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- PDB-6dc6: Crystal structure of human ubiquitin activating enzyme E1 (Uba1) ... -

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基本情報

登録情報
データベース: PDB / ID: 6dc6
タイトルCrystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin
要素
  • Ubiquitin-like modifier-activating enzyme 1
  • Ubiquitinユビキチン
キーワードSIGNALING PROTEIN/LIGASE / Ubiquitin (ユビキチン) / E1 / adenylation (アデニリル化) / thioester bond (チオエステル) / E2 / transthiolation / SIGNALING PROTEIN / SIGNALING PROTEIN-LIGASE complex
機能・相同性
機能・相同性情報


ユビキチン活性化酵素 / ubiquitin activating enzyme activity / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination ...ユビキチン活性化酵素 / ubiquitin activating enzyme activity / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / グリコーゲン合成 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / NF-kB is activated and signals survival / Regulation of PTEN localization / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / small-subunit processome / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / cytosolic ribosome / TICAM1, RIP1-mediated IKK complex recruitment / Gap-filling DNA repair synthesis and ligation in GG-NER / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling
類似検索 - 分子機能
Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain ...Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2 / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, UFD domain / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / ユビキチン活性化酵素 / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / Ubiquitin conserved site / Ubiquitin domain / 3-Layer(bba) Sandwich / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / ユビキチン様タンパク質 / Ubiquitin domain profile. / Zinc-binding ribosomal protein / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / NAD(P)-binding Rossmann-like Domain / Roll / Βバレル / ロスマンフォールド / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
PYROPHOSPHATE 2- / Ubiquitin-like modifier-activating enzyme 1 / Ubiquitin-ribosomal protein eS31 fusion 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 / 分子置換 / 解像度: 3.14 Å
データ登録者Lv, Z. / Yuan, L. / Williams, K.M. / Atkison, J.H. / Olsen, S.K.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115568 米国
引用ジャーナル: J. Biol. Chem. / 年: 2018
タイトル: Crystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity.
著者: Lv, Z. / Williams, K.M. / Yuan, L. / Atkison, J.H. / Olsen, S.K.
履歴
登録2018年5月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年10月10日Provider: repository / タイプ: Initial release
改定 1.12018年10月17日Group: Data collection / Database references / Structure summary
カテゴリ: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
改定 1.22018年12月5日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年10月11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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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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-like modifier-activating enzyme 1
B: Ubiquitin
C: Ubiquitin-like modifier-activating enzyme 1
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)245,27310
ポリマ－244,8244
非ポリマー4496
水0
1
A: Ubiquitin-like modifier-activating enzyme 1
B: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)122,6365
ポリマ－122,4122
非ポリマー2253
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-27 kcal/mol
Surface area46670 Å2
手法PISA
2
C: Ubiquitin-like modifier-activating enzyme 1
D: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)122,6365
ポリマ－122,4122
非ポリマー2253
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-26 kcal/mol
Surface area47650 Å2
手法PISA
単位格子
Length a, b, c (Å)104.999, 70.438, 188.851
Angle α, β, γ (deg.)90.000, 95.190, 90.000
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
11(chain A and (resseq 49:108 or (resid 109 and (name...
21(chain C and (resseq 49:108 or (resid 109 and (name...
12(chain B and ((resid 1 and (name N or name...
22(chain D and ((resid 1 and (name N or name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 49:108 or (resid 109 and (name...A0
211(chain C and (resseq 49:108 or (resid 109 and (name...C0
112(chain B and ((resid 1 and (name N or name...B1
122(chain B and ((resid 1 and (name N or name...B1 - 76
132(chain B and ((resid 1 and (name N or name...B1 - 76
142(chain B and ((resid 1 and (name N or name...B1 - 76
152(chain B and ((resid 1 and (name N or name...B1 - 76
162(chain B and ((resid 1 and (name N or name...B1 - 76
212(chain D and ((resid 1 and (name N or name...D1
222(chain D and ((resid 1 and (name N or name...D1 - 76
232(chain D and ((resid 1 and (name N or name...D1 - 76
242(chain D and ((resid 1 and (name N or name...D1 - 76
252(chain D and ((resid 1 and (name N or name...D1 - 76
262(chain D and ((resid 1 and (name N or name...D1 - 76

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 Ubiquitin-like modifier-activating enzyme 1 / Protein A1S9 / Ubiquitin-activating enzyme E1


分子量: 113504.680 Da / 分子数: 2 / 変異: C632A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBA1, A1S9T, UBE1 / プラスミド: pFastbac-HTB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P22314, ユビキチン活性化酵素
#2: タンパク質 Ubiquitin / ユビキチン


分子量: 8907.232 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pET29-NTEV / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62979
#3: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mg
#4: 化合物 ChemComp-POP / PYROPHOSPHATE 2- / ピロリン酸塩


分子量: 175.959 Da / 分子数: 2 / 由来タイプ: 合成 / 式: H2O7P2

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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: 2.86 Å3/Da / 溶媒含有率: 56.95 %
結晶化温度: 285 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 / 詳細: 0.1 M MgCl2, 0.2 M Tris HCl pH 8.0, 20% PEG 4000

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データ収集

回折平均測定温度: 108 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: RAYONIX MX300-HS / 検出器: CCD / 日付: 2015年12月16日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.15→50 Å / Num. obs: 46012 / % possible obs: 94.6 % / 冗長度: 2.9 % / Biso Wilson estimate: 70.5 Å2 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.088 / Rrim(I) all: 0.165 / Χ2: 0.946 / Net I/σ(I): 5.7 / Num. measured all: 133897
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.262.50.45945030.5920.3270.5660.49593.5
3.26-3.392.60.38245460.7460.2620.4660.56394.2
3.39-3.552.70.32845760.810.2230.3990.72694.8
3.55-3.732.80.25845900.8920.170.310.87694.9
3.73-3.972.80.21445980.9180.140.2571.01195.2
3.97-4.2730.15645890.9710.0980.1850.99295.6
4.27-4.73.10.14647110.9630.090.1711.14496.1
4.7-5.383.10.12746220.9750.0780.1491.28795.3
5.38-6.783.20.09846400.9830.0610.1161.05994.7
6.78-503.30.0846370.9860.0490.0951.00691.7

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
HKL-2000データ削減
HKL-2000データスケーリング
PDB_EXTRACT3.24データ抽出
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3CMM

3cmm


解像度: 3.14→41.702 Å / SU ML: 0.5 / 交差検証法: THROUGHOUT / σ(F): 1.41 / 位相誤差: 27.94 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.25 1997 4.35 %
Rwork0.2125 43931 -
obs0.2142 45928 94.51 %
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: 200.06 Å2 / Biso mean: 90.0623 Å2 / Biso min: 3.78 Å2
精密化ステップサイクル: final / 解像度: 3.14→41.702 Å
タンパク質核酸リガンド溶媒全体
原子数16866 0 22 0 16888
Biso mean--54.06 --
残基数----2140
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00317244
X-RAY DIFFRACTIONf_angle_d0.55423385
X-RAY DIFFRACTIONf_chiral_restr0.0412590
X-RAY DIFFRACTIONf_plane_restr0.0043077
X-RAY DIFFRACTIONf_dihedral_angle_d12.98410415
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A8103X-RAY DIFFRACTION10.741TORSIONAL
12C8103X-RAY DIFFRACTION10.741TORSIONAL
21B752X-RAY DIFFRACTION10.741TORSIONAL
22D752X-RAY DIFFRACTION10.741TORSIONAL
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 (%)
3.1401-3.21860.39111380.3413053319193
3.2186-3.30560.34771410.31213096323794
3.3056-3.40280.36671420.28683102324495
3.4028-3.51260.31861430.27653151329495
3.5126-3.63810.30251400.25273092323295
3.6381-3.78370.29661420.25083120326295
3.7837-3.95570.31571440.23593161330595
3.9557-4.16410.24311430.21183152329595
4.1641-4.42470.24171450.18643173331896
4.4247-4.76590.19651440.18063162330696
4.7659-5.24470.21921440.17783187333195
5.2447-6.00170.25751440.20363172331695
6.0017-7.55420.21381440.18973161330594
7.5542-41.70550.16691430.1583149329291
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)
11.50470.2035-0.26022.3540.92011.66520.23530.0937-0.0782-0.931-0.2634-0.2486-0.3473-0.43840.06960.74130.12590.27180.4789-0.01540.4737525.3829-79.2782378.99
23.05120.16721.08361.05520.39110.48380.2846-0.7572-0.39610.1808-0.1119-0.50240.1351-0.3785-0.17220.3375-0.00190.12040.74180.07530.7245545.6472-75.0024412.9038
31.1654-0.11060.02741.34420.55221.10020.0924-0.2430.1350.2222-0.2123-0.0485-0.3043-0.19040.08730.4822-0.04780.16660.56290.00860.4814526.1878-64.7808409.8227
48.35550.4201-4.01136.6141-1.92422.787-0.83080.2482-1.4511-0.1820.24140.06640.9545-0.30120.55130.6963-0.07350.48750.9555-0.03620.8242516.5739-95.4133395.5088
56.7896-3.8376-5.20946.60423.47214.4415-0.14440.1303-2.02720.46070.56140.69130.16550.0373-0.37810.93360.16990.62670.91660.16361.826514.9687-99.7506399.2005
67.93550.5323-2.71080.7742-2.23446.6307-0.2754-0.194-1.3710.457-0.21840.91740.8687-1.51010.48650.9164-0.25970.631.60430.20511.4731502.8395-97.061403.5763
76.80140.55374.67134.60361.89823.7139-0.2246-2.102-1.08722.1815-0.42770.29690.7629-0.22750.58630.82940.12220.19481.26230.2980.6478511.2577-91.4252406.8017
89.84932.14757.26212.74483.59247.30830.8732-1.0921-1.83851.8893-0.2865-0.02970.03120.1632-0.60920.7242-0.1685-0.00191.40780.39321.0073519.8186-92.6619407.0035
99.58380.74984.44914.3371-3.06494.80881.1-2.79820.2142.3199-0.67461.2544-0.4253-1.8821-0.41570.9585-0.33710.21390.9908-0.10390.7572515.4057-84.053402.4331
102.58140.61322.50480.23550.44612.6787-0.1767-0.5622-0.36440.31750.20730.8928-0.014-0.93620.01370.4078-0.00390.27140.7454-0.08050.8952507.3423-84.9697393.0415
113.22193.8635-5.11616.0531-7.14218.83820.7357-1.11.31632.84050.24783.1318-1.7109-1.3594-0.98210.8514-0.02920.26930.8923-0.20971.0581504.6864-83.8725402.565
128.8367-5.0652.79193.0027-1.5450.9126-0.60052.1144-0.5779-0.63411.48782.66380.3543-0.9532-0.8720.7975-0.55610.19051.58260.00121.2187500.9651-89.5109398.9283
138.12440.62271.94848.5361-6.09165.05590.14574.5474-2.9365-1.3382-1.00211.42851.013-0.49320.86020.5807-0.05920.23761.5259-0.3591.378503.9074-97.5267393.1046
146.30376.2149-6.94297.8498-8.10648.5706-0.67740.8961-2.5257-0.71580.5915-1.79031.569-0.84510.05840.9241-0.12030.31080.4064-0.05840.75514.0843-90.4094394.2322
155.79265.4603-5.66615.7536-4.3548.4082-0.1872-0.6221-1.01180.2363-0.162-2.49450.48061.44390.33850.43130.23770.00610.6224-0.12420.7305525.4077-75.9848396.3981
161.9130.45390.15240.3534-0.37152.690.2346-0.3506-0.18580.9697-0.14630.0099-0.23470.34610.37762.0666-0.17640.43380.61990.11780.4257491.968-63.6335475.4486
172.3717-3.27330.59317.25283.99758.620.43660.8315-1.9455-0.06630.38690.46351.50460.7726-0.59251.0030.1864-0.00980.7314-0.3131.5318493.4933-87.0615443.7691
180.6771-0.0384-0.95410.00550.0341.34720.1233-0.6553-0.31431.158-0.2628-0.6278-0.37340.83490.22642.2281-0.3454-0.26941.0270.28030.7415511.7246-61.2355480.3585
191.8015-1.0951-0.31620.9029-0.35941.45150.2381-0.0230.49240.8352-0.1451-0.1161-0.71860.3302-0.10471.8319-0.18040.25780.51330.01850.5739501.2356-40.5171460.9169
204.7353-1.44752.41051.1333-0.55311.4331-0.23380.97650.26450.2589-0.30870.0497-0.53070.43580.5730.806-0.12110.17490.78990.03890.53491.227-49.4677434.1396
212.5772-1.211.77496.2916-0.3921.984-0.0760.5207-0.24790.1907-0.0050.4186-0.0891-0.24850.11130.5309-0.05620.25560.811-0.23570.6383475.316-56.2929429.3756
221.84950.591-1.14271.8913-0.59062.72140.318-0.5339-0.0140.9717-0.4928-0.3554-0.32860.54170.18581.0338-0.1109-0.04910.45920.04250.4673510.7716-54.4142455.9561
238.2838-1.0209-3.60446.1127-0.1037.8680.21431.0840.5326-0.2182-0.3133-0.4419-0.8836-0.0580.11450.7362-0.13130.01560.74020.24670.6684523.3259-33.804433.2542
244.43483.8581-2.38888.3412-2.7656.5043-0.51140.687-1.8469-0.68050.2561-1.52480.21970.6710.23660.9259-0.3540.32041.0307-0.00981.3858516.4697-77.9078453.4169
259.4941-3.7317-0.55827.9553-0.96948.8781-0.36513.3749-1.8369-2.0029-0.3452-0.60790.8940.22470.68671.1197-0.07650.42471.4301-0.27410.9013515.8408-72.9163444.9464
266.9386-0.2317-4.15222.80353.0825.58420.454-0.2934-0.8460.1252-0.5051-0.67160.73330.91670.01780.9695-0.1129-0.01830.67570.3120.7824517.9868-67.3676454.8146
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 590 )A49 - 590
2X-RAY DIFFRACTION2chain 'A' and (resid 591 through 776 )A591 - 776
3X-RAY DIFFRACTION3chain 'A' and (resid 777 through 1057 )A777 - 1057
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 11 )B1 - 11
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 16 )B12 - 16
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 22 )B17 - 22
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 31 )B23 - 31
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 37 )B32 - 37
9X-RAY DIFFRACTION9chain 'B' and (resid 38 through 44 )B38 - 44
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 49 )B45 - 49
11X-RAY DIFFRACTION11chain 'B' and (resid 50 through 54 )B50 - 54
12X-RAY DIFFRACTION12chain 'B' and (resid 55 through 59 )B55 - 59
13X-RAY DIFFRACTION13chain 'B' and (resid 60 through 64 )B60 - 64
14X-RAY DIFFRACTION14chain 'B' and (resid 65 through 70 )B65 - 70
15X-RAY DIFFRACTION15chain 'B' and (resid 71 through 76 )B71 - 76
16X-RAY DIFFRACTION16chain 'C' and (resid 49 through 234 )C49 - 234
17X-RAY DIFFRACTION17chain 'C' and (resid 235 through 295 )C235 - 295
18X-RAY DIFFRACTION18chain 'C' and (resid 296 through 477 )C296 - 477
19X-RAY DIFFRACTION19chain 'C' and (resid 478 through 601 )C478 - 601
20X-RAY DIFFRACTION20chain 'C' and (resid 602 through 702 )C602 - 702
21X-RAY DIFFRACTION21chain 'C' and (resid 703 through 872 )C703 - 872
22X-RAY DIFFRACTION22chain 'C' and (resid 873 through 962 )C873 - 962
23X-RAY DIFFRACTION23chain 'C' and (resid 963 through 1057 )C963 - 1057
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 22 )D1 - 22
25X-RAY DIFFRACTION25chain 'D' and (resid 23 through 37 )D23 - 37
26X-RAY DIFFRACTION26chain 'D' and (resid 38 through 76 )D38 - 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