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- PDB-3o65: Crystal structure of a Josephin-ubiquitin complex: Evolutionary r... -

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基本情報

登録情報
データベース: PDB / ID: 3o65
タイトルCrystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity
要素
  • Putative ataxin-3-like protein
  • Ubiquitin
キーワードhydrolase/protein binding / Papain-like fold / Ubiquitin thiolesterase / hydrolase-protein binding complex
機能・相同性
機能・相同性情報


regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / nuclear inclusion body / cellular response to misfolded protein / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / exploration behavior / positive regulation of protein monoubiquitination / fat pad development ...regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / nuclear inclusion body / cellular response to misfolded protein / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / exploration behavior / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / protein quality control for misfolded or incompletely synthesized proteins / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / energy homeostasis / regulation of neuron apoptotic process / negative regulation of TORC1 signaling / 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 / 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 / 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 / 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 / neuron projection morphogenesis / 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
類似検索 - 分子機能
Cathepsin B; Chain A - #40 / Machado-Joseph disease protein / Unstructured region C-term to UIM in Ataxin3 / Josephin domain / Josephin / Josephin domain profile. / Josephin / S15/NS1, RNA-binding / Ubiquitin interaction motif / Ubiquitin-interacting motif. ...Cathepsin B; Chain A - #40 / Machado-Joseph disease protein / Unstructured region C-term to UIM in Ataxin3 / Josephin domain / Josephin / Josephin domain profile. / Josephin / S15/NS1, RNA-binding / Ubiquitin interaction motif / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Cathepsin B; Chain A / 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 / Helix Hairpins / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-B / Polyubiquitin-C / Ataxin-3-like protein
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 / 単波長異常分散 / 解像度: 2.7 Å
データ登録者Weeks, S.D. / Grasty, K.C. / Hernandez-Cuebas, L. / Loll, P.J.
引用ジャーナル: J.Biol.Chem. / 年: 2011
タイトル: Crystal Structure of a Josephin-Ubiquitin Complex: EVOLUTIONARY RESTRAINTS ON ATAXIN-3 DEUBIQUITINATING ACTIVITY.
著者: Weeks, S.D. / Grasty, K.C. / Hernandez-Cuebas, L. / Loll, P.J.
履歴
登録2010年7月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年11月24日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22017年11月8日Group: Refinement description / カテゴリ: software / Item: _software.name
改定 1.32024年11月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Putative ataxin-3-like protein
B: Ubiquitin
C: Putative ataxin-3-like protein
D: Ubiquitin
E: Putative ataxin-3-like protein
F: Ubiquitin
G: Putative ataxin-3-like protein
H: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)123,3009
ポリマ－123,2778
非ポリマー231
水2,738152
1
A: Putative ataxin-3-like protein
B: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)30,8423
ポリマ－30,8192
非ポリマー231
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-17 kcal/mol
Surface area12510 Å2
手法PISA
2
C: Putative ataxin-3-like protein
D: Ubiquitin


分子量 (理論値)分子数
合計 (水以外)30,8192
ポリマ－30,8192
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-9 kcal/mol
Surface area13340 Å2
手法PISA
3
E: Putative ataxin-3-like protein
F: Ubiquitin


分子量 (理論値)分子数
合計 (水以外)30,8192
ポリマ－30,8192
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-8 kcal/mol
Surface area13460 Å2
手法PISA
4
G: Putative ataxin-3-like protein
H: Ubiquitin


分子量 (理論値)分子数
合計 (水以外)30,8192
ポリマ－30,8192
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-9 kcal/mol
Surface area13570 Å2
手法PISA
5
A: Putative ataxin-3-like protein
B: Ubiquitin
C: Putative ataxin-3-like protein
D: Ubiquitin
E: Putative ataxin-3-like protein
F: Ubiquitin
G: Putative ataxin-3-like protein
H: Ubiquitin
ヘテロ分子

A: Putative ataxin-3-like protein
B: Ubiquitin
C: Putative ataxin-3-like protein
D: Ubiquitin
E: Putative ataxin-3-like protein
F: Ubiquitin
G: Putative ataxin-3-like protein
H: Ubiquitin
ヘテロ分子

A: Putative ataxin-3-like protein
B: Ubiquitin
C: Putative ataxin-3-like protein
D: Ubiquitin
E: Putative ataxin-3-like protein
F: Ubiquitin
G: Putative ataxin-3-like protein
H: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)369,89927
ポリマ－369,83024
非ポリマー693
水27015
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area64220 Å2
ΔGint-319 kcal/mol
Surface area126990 Å2
手法PISA
6
A: Putative ataxin-3-like protein
B: Ubiquitin
C: Putative ataxin-3-like protein
D: Ubiquitin
E: Putative ataxin-3-like protein
F: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)92,4817
ポリマ－92,4586
非ポリマー231
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint-58 kcal/mol
Surface area36490 Å2
手法PISA
7
A: Putative ataxin-3-like protein
C: Putative ataxin-3-like protein
E: Putative ataxin-3-like protein
G: Putative ataxin-3-like protein
ヘテロ分子

A: Putative ataxin-3-like protein
C: Putative ataxin-3-like protein
E: Putative ataxin-3-like protein
G: Putative ataxin-3-like protein
ヘテロ分子

A: Putative ataxin-3-like protein
C: Putative ataxin-3-like protein
E: Putative ataxin-3-like protein
G: Putative ataxin-3-like protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)267,33715
ポリマ－267,26812
非ポリマー693
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area33800 Å2
ΔGint-239 kcal/mol
Surface area99650 Å2
手法PISA
単位格子
Length a, b, c (Å)159.150, 159.150, 146.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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要素

#1: タンパク質
Putative ataxin-3-like protein / Machado-Joseph disease protein 1-like


分子量: 22272.348 Da / 分子数: 4 / 断片: Josephin domain / 由来タイプ: 組換発現
詳細: Protein expressed as a SUMO fusion. The isolated protein has an additional non-native glycine residue on the N-terminus that was necessary to facilitate cleavage of the SUMO fusion partner.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ATX3L, ATXN3L, MJDL / プラスミド: pETHSUL / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B834(DE3) / 参照: UniProt: Q9H3M9, EC: 3.1.2.15
#2: タンパク質
Ubiquitin


分子量: 8546.848 Da / 分子数: 4 / 由来タイプ: 組換発現
詳細: Protein expressed as a fusion with M. xenopii intein. Fusion cleaved with MESNA to generate Ubiqutitn 1-75 thioester. This was reacted with 2-chloroethylamine to yield a suicide substrate ...詳細: Protein expressed as a fusion with M. xenopii intein. Fusion cleaved with MESNA to generate Ubiqutitn 1-75 thioester. This was reacted with 2-chloroethylamine to yield a suicide substrate suitable for complex formation.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / プラスミド: pETXSH / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Rosetta(DE3) / 参照: UniProt: P0CG47, UniProt: P0CG48*PLUS
#3: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Na
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 152 / 由来タイプ: 天然 / 式: H2O
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: 4.33 Å3/Da / 溶媒含有率: 71.59 %
結晶化温度: 291 K / pH: 6.5
詳細: The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted ...詳細: The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K

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データ収集

放射光源由来: シンクロトロン / サイト: NSLS / ビームライン: X6A / 波長: 0.978 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2008年10月10日 / 詳細: Toroidal focusing mirror
放射モノクロメーター: Si(111) channel cut monochromator / 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: 0.978 Å / 相対比: 1
反射最高解像度: 2.7 Å / Num. obs: 112055 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 54.522 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.42
反射 シェル
解像度 (Å)最高解像度 (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.7-2.770.5881.622307779892.9
2.77-2.850.5022.6398938260100
2.85-2.930.4533.552077792299.9
2.93-3.020.3375.871942771199.8
3.02-3.120.2847.273491757599.6
3.12-3.230.2239.269140713499.2
3.23-3.350.17911.666655692198.8
3.35-3.490.14813.963873665898.2
3.49-3.640.12216.959639627997.8
3.64-3.820.10719.457832613798.4
3.82-4.030.092353835576798.2
4.03-4.270.08224.351298550398.8
4.27-4.560.07326.547718514698.6
4.56-4.930.0682844600482599.1
4.93-5.40.06727.741918446099.6
5.4-6.040.06328.438501404099.8
6.04-6.970.06129.534109358199.9
6.97-8.540.05232.3284663006100
8.54-12.080.04337219212340100
12.080.0437.3907699277.4

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位相決定

位相決定手法: 単波長異常分散
Phasing dmFOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.66 / 反射: 54832 / Reflection acentric: 51372 / Reflection centric: 3460
Phasing dm shell
解像度 (Å)FOM FOM acentricFOM centric反射Reflection acentricReflection centric
7.7-19.9030.930.950.8725292085444
4.8-7.70.880.890.7978507066784
3.9-4.80.870.870.8395328903629
3.4-3.90.750.760.6891988699499
2.9-3.40.510.510.441601215304708
2.7-2.90.260.260.2397119315396

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解析

ソフトウェア
名称バージョン分類NB
XSCALEデータスケーリング
RESOLVE2.14位相決定
PHENIX1.6.1_357精密化
PDB_EXTRACT3.1データ抽出
HKL-2000データ収集
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.7→19.903 Å / Occupancy max: 1 / Occupancy min: 0.56 / FOM work R set: 0.8532 / SU ML: 0.33 / σ(F): 0.04 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射
Rfree0.2242 2011 3.67 %
Rwork0.1763 --
obs0.1781 54826 93.08 %
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 / Bsol: 43.243 Å2 / ksol: 0.293 e/Å3
原子変位パラメータBiso max: 414.67 Å2 / Biso mean: 78.9387 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.9061 Å2-0 Å2-0 Å2
2--1.9061 Å2-0 Å2
3----3.8123 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→19.903 Å
タンパク質核酸リガンド溶媒全体
原子数8343 0 1 152 8496
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0098515
X-RAY DIFFRACTIONf_angle_d1.1411494
X-RAY DIFFRACTIONf_chiral_restr0.0741250
X-RAY DIFFRACTIONf_plane_restr0.0041509
X-RAY DIFFRACTIONf_dihedral_angle_d15.8883170
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7002-2.79650.2881870.23614884507187
2.7965-2.90810.28351970.21785060525791
2.9081-3.040.24241960.20835129532591
3.04-3.19970.2561910.20955124531591
3.1997-3.39920.24571910.20175119531091
3.3992-3.66020.26011990.18885217541692
3.6602-4.02580.22152050.15785326553194
4.0258-4.6020.18032090.14295494570396
4.602-5.77450.19482170.14885607582498
5.7745-19.90350.20532190.15995855607499
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)
11.555-0.0037-0.26270.1463-0.21880.3650.39030.27620.4297-0.1489-0.2714-0.3176-0.1671-0.0979-0.15080.1620.06830.03740.04910.02210.432113.039382.7079-7.1956
21.98011.2459-3.15210.8564-2.57948.4835-0.05120.091-0.5763-0.09180.34090.01850.6416-0.5576-0.30420.0910.0009-0.07760.0850.06350.735-0.982864.57818.7309
30.012-0.0975-0.01740.7811-0.76382.43050.1123-0.04820.03090.2090.19920.42420.2191-0.6483-0.1822-0.09110.10720.0017-0.119-0.02580.4413.164671.70747.2943
41.9406-0.4841-1.27680.904-0.20941.21340.0789-0.31350.20010.16920.0599-0.4732-0.1350.2239-0.00120.0230.0359-0.04740.0419-0.04260.487521.671983.92236.0919
50.1041-0.4999-0.00435.9997-2.241.4546-0.344-0.11910.1446-0.23410.0048-1.77340.29530.10880.23150.08210.03680.09420.1047-0.10360.599727.656977.4564-9.9296
63.07340.2964-2.78790.6155-0.27992.53830.0056-0.695-0.6332-0.088-0.1333-0.42920.39470.96240.27650.09340.1349-0.01390.29820.16540.696414.685362.875621.0116
78.8176-0.2641-0.80321.0677-0.21980.1287-0.2196-1.37560.58020.23650.2374-0.1199-0.04920.15620.04310.04510.085-0.03070.2411-0.03690.192113.269771.160528.1042
82.8512-3.00121.19614.3989-0.74440.7974-0.4897-0.89-0.54090.50090.81180.7716-0.163-0.1244-0.28190.12070.07770.03080.17870.13980.43625.056270.153821.2223
90.0938-0.6110.12125.1707-1.93481.9768-0.3633-0.6403-0.62440.33650.7761.4121-0.1178-0.4378-0.390.11740.04740.15510.46520.20460.49482.269466.463530.4808
101.98180.0723-0.80660.6546-0.10860.61290.0888-0.4638-0.3076-0.10380.27060.81550.04490.0761-0.22480.08030.0833-0.04860.13110.05440.49777.88866.937819.2017
110.4788-1.53661.23545.2451-4.12393.64520.05290.12210.0542-1.2154-0.1093-0.17570.86280.01970.05640.3444-0.04420.25460.046-0.03190.611722.3566105.1325-17.4812
120.02690.0670.23150.16390.41411.16120.02610.08410.2519-0.1192-0.01670.0993-0.1415-0.0225-0.23940.0932-0.01960.15280.04580.04010.595214.671127.7457-15.3318
130.40140.5086-0.62644.4256-0.74252.11820.3027-0.12950.3322-0.1968-0.3222-1.7134-0.00460.49880.00090.16210.02940.33840.0610.04980.927835.0421112.9655-15.5507
140.1170.06930.36170.18680.27921.3894-0.5330.5482-0.2018-0.1372-0.03650.0753-0.00950.940.49050.4793-0.12790.48390.86820.14511.802243.615115.4187-21.0017
153.2039-0.99030.64830.85740.61661.41590.2907-0.63260.18370.4386-0.0987-0.03020.31240.3653-0.1520.16-0.03310.080.1595-0.00910.717531.9812105.6802-6.4661
161.01882.2858-1.93246.7766-3.99324.0889-0.1344-0.32330.0976-0.2751-0.2789-1.1983-0.00430.65760.3490.1055-0.03910.00760.15010.0410.948630.8367140.3428-7.8202
172.41640.6485-1.68020.9356-0.02292.33190.1837-0.12840.1404-0.28010.0002-1.0758-0.06230.3695-0.05910.1438-0.03650.31180.13260.07971.081634.3388139.5995-16.9948
181.8981.59390.64992.49421.53541.0734-0.36250.1935-0.7703-0.59830.2024-0.3079-0.34770.06430.02710.2049-0.04410.25820.04070.09220.852327.2907137.3883-16.8109
190.5211-0.60730.73071.0965-1.29362.3108-0.11590.00330.3693-0.2062-0.3039-1.1841-0.39780.06230.35410.3551-0.10550.17390.06920.08040.87326.5793148.9405-11.1526
200.39790.1253-0.08741.6888-1.85212.04750.1935-0.0208-0.3614-0.52950.236-0.85250.2409-0.1738-0.39390.0978-0.01240.14830.02570.06070.619823.5422130.425-17.303
211.23460.24770.56090.23460.21260.33120.0843-0.3973-0.0173-0.0579-0.2117-0.20640.0113-0.44210.20110.35180.12450.22540.50290.00970.237619.693982.9611-33.5285
220.6302-0.33690.2660.7219-0.19640.13180.13220.6269-0.2006-1.2357-0.2433-0.0402-0.54540.34240.01451.10130.12390.34381.1315-0.11490.23224.748375.5774-61.0736
232.8001-0.3746-1.67942.00181.52993.75160.09210.5935-0.4682-0.55890.2032-1.00830.03430.2919-0.17790.39260.07040.33550.4214-0.07540.553130.565976.6593-35.8933
240.7206-0.5771-0.33140.55290.33520.33460.04880.0673-0.3055-0.25640.0367-0.24220.01740.19480.06340.32430.14310.31180.2122-0.01470.628732.400678.3661-30.3963
252.2018-3.2705-1.6525.49851.86171.78760.0854-0.05310.3503-0.1884-0.3006-0.23870.25690.27850.17760.16840.11430.28970.2034-0.00570.880740.340792.3197-14.6939
262.06750.5914-0.90110.458-0.77551.31470.32540.23930.2816-0.0653-0.7105-0.17320.52280.74320.41590.73940.36790.3371.60720.00390.706843.693974.4681-55.654
270.5407-0.38580.54951.1533-1.18091.27920.66021.3997-0.1835-0.2595-1.1352-0.080.10690.54110.20321.3030.54030.45511.4913-0.27670.870644.824663.4817-52.7889
284.1587-3.9343-3.52883.72813.33463.09040.71260.9626-0.0301-0.8961-0.5621-0.084-0.783-0.9672-0.10141.19190.40120.64961.4339-0.45511.067633.967265.2889-51.9529
290.21820.3134-0.38651.3324-1.54111.84840.0970.5607-0.2315-0.9937-1.0281-0.0330.95810.47080.76691.32330.38980.46341.7042-0.27060.992340.830964.5956-64.1752
301.96980.04961.1230.91570.47350.8730.48151.793-0.2026-0.9822-0.3172-0.0828-0.98230.065-0.29050.9106-0.13830.40551.4393-0.46050.621229.623770.3552-51.3881
310.7549-0.0334-0.19760.64060.15710.08770.09010.55780.0217-0.5062-0.135-0.04190.0284-0.31810.01670.85710.13360.2750.74890.14990.219918.482298.4105-45.8908
320.6793-0.0403-0.78590.02410.0870.96290.36940.13390.2549-0.1983-0.0689-0.6475-0.5797-0.0693-0.3990.95930.11620.70940.75690.24341.545340.2624110.1289-32.5203
330.67070.2315-0.61151.5183-0.22920.739-0.10840.71090.3252-0.1840.1666-0.47360.2618-0.6353-0.03441.13030.11360.51741.06430.29250.446727.5113105.0193-53.3431
341.12390.0694-0.23921.74270.340.11890.09061.09630.1424-1.35180.0577-0.2526-0.2875-0.5864-0.12521.35720.04540.13841.35980.34780.29614.1479105.2716-57.7379
350.58310.134-0.17730.2525-0.02860.0541-0.17240.70320.0052-0.52880.1603-0.0649-0.0432-0.2136-0.02061.7263-0.02330.39411.22250.29770.69315.706104.3274-61.9405
360.530.41220.41870.43250.37060.34260.06240.62910.1721-0.55510.3628-0.2869-0.59460.5268-0.27131.4378-0.32930.50991.70880.47091.294944.1963115.9426-51.8694
371.6107-0.47640.84760.1951-0.24080.4619-0.40220.2856-0.13810.0344-0.1871-0.06150.08290.90620.53811.0927-0.11410.51.28250.29550.837536.2957110.8657-47.0793
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:29)A1 - 29
2X-RAY DIFFRACTION2(chain A and resid 30:57)A30 - 57
3X-RAY DIFFRACTION3(chain A and resid 58:91)A58 - 91
4X-RAY DIFFRACTION4(chain A and resid 92:167)A92 - 167
5X-RAY DIFFRACTION5(chain A and resid 168:181)A168 - 181
6X-RAY DIFFRACTION6(chain B and resid 1:16)B1 - 16
7X-RAY DIFFRACTION7(chain B and resid 17:36)B17 - 36
8X-RAY DIFFRACTION8(chain B and resid 37:48)B37 - 48
9X-RAY DIFFRACTION9(chain B and resid 49:61)B49 - 61
10X-RAY DIFFRACTION10(chain B and resid 62:76)B62 - 76
11X-RAY DIFFRACTION11(chain C and resid 1:28)C1 - 28
12X-RAY DIFFRACTION12(chain C and resid 29:90)C29 - 90
13X-RAY DIFFRACTION13(chain C and resid 91:143)C91 - 143
14X-RAY DIFFRACTION14(chain C and resid 144:161)C144 - 161
15X-RAY DIFFRACTION15(chain C and resid 162:182)C162 - 182
16X-RAY DIFFRACTION16(chain D and resid 1:22)D1 - 22
17X-RAY DIFFRACTION17(chain D and resid 23:31)D23 - 31
18X-RAY DIFFRACTION18(chain D and resid 32:52)D32 - 52
19X-RAY DIFFRACTION19(chain D and resid 53:66)D53 - 66
20X-RAY DIFFRACTION20(chain D and resid 67:76)D67 - 76
21X-RAY DIFFRACTION21(Chain E and resid 1:28)E1 - 28
22X-RAY DIFFRACTION22(Chain E and resid 29:66)E29 - 66
23X-RAY DIFFRACTION23(Chain E and resid 67:149)E67 - 149
24X-RAY DIFFRACTION24(Chain E and resid 150:181)E150 - 181
25X-RAY DIFFRACTION25(Chain E and resid 182:187)E182 - 187
26X-RAY DIFFRACTION26(Chain F and resid 1:14)F1 - 14
27X-RAY DIFFRACTION27(Chain F and resid 15:37)F15 - 37
28X-RAY DIFFRACTION28(Chain F and resid 38:43)F38 - 43
29X-RAY DIFFRACTION29(Chain F and resid 44:67)F44 - 67
30X-RAY DIFFRACTION30(Chain F and resid 68:76)F68 - 76
31X-RAY DIFFRACTION31(Chain G and resid 2:45)G2 - 45
32X-RAY DIFFRACTION32(Chain G and resid 46:66)G46 - 66
33X-RAY DIFFRACTION33(Chain G and resid 67:107)G67 - 107
34X-RAY DIFFRACTION34(Chain G and resid 108:142)G108 - 142
35X-RAY DIFFRACTION35(Chain G and resid 143:181)G143 - 181
36X-RAY DIFFRACTION36(Chain H and resid 1:64)H1 - 64
37X-RAY DIFFRACTION37(Chain H and resid 65:76)H65 - 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