15.357923.7632
266.46521.3541-1.90294.6332-0.29327.00750.13750.3359-0.350.26250.3006-0.01460.9055-0.6655-0.43690.7982-0.1091-0.13680.62850.02770.651813.3174.438111.2925
275.4869-5.68824.79887.8393-5.99244.974-1.13922.10192.062-1.04780.2448-2.5479-2.03751.1574-0.36862.2254-0.2163-0.0071.80850.28581.578619.831810.5223-5.3768
286.07690.49121.47743.63912.34833.77830.0521.2574-0.9272-1.03110.5657-1.1698-0.72031.8013-0.75241.4046-0.01620.23071.6306-0.2781.173429.79441.6672-2.6829
295.58670.46061.60051.36850.66225.1168-0.4674-0.87670.55060.13350.14260.5808-0.9093-0.45210.48391.07070.14230.17840.7967-0.0081.610568.599236.044519.2877
302.92991.2403-0.43435.19822.78245.41570.1715-0.34310.29410.0731-0.18980.31910.2426-1.5760.03630.81820.10090.14980.65180.1341.575462.457126.529110.7349
312.42211.5328-0.3886.88391.26826.12960.0653-0.24040.02130.64540.2939-0.50240.8753-0.0343-0.27840.75550.04430.12760.57370.11391.435171.229221.394710.3236
321.11360.62010.29463.9671.01415.7689-0.36940.71880.9669-0.99510.8594-0.1727-1.06940.8231-0.36520.7528-0.02030.23190.49770.02111.508174.012930.10255.8327
335.4795-2.64560.05065.9543-0.50457.46440.7790.53340.77590.649-0.5548-2.00121.762-0.00570.11911.74670.02280.17051.5936-0.05211.651568.792115.8513-6.8833
342.98021.04940.1873.0993-1.18713.10380.5918-0.38370.5571-0.3243-0.5311.7648-0.5782-0.16910.94121.3569-0.3427-0.02581.22290.23662.19354.037917.96120.6064
352.22564.1469-1.18119.1748-0.38894.9899-0.049-0.9335-1.54090.39-0.4719-1.70181.04821.170.36640.58560.1248-0.0530.76290.0210.613469.5474-40.731917.5713
365.66021.29-1.84424.3864-3.83059.7217-0.4002-0.3950.8588-0.46010.295-1.23620.00770.01590.21510.5909-0.04950.06780.67980.05470.619372.1184-29.707510.5053
373.4189-0.98951.55087.3227-2.49055.17140.0707-0.1750.01880.0745-0.01010.0284-0.4579-0.4057-0.04290.48230.06680.06450.5525-0.02910.442261.2894-28.46769.214
382.8495-3.21640.62068.9111-2.91514.02350.17320.3118-0.2635-1.04450.20640.27970.3118-0.4183-0.33160.5744-0.0382-0.02520.5369-0.01740.38659.4212-34.042.0631
395.33534.7431-0.46875.8754-0.88152.12950.01782.0167-1.1166-0.66250.35921.774-0.4771-2.2801-0.07381.36260.1369-0.15751.5320.11650.821752.3903-24.8412-10.0808
404.99210.78460.87774.26161.5277.841-0.27820.33960.6828-0.3556-0.54570.153-1.6323-0.08250.22571.32260.03030.09880.86540.19450.874960.5771-14.0003-2.5495
414.2458-0.95712.02983.3439-0.50524.1708-0.26260.84160.8361-0.1379-0.2633-0.7354-0.69611.56460.16580.8635-0.0547-0.08881.01470.08680.711714.305239.4502-16.0983
425.5422-2.3724-3.36246.8707-1.50956.0174-0.78611.2464-1.2139-1.40590.3087-1.43821.07631.20220.29811.25750.11980.14360.9046-0.07170.690713.585531.1109-18.8313
432.9688-0.57270.28324.0285-1.93455.64480.1336-0.0133-1.07150.06370.1886-0.02631.1914-0.00780.13261.13880.0691-0.02340.785-0.09410.7715.806133.0254-12.4985
443.2391-2.49911.40842.4962-0.87746.9284-0.03820.5942-0.61110.9735-0.52520.60260.07320.97690.33530.99790.10760.01260.7383-0.0030.68779.737738.41-11.0267
450.9271-0.3507-1.22143.36320.55924.52820.2962-0.0907-1.25040.0053-0.39071.28580.1169-1.17430.0831.08570.09620.19711.3664-0.45791.787531.5698-48.0573-10.4849
462.748-0.5389-0.25612.1209-0.56864.34090.46371.57130.78660.3512-1.11260.7946-0.02440.25730.16960.8248-0.03840.05360.935-0.19241.325439.5409-50.5212-17.0743
471.3561-0.41010.08163.8985-1.47034.9420.4454-0.4747-0.1405-0.2941-0.6716-0.0901-0.46422.82290.20211.0287-0.50880.43721.5117-0.54731.436944.2133-47.1882-7.9166
481.44580.5456-0.27842.2487-0.26048.69850.1797-0.8770.13061.414-0.3326-0.4211.37060.15030.30270.5724-0.20910.15621.0229-0.43661.393241.9509-59.4266-9.0367
496.12621.39050.65082.4030.38125.82980.60540.6651-0.0549-0.84120.08420.37280.8172-0.09310.20390.9178-0.19580.13761.2634-0.30211.479633.1593-61.3345-12.6882
500.6201-0.1458-0.57626.95310.16338.00820.6988-0.90260.26510.4398-0.98551.0212-1.4557-1.24440.11720.9732-0.21530.12661.0081-0.16491.55337.0227-50.0949-4.4749
518.08350.06181.80520.0934-0.40122.09720.4305-0.1990.53210.8771-2.28780.88381.2251-0.64251.38111.8856-0.2553-0.21422.4582-0.46611.736547.9532-39.6843-0.5141
523.7726-0.5369-1.8593.05721.56239.6614-1.0710.2776-1.17830.8159-0.8004-0.97361.43011.08831.58551.72050.17940.2491.27830.28961.03697.99446.8303-10.8762
530.0734-0.0244-0.110.1231-0.04550.15350.25970.09-0.3701-1.41280.03070.83770.5167-0.7622-0.12881.08320.13920.29851.02470.23721.2568102.837116.4303-20.9094
544.1556-0.1802-0.38453.72070.79845.0053-0.19591.0723-0.3944-0.93810.41640.81950.89790.5801-0.04871.32870.11140.01881.29640.08750.97792.562714.2613-16.357
552.00630.00713.32514.6051-0.67146.8801-1.3198-0.52891.4709-0.17810.38461.15440.0426-1.48790.93551.11750.30470.24131.46440.23991.16189.976117.0336-8.7849
561.47221.25421.3213.8282-3.11127.480.11880.86921.23950.3095-0.34880.1332-0.36351.76-0.02651.0940.23670.08041.13190.20.9146101.836122.0474-8.4079
576.41161.2696-0.49829.21981.98420.4869-0.7324-0.15070.25680.67990.9513-2.15360.1961.94410.08940.97250.2310.21831.2830.09460.9501107.758615.8769-13.9106
584.28572.39372.49875.6481-0.19657.4244-0.2781-1.91391.25450.5095-1.02291.85870.5979-0.87-0.28071.56480.48530.67651.17580.38320.926594.829513.6515-4.6254
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 4 through 35 )H4 - 35
2X-RAY DIFFRACTION2chain 'H' and (resid 36 through 51 )H36 - 51
3X-RAY DIFFRACTION3chain 'H' and (resid 52 through 68 )H52 - 68
4X-RAY DIFFRACTION4chain 'H' and (resid 69 through 87 )H69 - 87
5X-RAY DIFFRACTION5chain 'H' and (resid 88 through 97 )H88 - 97
6X-RAY DIFFRACTION6chain 'H' and (resid 98 through 107 )H98 - 107
7X-RAY DIFFRACTION7chain 'H' and (resid 108 through 136 )H108 - 136
8X-RAY DIFFRACTION8chain 'H' and (resid 137 through 145 )H137 - 145
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 21 )B5 - 21
10X-RAY DIFFRACTION10chain 'B' and (resid 22 through 30 )B22 - 30
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 78 )B31 - 78
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 114 )B79 - 114
13X-RAY DIFFRACTION13chain 'B' and (resid 115 through 134 )B115 - 134
14X-RAY DIFFRACTION14chain 'B' and (resid 135 through 145 )B135 - 145
15X-RAY DIFFRACTION15chain 'E' and (resid 5 through 21 )E5 - 21
16X-RAY DIFFRACTION16chain 'E' and (resid 22 through 30 )E22 - 30
17X-RAY DIFFRACTION17chain 'E' and (resid 31 through 44 )E31 - 44
18X-RAY DIFFRACTION18chain 'E' and (resid 45 through 68 )E45 - 68
19X-RAY DIFFRACTION19chain 'E' and (resid 69 through 87 )E69 - 87
20X-RAY DIFFRACTION20chain 'E' and (resid 88 through 97 )E88 - 97
21X-RAY DIFFRACTION21chain 'E' and (resid 98 through 107 )E98 - 107
22X-RAY DIFFRACTION22chain 'E' and (resid 108 through 114 )E108 - 114
23X-RAY DIFFRACTION23chain 'E' and (resid 115 through 127 )E115 - 127
24X-RAY DIFFRACTION24chain 'E' and (resid 128 through 137 )E128 - 137
25X-RAY DIFFRACTION25chain 'E' and (resid 138 through 145 )E138 - 145
26X-RAY DIFFRACTION26chain 'G' and (resid 1 through 113 )G1 - 113
27X-RAY DIFFRACTION27chain 'G' and (resid 114 through 122 )G114 - 122
28X-RAY DIFFRACTION28chain 'G' and (resid 123 through 152 )G123 - 152
29X-RAY DIFFRACTION29chain 'D' and (resid 4 through 30 )D4 - 30
30X-RAY DIFFRACTION30chain 'D' and (resid 31 through 57 )D31 - 57
31X-RAY DIFFRACTION31chain 'D' and (resid 58 through 86 )D58 - 86
32X-RAY DIFFRACTION32chain 'D' and (resid 87 through 113 )D87 - 113
33X-RAY DIFFRACTION33chain 'D' and (resid 114 through 132 )D114 - 132
34X-RAY DIFFRACTION34chain 'D' and (resid 133 through 152 )D133 - 152
35X-RAY DIFFRACTION35chain 'A' and (resid 3 through 17 )A3 - 17
36X-RAY DIFFRACTION36chain 'A' and (resid 18 through 27 )A18 - 27
37X-RAY DIFFRACTION37chain 'A' and (resid 28 through 76 )A28 - 76
38X-RAY DIFFRACTION38chain 'A' and (resid 77 through 113 )A77 - 113
39X-RAY DIFFRACTION39chain 'A' and (resid 114 through 132 )A114 - 132
40X-RAY DIFFRACTION40chain 'A' and (resid 133 through 152 )A133 - 152
41X-RAY DIFFRACTION41chain 'I' and (resid 1 through 22 )I1 - 22
42X-RAY DIFFRACTION42chain 'I' and (resid 23 through 34 )I23 - 34
43X-RAY DIFFRACTION43chain 'I' and (resid 35 through 59 )I35 - 59
44X-RAY DIFFRACTION44chain 'I' and (resid 60 through 74 )I60 - 74
45X-RAY DIFFRACTION45chain 'C' and (resid 1 through 16 )C1 - 16
46X-RAY DIFFRACTION46chain 'C' and (resid 17 through 34 )C17 - 34
47X-RAY DIFFRACTION47chain 'C' and (resid 35 through 44 )C35 - 44
48X-RAY DIFFRACTION48chain 'C' and (resid 45 through 56 )C45 - 56
49X-RAY DIFFRACTION49chain 'C' and (resid 57 through 65 )C57 - 65
50X-RAY DIFFRACTION50chain 'C' and (resid 66 through 71 )C66 - 71
51X-RAY DIFFRACTION51chain 'C' and (resid 72 through 76 )C72 - 76
52X-RAY DIFFRACTION52chain 'F' and (resid 1 through 16 )F1 - 16
53X-RAY DIFFRACTION53chain 'F' and (resid 17 through 22 )F17 - 22
54X-RAY DIFFRACTION54chain 'F' and (resid 23 through 34 )F23 - 34
55X-RAY DIFFRACTION55chain 'F' and (resid 35 through 44 )F35 - 44
56X-RAY DIFFRACTION56chain 'F' and (resid 45 through 54 )F45 - 54
57X-RAY DIFFRACTION57chain 'F' and (resid 55 through 65 )F55 - 65
58X-RAY DIFFRACTION58chain 'F' and (resid 66 through 73 )F66 - 73

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万見について

-
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