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- PDB-4ddg: Crystal structure of human OTUB1/UbcH5b~Ub/Ub -

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基本情報

登録情報
データベース: PDB / ID: 4ddg
タイトルCrystal structure of human OTUB1/UbcH5b~Ub/Ub
要素
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
キーワードHYDROLASE/LIGASE / inhibition / HYDROLASE-LIGASE complex
機能・相同性
機能・相同性情報


negative regulation of double-strand break repair / ubiquitin-protein transferase inhibitor activity / deNEDDylase activity / protein K48-linked deubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein deubiquitination / protein K48-linked ubiquitination / protein autoubiquitination ...negative regulation of double-strand break repair / ubiquitin-protein transferase inhibitor activity / deNEDDylase activity / protein K48-linked deubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein deubiquitination / protein K48-linked ubiquitination / protein autoubiquitination / 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 / positive regulation of TORC1 signaling / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / 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 / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / ubiquitin binding / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Translesion synthesis by POLI / 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 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / Regulation of NF-kappa B signaling / 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 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Negative regulation of FGFR2 signaling / Regulation of TNFR1 signaling / Negative regulation of FGFR4 signaling / Degradation of AXIN / Stabilization of p53 / Hh mutants are degraded by ERAD
類似検索 - 分子機能
Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. ...Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / 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 / Papain-like cysteine peptidase superfamily / : / 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 / Phosphorylase Kinase; domain 1 / Roll / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin thioesterase OTUB1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2987 Å
データ登録者Juang, Y.C. / Sanches, M. / Sicheri, F.
引用ジャーナル: Mol.Cell / 年: 2012
タイトル: OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function.
著者: Juang, Y.C. / Landry, M.C. / Sanches, M. / Vittal, V. / Leung, C.C. / Ceccarelli, D.F. / Mateo, A.R. / Pruneda, J.N. / Mao, D.Y. / Szilard, R.K. / Orlicky, S. / Munro, M. / Brzovic, P.S. / ...著者: Juang, Y.C. / Landry, M.C. / Sanches, M. / Vittal, V. / Leung, C.C. / Ceccarelli, D.F. / Mateo, A.R. / Pruneda, J.N. / Mao, D.Y. / Szilard, R.K. / Orlicky, S. / Munro, M. / Brzovic, P.S. / Klevit, R.E. / Sicheri, F. / Durocher, D.
履歴
登録2012年1月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年2月22日Provider: repository / タイプ: Initial release
改定 1.12012年5月23日Group: Other
改定 1.22017年8月2日Group: Source and taxonomy / カテゴリ: entity_src_gen
改定 1.32017年11月15日Group: Refinement description / カテゴリ: software
改定 1.42023年9月13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 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
改定 1.52024年11月27日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
B: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
C: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C
J: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
K: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
L: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
M: Polyubiquitin-C
N: Polyubiquitin-C
O: Polyubiquitin-C
P: Polyubiquitin-C
Q: Polyubiquitin-C
R: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)377,61718
ポリマ－377,61718
非ポリマー00
水00
1
A: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
B: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
C: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)188,8099
ポリマ－188,8099
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-69 kcal/mol
Surface area63270 Å2
手法PISA
2
J: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
K: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
L: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
M: Polyubiquitin-C
N: Polyubiquitin-C
O: Polyubiquitin-C
P: Polyubiquitin-C
Q: Polyubiquitin-C
R: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)188,8099
ポリマ－188,8099
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-66 kcal/mol
Surface area63600 Å2
手法PISA
単位格子
Length a, b, c (Å)134.566, 104.928, 148.479
Angle α, β, γ (deg.)90.00, 104.19, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11G
21H
31I
41Q
51P
61R
12A
22B
32C
42J
52K
62L
13A
23B
33C
43J
53K
63L
14D
24E
34F
44N
54M
64O

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYchain 'G'GG1 - 761 - 76
21METMETGLYGLYchain 'H'HH1 - 761 - 76
31METMETGLYGLYchain 'I'II1 - 761 - 76
41METMETGLYGLYchain 'Q'QQ1 - 761 - 76
51METMETGLYGLYchain 'P'PP1 - 761 - 76
61METMETGLYGLYchain 'R'RR1 - 761 - 76
12ALAALAALAALAchain 'A' and (resseq 1:150 ) and (not element H) and (not element D)AA02
22ALAALAALAALAchain 'B' and (resseq 1:150 ) and (not element H) and (not element D)BB02
32ALAALAALAALAchain 'C' and (resseq 1:150 ) and (not element H) and (not element D)CC02
42ALAALAALAALAchain 'J' and (resseq 1:150 ) and (not element H) and (not element D)JJ02
52ALAALAALAALAchain 'K' and (resseq 1:150 ) and (not element H) and (not element D)KK02
62ALAALAALAALAchain 'L' and (resseq 1:150 ) and (not element H) and (not element D)LL02
13ALAALAALAALAchain 'A' and (resseq 1025:1271 ) and (not element H) and (not element D)AA02
23ALAALAALAALAchain 'B' and (resseq 1025:1271 ) and (not element H) and (not element D)BB02
33ALAALAALAALAchain 'C' and (resseq 1025:1271 ) and (not element H) and (not element D)CC02
43ALAALAALAALAchain 'J' and (resseq 1025:1271 ) and (not element H) and (not element D)JJ02
53ALAALAALAALAchain 'K' and (resseq 1025:1271 ) and (not element H) and (not element D)KK02
63ALAALAALAALAchain 'L' and (resseq 1025:1271 ) and (not element H) and (not element D)LL02
14METMETGLYGLYchain 'D'DD1 - 761 - 76
24METMETGLYGLYchain 'E'EE1 - 761 - 76
34METMETGLYGLYchain 'F'FF1 - 761 - 76
44METMETGLYGLYchain 'N'NN1 - 761 - 76
54METMETGLYGLYchain 'M'MM1 - 761 - 76
64METMETGLYGLYchain 'O'OO1 - 761 - 76

NCSアンサンブル:
ID
1
2
3
4
詳細The biological complex defined by the author consists of: Complex 1: chain H, chain E, residues 1 to 147 of chain C, and residues 1025-1271 of Chain B; Complex 2: chain G, chain D, residues 1 to 147 of chain B, and residues 1025-1271 of Chain A; Complex 3: chain I, chain F, residues 1 to 147 of chain A, and residues 1025-1271 of Chain C; Complex 4: chain Q, chain N, residues 1 to 147 of chain L, and residues 1025-1271 of Chain K; Complex 5: chain P, chain M, residues 1 to 147 of chain K, and residues 1025-1271 of Chain J; Complex 6: chain R, chain O, residues 1 to 147 of chain J, and residues 1025-1271 of Chain L

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要素

#1: タンパク質
Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / Deubiquitinating enzyme OTUB1 / OTU domain-containing ubiquitin aldehyde-binding protein 1 / Otubain-1 / hOTU1 / Ubiquitin-specific-processing protease OTUB1


分子量: 45782.543 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト)
遺伝子: E2, HSPC263, OTB1, OTU1, OTUB1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21
参照: UniProt: P62837, UniProt: Q96FW1, ubiquitin-protein ligase, ubiquitinyl hydrolase 1
#2: タンパク質
Polyubiquitin-C / Ubiquitin


分子量: 8576.831 Da / 分子数: 12 / 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 (大腸菌) / 参照: UniProt: P0CG48
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: 2.69 Å3/Da / 溶媒含有率: 54.28 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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データ収集

回折平均測定温度: 198.25 K
放射光源由来: シンクロトロン / サイト: CLSI / ビームライン: 08ID-1 / 波長: 0.97949 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2011年12月12日
放射モノクロメーター: ACCEL/BRUKER double crystal monochromator (DCM)
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: 0.97949 Å / 相対比: 1
反射解像度: 3.2987→49.29 Å / Num. all: 60666 / Num. obs: 60387 / % possible obs: 99.54 %
反射 シェル解像度: 3.2987→3.5 Å / % possible all: 97.6

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解析

ソフトウェア
名称バージョン分類
MxDCデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.7.1_743)精密化
XDSデータ削減
XDS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 ENTRY 2ESK AND 2ZFY

2esk

2zfy


解像度: 3.2987→49.121 Å / SU ML: 0.4 / σ(F): 1.99 / 位相誤差: 33.26 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射
Rfree0.2802 3053 5.06 %
Rwork0.2332 --
obs0.2356 60385 99.54 %
all-60402 -
溶媒の処理減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 110.304 Å2 / ksol: 0.311 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--4.7794 Å20 Å2-2.5662 Å2
2--3.1302 Å2-0 Å2
3---1.6492 Å2
精密化ステップサイクル: LAST / 解像度: 3.2987→49.121 Å
タンパク質核酸リガンド溶媒全体
原子数26568 0 0 0 26568
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00427126
X-RAY DIFFRACTIONf_angle_d0.93836660
X-RAY DIFFRACTIONf_dihedral_angle_d16.51110326
X-RAY DIFFRACTIONf_chiral_restr0.074032
X-RAY DIFFRACTIONf_plane_restr0.0054782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11G601X-RAY DIFFRACTIONPOSITIONAL0.001
12H601X-RAY DIFFRACTIONPOSITIONAL0.001
13I601X-RAY DIFFRACTIONPOSITIONAL0.001
14Q601X-RAY DIFFRACTIONPOSITIONAL0.001
15P601X-RAY DIFFRACTIONPOSITIONAL0.001
16R601X-RAY DIFFRACTIONPOSITIONAL0.001
21A1191X-RAY DIFFRACTIONPOSITIONAL0.003
22B1191X-RAY DIFFRACTIONPOSITIONAL0.003
23C1191X-RAY DIFFRACTIONPOSITIONAL0.003
24J1191X-RAY DIFFRACTIONPOSITIONAL0.002
25K1191X-RAY DIFFRACTIONPOSITIONAL0.002
26L1191X-RAY DIFFRACTIONPOSITIONAL0.003
31A2026X-RAY DIFFRACTIONPOSITIONAL0.002
32B2026X-RAY DIFFRACTIONPOSITIONAL0.002
33C2026X-RAY DIFFRACTIONPOSITIONAL0.002
34J2026X-RAY DIFFRACTIONPOSITIONAL0.001
35K2026X-RAY DIFFRACTIONPOSITIONAL0.002
36L2026X-RAY DIFFRACTIONPOSITIONAL0.002
41D601X-RAY DIFFRACTIONPOSITIONAL0.001
42E601X-RAY DIFFRACTIONPOSITIONAL0.001
43F601X-RAY DIFFRACTIONPOSITIONAL0.001
44N601X-RAY DIFFRACTIONPOSITIONAL0.001
45M601X-RAY DIFFRACTIONPOSITIONAL0.001
46O601X-RAY DIFFRACTIONPOSITIONAL0.001
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2987-3.35020.39611360.37652567X-RAY DIFFRACTION99
3.3502-3.40520.42591450.37182578X-RAY DIFFRACTION100
3.4052-3.46390.41291280.36972597X-RAY DIFFRACTION99
3.4639-3.52680.41141240.32822601X-RAY DIFFRACTION100
3.5268-3.59460.3751390.32472582X-RAY DIFFRACTION100
3.5946-3.6680.40921260.32162610X-RAY DIFFRACTION100
3.668-3.74770.34551450.2932621X-RAY DIFFRACTION100
3.7477-3.83490.35671430.27482588X-RAY DIFFRACTION100
3.8349-3.93070.33761410.28182564X-RAY DIFFRACTION99
3.9307-4.0370.30171540.24652607X-RAY DIFFRACTION100
4.037-4.15570.27741350.2452619X-RAY DIFFRACTION100
4.1557-4.28980.3141380.22612564X-RAY DIFFRACTION100
4.2898-4.4430.26981300.21222635X-RAY DIFFRACTION100
4.443-4.62070.25261250.20752641X-RAY DIFFRACTION100
4.6207-4.83090.27471410.19862591X-RAY DIFFRACTION100
4.8309-5.08530.25761450.21162598X-RAY DIFFRACTION100
5.0853-5.40360.27331380.21832610X-RAY DIFFRACTION100
5.4036-5.82020.27141400.24162654X-RAY DIFFRACTION100
5.8202-6.40470.32061470.25072627X-RAY DIFFRACTION100
6.4047-7.32890.26881710.20212607X-RAY DIFFRACTION100
7.3289-9.22360.19911330.17382659X-RAY DIFFRACTION100
9.2236-49.12680.16841290.17722612X-RAY DIFFRACTION95
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)
14.0807-0.54620.32554.9080.94393.3389-0.419-0.8663-0.26640.54220.5825-0.4760.47961.8712-0.20260.94190.14920.16581.63360.00610.4728-58.9105-14.46029.1567
20.4574-0.38890.25190.6582-0.41360.2849-1.0755-0.82521.45521.0662-0.0036-0.6423-1.5783-0.1924-0.48981.93240.3414-1.60011.0264-0.23341.8534-22.93399.875417.1484
33.078-0.57960.47055.10690.15214.0853-0.2898-0.10990.28450.5541-0.2047-0.23870.18620.1770.5010.1894-0.0208-0.05780.30640.02510.2552-36.0794-9.0058-9.4012
42.3740.0549-0.31741.5529-0.53223.31430.05980.2840.8090.37170.4770.5065-0.964-0.5032-0.28430.42010.12920.13670.41430.30350.7802-54.331913.8772-42.3539
53.3648-0.077-0.98243.19540.32383.83010.2069-0.2358-0.2104-0.27640.08820.02130.37180.2477-0.03520.4495-0.03270.40840.32320.34310.1768-70.490441.049720.0663
63.4590.66620.28952.146-0.39613.1508-0.43520.3382-0.5676-0.03130.1473-0.1456-0.12640.00080.29780.37690.01080.10250.32280.02320.0702-45.202355.8861-10.6272
72.9494-1.18230.69372.0690.7833.731-1.1612-0.06340.97710.2854-0.8336-1.6717-1.25011.02781.11791.12410.0984-0.47241.5070.82552.3957-1.9547-6.997321.3419
84.13830.65121.72962.7618-0.10123.957-0.12680.4125-0.9753-0.3865-0.1439-0.61250.52771.46680.3010.24640.00240.12070.77110.16950.5682-56.1234-3.5318-63.2212
91.16080.1223-0.55182.11241.93583.71890.09780.9546-1.1516-0.242-0.0184-0.97431.18291.03090.28481.08330.2070.42931.5423-0.4931.3303-31.184635.142-21.2524
103.45971.2149-0.65222.2868-0.05460.1409-0.7744-1.9095-0.59161.03450.246-0.2977-0.7385-1.50420.07581.19770.7024-0.09692.435-0.16441.0369-31.3618-12.909626.6998
111.69240.4790.43953.6849-0.14954.8960.1682-0.40190.3535-0.0156-0.26450.04040.7237-0.3778-0.01910.12590.0235-0.15480.7978-0.09380.3539-98.122247.760941.5723
125.20070.402-2.00172.57060.9272.9649-0.5086-0.1912-1.7469-0.0422-0.26820.59530.8081-0.29660.43230.3589-0.21970.2470.5334-0.16810.924-92.0553-15.475-6.5831
133.590.93150.74163.8721-0.35532.15680.00850.0968-0.1019-0.0482-0.23110.05520.01-0.57210.19690.44710.11710.07011.39320.26911.10179.8367-13.3747-80.2532
142.55070.24750.98594.7121-0.28893.7965-0.3027-0.10470.4058-0.1071-0.0958-0.4224-0.77950.05520.36950.41780.0522-0.1560.66580.07190.5706-13.0959-8.5163-61.5791
152.2311-0.6458-0.60114.19690.02213.0654-0.14860.17420.4181-0.3245-0.0793-0.2555-0.710.4860.22040.7401-0.1225-0.33610.45660.11840.5977-26.940410.6581-87.4801
161.18210.60020.36481.1696-0.37972.0293-0.4755-0.53481.26910.2594-0.0378-0.7963-0.56070.8415-2.2680.20540.0083-0.8521.3101-0.74131.99974.872813.396-27.3988
172.96240.3984-1.2623.4864-1.5033.667-0.09640.20170.4343-0.4078-0.09790.16910.1852-0.54540.09820.4329-0.10120.08711.3269-0.40341.266421.52541.502-93.1211
182.9861-0.42220.27132.97040.17752.4779-0.438-0.3978-0.39930.22890.317-0.3195-0.33120.27660.0830.3013-0.01860.00320.4407-0.1350.1486-4.0556.3017-61.992
194.47890.6505-0.68031.6485-1.08443.2077-0.8028-0.54620.13120.1359-0.12530.47740.5436-0.57210.83721.1272-0.1738-0.19820.7074-0.23810.8545-47.1965-7.0626-92.1962
201.83570.430.43480.9924-0.21242.3652-0.1334-0.452-0.89320.0405-0.5350.2396-0.0706-1.2376-0.29570.47760.1036-0.36641.6826-0.4341.53236.9972-4.6255-7.2317
211.94950.093-0.07823.0763-1.28244.24980.098-1.6565-1.49530.5155-0.18930.79281.4231-0.48870.10021.0656-0.03510.42371.49180.49721.3305-18.051435.1583-52.1277
224.7753-0.60571.23683.24710.0322.73220.3415-0.5625-1.1439-0.509-0.1719-0.13260.04381.1875-0.09630.67570.00250.00150.8090.23990.8103-17.7606-11.2334-97.5855
231.0545-0.52680.73342.06160.7664.5475-0.15280.74910.7884-0.1670.19410.28220.4024-0.40810.07180.3084-0.3418-0.3720.91250.31040.758649.308347.2202-114.8069
244.81750.7614-1.87754.0405-0.89933.2463-0.6080.1884-1.83030.10670.0333-0.35320.4703-0.28670.47160.50160.0060.1770.57360.04140.902842.9515-14.7086-64.1468
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:147)
2X-RAY DIFFRACTION2chain 'A' and (resseq 1025:1271)
3X-RAY DIFFRACTION3chain 'B' and (resseq -1:147)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1025:1271)
5X-RAY DIFFRACTION5chain 'C' and (resseq -1:147)
6X-RAY DIFFRACTION6chain 'C' and (resseq 1025:1271)
7X-RAY DIFFRACTION7chain 'D' and (resseq 1:76)
8X-RAY DIFFRACTION8chain 'E' and (resseq 1:76)
9X-RAY DIFFRACTION9chain 'F' and (resseq 1:76)
10X-RAY DIFFRACTION10chain 'G' and (resseq 1:76)
11X-RAY DIFFRACTION11chain 'H' and (resseq 1:76)
12X-RAY DIFFRACTION12chain 'I' and (resseq 1:76)
13X-RAY DIFFRACTION13chain 'J' and (resseq -1:147)
14X-RAY DIFFRACTION14chain 'K' and (resseq -1:147)
15X-RAY DIFFRACTION15chain 'J' and (resseq 1025:1271)
16X-RAY DIFFRACTION16chain 'K' and (resseq 1025:1271)
17X-RAY DIFFRACTION17chain 'L' and (resseq -1:147)
18X-RAY DIFFRACTION18chain 'L' and (resseq 1025:1271)
19X-RAY DIFFRACTION19chain 'M' and (resseq 1:76)
20X-RAY DIFFRACTION20chain 'N' and (resseq 1:76)
21X-RAY DIFFRACTION21chain 'O' and (resseq 1:76)
22X-RAY DIFFRACTION22chain 'P' and (resseq 1:76)
23X-RAY DIFFRACTION23chain 'Q' and (resseq 1:76)
24X-RAY DIFFRACTION24chain 'R' and (resseq 1:76)

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る