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- PDB-4ksl: Gumby/Fam105B in complex with linear di-ubiquitin -

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基本情報

登録情報
データベース: PDB / ID: 4ksl
タイトルGumby/Fam105B in complex with linear di-ubiquitin
要素
  • Polyubiquitin-C
  • Protein FAM105B
キーワードHYDROLASE / OTU domain / deubiquitinase / linear diubiquitin
機能・相同性
機能・相同性情報


protein linear deubiquitination / LUBAC complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / cysteine-type peptidase activity / Maturation of protein E / Maturation of protein E ...protein linear deubiquitination / LUBAC complex / nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of tumor necrosis factor-mediated signaling pathway / regulation of canonical Wnt signaling pathway / sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / cysteine-type peptidase activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR2 signaling / Iron uptake and transport / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Recognition of DNA damage by PCNA-containing replication complex / Stabilization of p53 / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / EGFR downregulation
類似検索 - 分子機能
Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family ...Ubiquitin thioesterase otulin / FAM105 / Peptidase family C101 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-C / Ubiquitin thioesterase otulin
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: 2.83 Å
データ登録者Juang, Y.-C. / Ceccarelli, D.F. / Sicheri, F.
引用ジャーナル: Nature / : 2013
タイトル: The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis.
著者: Rivkin, E. / Almeida, S.M. / Ceccarelli, D.F. / Juang, Y.C. / MacLean, T.A. / Srikumar, T. / Huang, H. / Dunham, W.H. / Fukumura, R. / Xie, G. / Gondo, Y. / Raught, B. / Gingras, A.C. / Sicheri, F. / Cordes, S.P.
履歴
登録2013年5月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年6月5日Provider: repository / タイプ: Initial release
改定 1.12013年7月3日Group: Database references
改定 1.22014年11月12日Group: Structure summary
改定 1.32024年2月28日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
改定 1.42024年4月3日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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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: Protein FAM105B
D: Polyubiquitin-C
B: Protein FAM105B
C: Polyubiquitin-C
E: Protein FAM105B
F: Polyubiquitin-C
G: Protein FAM105B
H: Polyubiquitin-C
I: Protein FAM105B
J: Polyubiquitin-C
K: Protein FAM105B
L: Polyubiquitin-C
M: Protein FAM105B
N: Polyubiquitin-C
O: Protein FAM105B
P: Polyubiquitin-C
Q: Protein FAM105B
R: Polyubiquitin-C
S: Protein FAM105B
T: Polyubiquitin-C
U: Protein FAM105B
V: Polyubiquitin-C
W: Protein FAM105B
X: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)593,92524
ポリマ-593,92524
非ポリマー00
00
1
A: Protein FAM105B
D: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-7 kcal/mol
Surface area19030 Å2
手法PISA
2
B: Protein FAM105B
C: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-5 kcal/mol
Surface area19060 Å2
手法PISA
3
E: Protein FAM105B
F: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-4 kcal/mol
Surface area18820 Å2
手法PISA
4
G: Protein FAM105B
H: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-2 kcal/mol
Surface area18730 Å2
手法PISA
5
I: Protein FAM105B
J: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-6 kcal/mol
Surface area19120 Å2
手法PISA
6
K: Protein FAM105B
L: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-5 kcal/mol
Surface area19230 Å2
手法PISA
7
M: Protein FAM105B
N: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-9 kcal/mol
Surface area19060 Å2
手法PISA
8
O: Protein FAM105B
P: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-4 kcal/mol
Surface area19270 Å2
手法PISA
9
Q: Protein FAM105B
R: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-3 kcal/mol
Surface area19010 Å2
手法PISA
10
S: Protein FAM105B
T: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-5 kcal/mol
Surface area18890 Å2
手法PISA
11
U: Protein FAM105B
V: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-6 kcal/mol
Surface area19030 Å2
手法PISA
12
W: Protein FAM105B
X: Polyubiquitin-C


分子量 (理論値)分子数
合計 (水以外)49,4942
ポリマ-49,4942
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-6 kcal/mol
Surface area18670 Å2
手法PISA
単位格子
Length a, b, c (Å)183.622, 186.087, 219.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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要素

#1: タンパク質
Protein FAM105B


分子量: 32041.746 Da / 分子数: 12 / 断片: OTU domain (unp residues 79-352) / 変異: C129A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FAM105B / プラスミド: pRoEX / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q96BN8
#2: タンパク質
Polyubiquitin-C / Ubiquitin


分子量: 17452.031 Da / 分子数: 12 / 断片: linear diubiquitin (unp residues 76-228) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBC / プラスミド: pETm30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0CG48

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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: 3.16 Å3/Da / 溶媒含有率: 61.07 %
結晶化温度: 298 K / pH: 5.5
詳細: 100mM acetate, 100mM CaCl2, 100 mM glycine, 2.5M sodium formate, 24% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9792
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年2月27日
放射モノクロメーター: SI(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9792 Å / 相対比: 1
反射解像度: 2.83→50 Å / Num. obs: 173426 / % possible obs: 99.9 % / Observed criterion σ(I): 1.37
反射 シェル解像度: 2.8→2.9 Å / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
ADSCQuantumデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.1_1168)精密化
HKL-3000データ削減
HKL-3000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: GUMBY/FAM105B UBIQUITIN

解像度: 2.83→50 Å / SU ML: 0.36 / σ(F): 1.37 / 位相誤差: 29.81 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.254 8692 5.01 %
Rwork0.224 --
obs0.226 173426 96.7 %
all-173695 -
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.83→50 Å
タンパク質核酸リガンド溶媒全体
原子数40089 0 0 0 40089
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00440819
X-RAY DIFFRACTIONf_angle_d0.97955125
X-RAY DIFFRACTIONf_dihedral_angle_d13.68215731
X-RAY DIFFRACTIONf_chiral_restr0.0666218
X-RAY DIFFRACTIONf_plane_restr0.0047053
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8286-2.86080.3833970.33921725X-RAY DIFFRACTION31
2.8608-2.89440.37162300.33664399X-RAY DIFFRACTION78
2.8944-2.92970.35362900.33125568X-RAY DIFFRACTION99
2.9297-2.96680.35683110.325630X-RAY DIFFRACTION100
2.9668-3.00580.34742990.3285620X-RAY DIFFRACTION100
3.0058-3.0470.33662830.31635645X-RAY DIFFRACTION100
3.047-3.09050.33642860.30595603X-RAY DIFFRACTION100
3.0905-3.13660.34112910.28865618X-RAY DIFFRACTION100
3.1366-3.18560.30443170.29165621X-RAY DIFFRACTION100
3.1856-3.23790.32153010.29495612X-RAY DIFFRACTION100
3.2379-3.29370.34952870.285651X-RAY DIFFRACTION100
3.2937-3.35360.27282930.28065634X-RAY DIFFRACTION100
3.3536-3.41810.32783410.2675566X-RAY DIFFRACTION100
3.4181-3.48780.29392800.26125683X-RAY DIFFRACTION100
3.4878-3.56360.29572700.24945629X-RAY DIFFRACTION100
3.5636-3.64650.26452810.24885683X-RAY DIFFRACTION100
3.6465-3.73770.29033010.24155649X-RAY DIFFRACTION100
3.7377-3.83870.2662990.22625658X-RAY DIFFRACTION100
3.8387-3.95160.26112750.21785670X-RAY DIFFRACTION100
3.9516-4.07910.24922870.21355688X-RAY DIFFRACTION100
4.0791-4.22480.2542820.19425677X-RAY DIFFRACTION100
4.2248-4.39390.20433230.19045628X-RAY DIFFRACTION100
4.3939-4.59370.19773050.17125676X-RAY DIFFRACTION100
4.5937-4.83570.20992880.17125707X-RAY DIFFRACTION100
4.8357-5.13840.19813200.18665700X-RAY DIFFRACTION100
5.1384-5.53470.23883080.19365706X-RAY DIFFRACTION100
5.5347-6.09080.23993080.20545743X-RAY DIFFRACTION100
6.0908-6.97010.2373250.21335706X-RAY DIFFRACTION99
6.9701-8.77390.21652950.18785822X-RAY DIFFRACTION100
8.7739-50.05440.1893190.18925817X-RAY DIFFRACTION97
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.5969-3.3688-0.16644.82411.78371.8293-0.2672-0.5218-0.00740.25110.2019-0.03250.16560.37510.07990.8634-0.0547-0.02150.6188-0.01740.4372-21.507330.2729-4.5605
23.16721.47160.67373.70691.20052.65570.2078-0.020.5123-0.2234-0.49830.47630.0525-0.49390.22280.5955-0.00580.06220.7955-0.13830.6374-45.826436.3833-13.357
36.48231.6304-0.99034.1127-1.61760.8804-0.277-0.0026-0.47310.4103-0.03581.14060.8027-1.7675-0.04890.6841-0.13050.20621.0416-0.23211.0736-58.783122.761-18.4127
44.9345.22965.74165.17635.84736.55750.5643-0.82620.62021.0358-1.06511.15420.2158-0.73160.61610.60230.0471-0.0760.9197-0.16350.7912-55.054637.3908-10.6705
55.0387-2.28850.18292.30830.93598.31870.0492-0.84260.26180.4170.30290.63290.2125-0.5463-0.22590.7274-0.14860.09140.8424-0.12050.6134-43.848743.1821-0.7781
64.5449-0.89811.44392.82271.2738.9034-0.12440.08660.0048-0.1113-0.70920.3560.0342-0.61120.88720.7147-0.0497-0.07550.7482-0.15310.7609-49.392830.5001-20.9713
73.96550.15350.93664.74082.08334.15640.01230.6438-0.3537-0.4896-0.23470.5933-0.0761-0.24460.17750.6951-0.0819-0.02390.8735-0.13480.7137-43.086125.2187-25.9491
84.218-1.06910.45174.7140.12321.93180.02870.24740.0149-0.0497-0.1108-0.01790.11570.08650.06270.6555-0.0420.02360.65220.04780.6213-29.840635.3081-16.6616
90.70032.30971.35317.38354.28662.42920.75241.63541.5313-1.23410.0878-1.55990.21960.5931-0.43471.00070.13430.02171.6887-0.07650.6995-22.157724.2646-35.485
104.45161.02091.70074.60160.95138.62040.12741.6637-0.9563-0.89630.0479-1.01960.4111.7821-0.17961.07070.2218-0.03861.6331-0.34420.8159-21.619913.0585-34.533
113.6467-1.88635.18795.7941-2.02758.60230.22411.3743-0.5553-0.1107-0.13550.6363-0.03121.7951-0.19380.9310.22870.02651.2287-0.14180.7226-31.357116.6961-31.1761
126.146-1.7094-0.19927.40373.02892.0403-0.1131.21020.2897-0.67430.107-0.00440.930.9639-0.04160.96320.19430.15971.4867-0.10260.7325-28.756716.1973-42.316
136.09261.7735-4.48573.082-2.42193.89130.517-0.11160.0949-0.26720.40470.5881.31410.4038-0.88860.7541-0.0529-0.02650.77310.08360.5701-33.624419.7407-20.3436
143.1668-3.64833.39224.3708-4.27353.94010.2131-0.91330.74331.1047-0.1856-0.4807-0.5831-0.4272-0.30530.979-0.055-0.00780.75780.01750.5528-28.438617.17381.959
152.7899-0.57442.53284.4152-0.7435.21540.47380.3167-0.32350.4458-0.2823-0.05350.80210.3491-0.03550.8914-0.05790.07590.6314-0.10110.6653-23.022111.6416-6.0964
163.4445-0.52481.94562.39321.43642.46780.4431-0.3149-0.2376-1.34430.2041-0.32322.03460.6722-1.230.9377-0.0190.03230.9294-0.07080.9235-30.98963.6534-6.2822
174.2159-1.03072.23034.3477-1.10816.93920.12780.2629-0.44450.32060.11280.36370.6605-0.6829-0.10371.0824-0.23340.10660.7465-0.09830.7477-31.45919.1661-2.4758
184.10535.3237-0.20157.8332-1.57993.0969-0.58290.7707-0.0547-0.41120.4465-0.2612-0.3553-0.00230.19460.6443-0.0081-0.04510.4816-0.08610.567486.516430.7069-108.9183
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1891.256-0.04120.55551.85120.4070.60790.97470.24560.68520.1021-0.33910.1457-1.56830.7772-0.52072.46960.38810.58531.69170.36451.661881.806183.9081-57.2312
1907.3151-0.20285.91788.1090.42334.8288-1.12960.1224-0.70571.66662.20230.5532-1.58370.6633-0.75121.86230.12050.27821.48580.08340.93579.651971.8805-58.5453
1915.93210.3408-0.29243.9607-2.84296.0061-0.56560.2445-0.2755-2.9589-0.2893-1.0557-0.3231-0.89820.83672.2546-0.09040.36990.82430.03060.944887.280875.3515-37.4503
1928.9338-2.9704-0.02978.66912.85981.14870.55970.17320.1207-1.64710.4835-0.0766-1.51130.5667-0.90731.3487-0.04760.21740.79060.0290.853382.325377.9028-19.3886
1938.02462.34280.73715.1317-0.95743.02420.51660.48850.5905-0.4334-0.12730.0217-0.3045-0.0063-0.26751.66320.17560.18170.6822-0.05090.711474.58283.4091-20.8801
1943.63962.5097-0.58342.312-2.12394.75430.26230.05841.407-2.27860.2460.67310.18590.2707-0.01952.03060.10820.27340.78440.03521.123881.874889.6604-27.2267
1954.7114-1.6727-2.72853.77522.22774.35170.91660.10660.8494-0.217-0.2844-0.5587-0.68360.3562-0.71171.699-0.01650.18910.6197-0.07430.90181.903184.3316-17.48
1967.98756.33281.92926.18050.58853.3885-0.37050.23610.1516-0.44240.09450.07370.06750.02360.3630.71570.03430.04320.35860.03690.4435-17.603463.7022-92.6164
1976.76621.36970.04863.71542.23821.18110.1362-0.1125-0.61450.3548-0.1156-0.1902-0.23210.17340.05750.8189-0.01220.03610.59360.190.4803-18.410862.2038-85.3968
1984.81910.62550.04854.65810.33832.96020.3588-0.79740.49560.4908-0.27581.2089-0.3732-0.5578-0.0260.69290.03990.18060.7692-0.03550.792-46.920863.6544-78.2812
1996.11751.01990.54692.01744.33289.77890.03110.0368-0.0782-0.11750.28-0.3325-0.4127-0.5352-0.50930.62550.0886-0.02520.73060.1640.6612-39.363653.9272-92.8871
2005.75750.77880.02917.43044.42123.07090.3326-1.18670.3410.7864-1.17410.78610.2553-0.95581.07690.7572-0.09710.20990.9235-0.08530.8389-42.724767.9127-72.847
2013.72921.1864-2.1893.0822-0.25765.80950.472-1.66250.45980.8108-0.58720.7296-0.58630.1413-0.06081.0494-0.14960.27161.1619-0.19550.8214-36.127673.9996-66.8907
2025.24970.7014-1.10163.59031.46581.75760.3062-0.9499-0.25170.599-0.1489-0.0447-0.201-0.4094-0.14190.7192-0.04130.02440.71270.17420.4937-25.900160.2303-75.8031
2030.40160.88331.46582.68320.69814.68860.5877-1.27470.20561.4659-0.8025-0.0745-1.02430.65340.11191.5646-0.57380.10461.6943-0.05920.6998-17.964576.5103-58.9767
2048.10340.9826-0.81924.3714-2.01474.03820.03-0.26910.85980.02110.10280.149-0.4709-0.0699-0.06430.75950.02550.01440.4222-0.020.518-16.944382.4821-89.6503
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 79 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 183 )
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 203 )
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 222 )
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 248 )
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 298 )
8X-RAY DIFFRACTION8chain 'A' and (resid 299 through 348 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 16 )
10X-RAY DIFFRACTION10chain 'D' and (resid 17 through 34 )
11X-RAY DIFFRACTION11chain 'D' and (resid 35 through 50 )
12X-RAY DIFFRACTION12chain 'D' and (resid 51 through 68 )
13X-RAY DIFFRACTION13chain 'D' and (resid 69 through 1001 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1002 through 1016 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1017 through 1044 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1045 through 1056 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1057 through 1073 )
18X-RAY DIFFRACTION18chain 'B' and (resid 79 through 100 )
19X-RAY DIFFRACTION19chain 'B' and (resid 101 through 128 )
20X-RAY DIFFRACTION20chain 'B' and (resid 129 through 151 )
21X-RAY DIFFRACTION21chain 'B' and (resid 152 through 183 )
22X-RAY DIFFRACTION22chain 'B' and (resid 184 through 203 )
23X-RAY DIFFRACTION23chain 'B' and (resid 204 through 222 )
24X-RAY DIFFRACTION24chain 'B' and (resid 223 through 248 )
25X-RAY DIFFRACTION25chain 'B' and (resid 249 through 262 )
26X-RAY DIFFRACTION26chain 'B' and (resid 263 through 298 )
27X-RAY DIFFRACTION27chain 'B' and (resid 299 through 348 )
28X-RAY DIFFRACTION28chain 'C' and (resid 0 through 1001 )
29X-RAY DIFFRACTION29chain 'C' and (resid 1002 through 1055 )
30X-RAY DIFFRACTION30chain 'C' and (resid 1056 through 1073 )
31X-RAY DIFFRACTION31chain 'E' and (resid 79 through 100 )
32X-RAY DIFFRACTION32chain 'E' and (resid 101 through 128 )
33X-RAY DIFFRACTION33chain 'E' and (resid 129 through 151 )
34X-RAY DIFFRACTION34chain 'E' and (resid 152 through 183 )
35X-RAY DIFFRACTION35chain 'E' and (resid 184 through 203 )
36X-RAY DIFFRACTION36chain 'E' and (resid 204 through 222 )
37X-RAY DIFFRACTION37chain 'E' and (resid 223 through 248 )
38X-RAY DIFFRACTION38chain 'E' and (resid 249 through 287 )
39X-RAY DIFFRACTION39chain 'E' and (resid 288 through 327 )
40X-RAY DIFFRACTION40chain 'E' and (resid 328 through 348 )
41X-RAY DIFFRACTION41chain 'F' and (resid 0 through 22 )
42X-RAY DIFFRACTION42chain 'F' and (resid 23 through 40 )
43X-RAY DIFFRACTION43chain 'F' and (resid 41 through 55 )
44X-RAY DIFFRACTION44chain 'F' and (resid 56 through 68 )
45X-RAY DIFFRACTION45chain 'F' and (resid 69 through 76 )
46X-RAY DIFFRACTION46chain 'F' and (resid 1001 through 1006 )
47X-RAY DIFFRACTION47chain 'F' and (resid 1007 through 1022 )
48X-RAY DIFFRACTION48chain 'F' and (resid 1023 through 1044 )
49X-RAY DIFFRACTION49chain 'F' and (resid 1045 through 1054 )
50X-RAY DIFFRACTION50chain 'F' and (resid 1055 through 1065 )
51X-RAY DIFFRACTION51chain 'F' and (resid 1066 through 1073 )
52X-RAY DIFFRACTION52chain 'G' and (resid 79 through 100 )
53X-RAY DIFFRACTION53chain 'G' and (resid 101 through 116 )
54X-RAY DIFFRACTION54chain 'G' and (resid 117 through 128 )
55X-RAY DIFFRACTION55chain 'G' and (resid 129 through 151 )
56X-RAY DIFFRACTION56chain 'G' and (resid 152 through 183 )
57X-RAY DIFFRACTION57chain 'G' and (resid 184 through 203 )
58X-RAY DIFFRACTION58chain 'G' and (resid 204 through 222 )
59X-RAY DIFFRACTION59chain 'G' and (resid 223 through 248 )
60X-RAY DIFFRACTION60chain 'G' and (resid 249 through 262 )
61X-RAY DIFFRACTION61chain 'G' and (resid 263 through 348 )
62X-RAY DIFFRACTION62chain 'H' and (resid 1 through 76 )
63X-RAY DIFFRACTION63chain 'H' and (resid 1001 through 1073 )
64X-RAY DIFFRACTION64chain 'I' and (resid 79 through 100 )
65X-RAY DIFFRACTION65chain 'I' and (resid 101 through 128 )
66X-RAY DIFFRACTION66chain 'I' and (resid 129 through 151 )
67X-RAY DIFFRACTION67chain 'I' and (resid 152 through 203 )
68X-RAY DIFFRACTION68chain 'I' and (resid 204 through 222 )
69X-RAY DIFFRACTION69chain 'I' and (resid 223 through 248 )
70X-RAY DIFFRACTION70chain 'I' and (resid 249 through 279 )
71X-RAY DIFFRACTION71chain 'I' and (resid 280 through 298 )
72X-RAY DIFFRACTION72chain 'I' and (resid 299 through 328 )
73X-RAY DIFFRACTION73chain 'I' and (resid 329 through 348 )
74X-RAY DIFFRACTION74chain 'J' and (resid 0 through 22 )
75X-RAY DIFFRACTION75chain 'J' and (resid 23 through 34 )
76X-RAY DIFFRACTION76chain 'J' and (resid 35 through 50 )
77X-RAY DIFFRACTION77chain 'J' and (resid 51 through 60 )
78X-RAY DIFFRACTION78chain 'J' and (resid 61 through 68 )
79X-RAY DIFFRACTION79chain 'J' and (resid 69 through 1001 )
80X-RAY DIFFRACTION80chain 'J' and (resid 1002 through 1011 )
81X-RAY DIFFRACTION81chain 'J' and (resid 1012 through 1022 )
82X-RAY DIFFRACTION82chain 'J' and (resid 1023 through 1044 )
83X-RAY DIFFRACTION83chain 'J' and (resid 1045 through 1056 )
84X-RAY DIFFRACTION84chain 'J' and (resid 1057 through 1065 )
85X-RAY DIFFRACTION85chain 'J' and (resid 1066 through 1073 )
86X-RAY DIFFRACTION86chain 'K' and (resid 79 through 100 )
87X-RAY DIFFRACTION87chain 'K' and (resid 101 through 128 )
88X-RAY DIFFRACTION88chain 'K' and (resid 129 through 164 )
89X-RAY DIFFRACTION89chain 'K' and (resid 165 through 180 )
90X-RAY DIFFRACTION90chain 'K' and (resid 181 through 203 )
91X-RAY DIFFRACTION91chain 'K' and (resid 204 through 222 )
92X-RAY DIFFRACTION92chain 'K' and (resid 223 through 248 )
93X-RAY DIFFRACTION93chain 'K' and (resid 249 through 287 )
94X-RAY DIFFRACTION94chain 'K' and (resid 288 through 348 )
95X-RAY DIFFRACTION95chain 'L' and (resid 0 through 22 )
96X-RAY DIFFRACTION96chain 'L' and (resid 23 through 50 )
97X-RAY DIFFRACTION97chain 'L' and (resid 51 through 59 )
98X-RAY DIFFRACTION98chain 'L' and (resid 60 through 76 )
99X-RAY DIFFRACTION99chain 'L' and (resid 1001 through 1022 )
100X-RAY DIFFRACTION100chain 'L' and (resid 1023 through 1034 )
101X-RAY DIFFRACTION101chain 'L' and (resid 1035 through 1044 )
102X-RAY DIFFRACTION102chain 'L' and (resid 1045 through 1054 )
103X-RAY DIFFRACTION103chain 'L' and (resid 1055 through 1065 )
104X-RAY DIFFRACTION104chain 'L' and (resid 1066 through 1073 )
105X-RAY DIFFRACTION105chain 'M' and (resid 79 through 114 )
106X-RAY DIFFRACTION106chain 'M' and (resid 115 through 128 )
107X-RAY DIFFRACTION107chain 'M' and (resid 129 through 151 )
108X-RAY DIFFRACTION108chain 'M' and (resid 152 through 186 )
109X-RAY DIFFRACTION109chain 'M' and (resid 187 through 222 )
110X-RAY DIFFRACTION110chain 'M' and (resid 223 through 248 )
111X-RAY DIFFRACTION111chain 'M' and (resid 249 through 306 )
112X-RAY DIFFRACTION112chain 'M' and (resid 307 through 348 )
113X-RAY DIFFRACTION113chain 'N' and (resid 0 through 6 )
114X-RAY DIFFRACTION114chain 'N' and (resid 7 through 22 )
115X-RAY DIFFRACTION115chain 'N' and (resid 23 through 34 )
116X-RAY DIFFRACTION116chain 'N' and (resid 35 through 50 )
117X-RAY DIFFRACTION117chain 'N' and (resid 51 through 60 )
118X-RAY DIFFRACTION118chain 'N' and (resid 61 through 68 )
119X-RAY DIFFRACTION119chain 'N' and (resid 69 through 1001 )
120X-RAY DIFFRACTION120chain 'N' and (resid 1002 through 1011 )
121X-RAY DIFFRACTION121chain 'N' and (resid 1012 through 1022 )
122X-RAY DIFFRACTION122chain 'N' and (resid 1023 through 1034 )
123X-RAY DIFFRACTION123chain 'N' and (resid 1035 through 1050 )
124X-RAY DIFFRACTION124chain 'N' and (resid 1051 through 1059 )
125X-RAY DIFFRACTION125chain 'N' and (resid 1060 through 1073 )
126X-RAY DIFFRACTION126chain 'O' and (resid 79 through 116 )
127X-RAY DIFFRACTION127chain 'O' and (resid 117 through 169 )
128X-RAY DIFFRACTION128chain 'O' and (resid 170 through 184 )
129X-RAY DIFFRACTION129chain 'O' and (resid 185 through 203 )
130X-RAY DIFFRACTION130chain 'O' and (resid 204 through 222 )
131X-RAY DIFFRACTION131chain 'O' and (resid 223 through 248 )
132X-RAY DIFFRACTION132chain 'O' and (resid 249 through 298 )
133X-RAY DIFFRACTION133chain 'O' and (resid 299 through 348 )
134X-RAY DIFFRACTION134chain 'P' and (resid 1 through 16 )
135X-RAY DIFFRACTION135chain 'P' and (resid 17 through 34 )
136X-RAY DIFFRACTION136chain 'P' and (resid 35 through 55 )
137X-RAY DIFFRACTION137chain 'P' and (resid 56 through 76 )
138X-RAY DIFFRACTION138chain 'P' and (resid 1001 through 1007 )
139X-RAY DIFFRACTION139chain 'P' and (resid 1008 through 1022 )
140X-RAY DIFFRACTION140chain 'P' and (resid 1023 through 1044 )
141X-RAY DIFFRACTION141chain 'P' and (resid 1045 through 1056 )
142X-RAY DIFFRACTION142chain 'P' and (resid 1057 through 1065 )
143X-RAY DIFFRACTION143chain 'P' and (resid 1066 through 1073 )
144X-RAY DIFFRACTION144chain 'Q' and (resid 79 through 100 )
145X-RAY DIFFRACTION145chain 'Q' and (resid 101 through 116 )
146X-RAY DIFFRACTION146chain 'Q' and (resid 117 through 141 )
147X-RAY DIFFRACTION147chain 'Q' and (resid 142 through 164 )
148X-RAY DIFFRACTION148chain 'Q' and (resid 165 through 187 )
149X-RAY DIFFRACTION149chain 'Q' and (resid 188 through 222 )
150X-RAY DIFFRACTION150chain 'Q' and (resid 223 through 248 )
151X-RAY DIFFRACTION151chain 'Q' and (resid 249 through 279 )
152X-RAY DIFFRACTION152chain 'Q' and (resid 280 through 297 )
153X-RAY DIFFRACTION153chain 'Q' and (resid 298 through 327 )
154X-RAY DIFFRACTION154chain 'Q' and (resid 328 through 348 )
155X-RAY DIFFRACTION155chain 'R' and (resid 0 through 1007 )
156X-RAY DIFFRACTION156chain 'R' and (resid 1008 through 1073 )
157X-RAY DIFFRACTION157chain 'S' and (resid 79 through 100 )
158X-RAY DIFFRACTION158chain 'S' and (resid 101 through 128 )
159X-RAY DIFFRACTION159chain 'S' and (resid 129 through 203 )
160X-RAY DIFFRACTION160chain 'S' and (resid 204 through 222 )
161X-RAY DIFFRACTION161chain 'S' and (resid 223 through 248 )
162X-RAY DIFFRACTION162chain 'S' and (resid 249 through 309 )
163X-RAY DIFFRACTION163chain 'S' and (resid 310 through 348 )
164X-RAY DIFFRACTION164chain 'T' and (resid 1 through 7 )
165X-RAY DIFFRACTION165chain 'T' and (resid 8 through 22 )
166X-RAY DIFFRACTION166chain 'T' and (resid 23 through 34 )
167X-RAY DIFFRACTION167chain 'T' and (resid 35 through 54 )
168X-RAY DIFFRACTION168chain 'T' and (resid 55 through 69 )
169X-RAY DIFFRACTION169chain 'T' and (resid 70 through 1001 )
170X-RAY DIFFRACTION170chain 'T' and (resid 1002 through 1011 )
171X-RAY DIFFRACTION171chain 'T' and (resid 1012 through 1022 )
172X-RAY DIFFRACTION172chain 'T' and (resid 1023 through 1049 )
173X-RAY DIFFRACTION173chain 'T' and (resid 1050 through 1059 )
174X-RAY DIFFRACTION174chain 'T' and (resid 1060 through 1073 )
175X-RAY DIFFRACTION175chain 'U' and (resid 79 through 115 )
176X-RAY DIFFRACTION176chain 'U' and (resid 116 through 128 )
177X-RAY DIFFRACTION177chain 'U' and (resid 129 through 153 )
178X-RAY DIFFRACTION178chain 'U' and (resid 154 through 183 )
179X-RAY DIFFRACTION179chain 'U' and (resid 184 through 203 )
180X-RAY DIFFRACTION180chain 'U' and (resid 204 through 222 )
181X-RAY DIFFRACTION181chain 'U' and (resid 223 through 248 )
182X-RAY DIFFRACTION182chain 'U' and (resid 249 through 261 )
183X-RAY DIFFRACTION183chain 'U' and (resid 262 through 287 )
184X-RAY DIFFRACTION184chain 'U' and (resid 288 through 348 )
185X-RAY DIFFRACTION185chain 'V' and (resid 0 through 7 )
186X-RAY DIFFRACTION186chain 'V' and (resid 8 through 22 )
187X-RAY DIFFRACTION187chain 'V' and (resid 23 through 33 )
188X-RAY DIFFRACTION188chain 'V' and (resid 34 through 50 )
189X-RAY DIFFRACTION189chain 'V' and (resid 51 through 59 )
190X-RAY DIFFRACTION190chain 'V' and (resid 60 through 69 )
191X-RAY DIFFRACTION191chain 'V' and (resid 70 through 76 )
192X-RAY DIFFRACTION192chain 'V' and (resid 1001 through 1022 )
193X-RAY DIFFRACTION193chain 'V' and (resid 1023 through 1049 )
194X-RAY DIFFRACTION194chain 'V' and (resid 1050 through 1059 )
195X-RAY DIFFRACTION195chain 'V' and (resid 1060 through 1073 )
196X-RAY DIFFRACTION196chain 'W' and (resid 79 through 100 )
197X-RAY DIFFRACTION197chain 'W' and (resid 101 through 128 )
198X-RAY DIFFRACTION198chain 'W' and (resid 129 through 203 )
199X-RAY DIFFRACTION199chain 'W' and (resid 204 through 222 )
200X-RAY DIFFRACTION200chain 'W' and (resid 223 through 248 )
201X-RAY DIFFRACTION201chain 'W' and (resid 249 through 287 )
202X-RAY DIFFRACTION202chain 'W' and (resid 288 through 348 )
203X-RAY DIFFRACTION203chain 'X' and (resid 1 through 76 )
204X-RAY DIFFRACTION204chain 'X' and (resid 1001 through 1073 )

+
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

-
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