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- PDB-4zux: SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome -

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基本情報

登録情報
データベース: PDB / ID: 4zux
タイトルSAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome
要素
  • (DNA (145-MER)) x 2
  • (SAGA-associated factor ...) x 2
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4ヒストンH4
  • Polyubiquitin-B
  • Transcription and mRNA export factor SUS1
  • Ubiquitin carboxyl-terminal hydrolase 8
キーワードHydrolase/DNA / DUB / deubiquitinase (脱ユビキチン化酵素) / USP / chromatin (クロマチン) / eraser / nucleosome (ヌクレオソーム) / modified histone / macromolecular complex / Hydrolase-DNA complex
機能・相同性
機能・相同性情報


RITS complex assembly / DUBm complex / : / regulation of nucleocytoplasmic transport / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear mRNA surveillance / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / hypothalamus gonadotrophin-releasing hormone neuron development ...RITS complex assembly / DUBm complex / : / regulation of nucleocytoplasmic transport / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear mRNA surveillance / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / hypothalamus gonadotrophin-releasing hormone neuron development / SAGA complex / female meiosis I / positive regulation of protein monoubiquitination / poly(A)+ mRNA export from nucleus / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / enzyme activator activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of proteasomal protein catabolic process / mRNA export from nucleus / 核膜孔 / energy homeostasis / regulation of neuron apoptotic 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 / 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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / 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 / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / 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 / RNA splicing / neuron projection morphogenesis / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / 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
類似検索 - 分子機能
Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / ENY2/SUS1 / SAGA complex, Sgf11 subunit / SAGA-associated factor 73, zinc finger domain / Sgf11 (transcriptional regulation protein) / Zinc finger domain / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 ...Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / ENY2/SUS1 / SAGA complex, Sgf11 subunit / SAGA-associated factor 73, zinc finger domain / Sgf11 (transcriptional regulation protein) / Zinc finger domain / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAGA-associated factor 73 / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Serum Albumin; Chain A, Domain 1 / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Histone, subunit A / Histone, subunit A / Cysteine proteinases / Cathepsin B; Chain A / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Histone H2B signature. / ヒストンH2B / ヒストンH2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / ヒストンH2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / ヒストンH4 / ヒストンH4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Papain-like cysteine peptidase superfamily / Histone H3 signature 1. / Ubiquitin conserved site / Ubiquitin domain / Histone H3 signature 2. / ヒストンH3 / Histone H3/CENP-A / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ubiquitin family / Ubiquitin homologues / ユビキチン様タンパク質 / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
デオキシリボ核酸 / DNA (> 10) / DNA (> 100) / SAGA-associated factor 11 / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 8 / SAGA-associated factor 73 / ヒストンH4 ...デオキシリボ核酸 / DNA (> 10) / DNA (> 100) / SAGA-associated factor 11 / Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-B / Ubiquitin carboxyl-terminal hydrolase 8 / SAGA-associated factor 73 / ヒストンH4 / Histone H3.2 / SAGA-associated factor 11 / Transcription and mRNA export factor SUS1
類似検索 - 構成要素
生物種Xenopus laevis (アフリカツメガエル)
synthetic construct (人工物)
Saccharomyces cerevisiae (パン酵母)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 解像度: 3.82 Å
データ登録者Morgan, M. / Wolberger, C.
引用ジャーナル: Science / 年: 2016
タイトル: Structural basis for histone H2B deubiquitination by the SAGA DUB module.
著者: Morgan, M.T. / Haj-Yahya, M. / Ringel, A.E. / Bandi, P. / Brik, A. / Wolberger, C.
履歴
登録2015年5月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年2月24日Provider: repository / タイプ: Initial release
改定 1.12016年3月2日Group: Derived calculations
改定 1.22016年3月9日Group: Database references

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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: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (145-MER)
J: DNA (145-MER)
K: Histone H3.2
L: Histone H4
M: Histone H2A type 1
N: Histone H2B 1.1
O: Histone H3.2
P: Histone H4
Q: Histone H2A type 1
R: Histone H2B 1.1
S: DNA (145-MER)
T: DNA (145-MER)
U: Ubiquitin carboxyl-terminal hydrolase 8
V: Transcription and mRNA export factor SUS1
W: SAGA-associated factor 11
X: Polyubiquitin-B
Y: SAGA-associated factor 73
Z: Ubiquitin carboxyl-terminal hydrolase 8
a: Transcription and mRNA export factor SUS1
b: SAGA-associated factor 11
c: Polyubiquitin-B
d: SAGA-associated factor 73
e: Ubiquitin carboxyl-terminal hydrolase 8
f: Transcription and mRNA export factor SUS1
g: SAGA-associated factor 11
h: Polyubiquitin-B
i: SAGA-associated factor 73
j: Ubiquitin carboxyl-terminal hydrolase 8
k: Transcription and mRNA export factor SUS1
l: SAGA-associated factor 11
m: Polyubiquitin-B
n: SAGA-associated factor 73
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)784,45072
ポリマ－782,35740
非ポリマー2,09332
水0
1
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (145-MER)
J: DNA (145-MER)
U: Ubiquitin carboxyl-terminal hydrolase 8
V: Transcription and mRNA export factor SUS1
W: SAGA-associated factor 11
X: Polyubiquitin-B
Y: SAGA-associated factor 73
Z: Ubiquitin carboxyl-terminal hydrolase 8
a: Transcription and mRNA export factor SUS1
b: SAGA-associated factor 11
c: Polyubiquitin-B
d: SAGA-associated factor 73
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)392,22536
ポリマ－391,17920
非ポリマー1,04716
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
K: Histone H3.2
L: Histone H4
M: Histone H2A type 1
N: Histone H2B 1.1
O: Histone H3.2
P: Histone H4
Q: Histone H2A type 1
R: Histone H2B 1.1
S: DNA (145-MER)
T: DNA (145-MER)
e: Ubiquitin carboxyl-terminal hydrolase 8
f: Transcription and mRNA export factor SUS1
g: SAGA-associated factor 11
h: Polyubiquitin-B
i: SAGA-associated factor 73
j: Ubiquitin carboxyl-terminal hydrolase 8
k: Transcription and mRNA export factor SUS1
l: SAGA-associated factor 11
m: Polyubiquitin-B
n: SAGA-associated factor 73
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)392,22536
ポリマ－391,17920
非ポリマー1,04716
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)178.804, 179.174, 353.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 7種, 28分子 AEKOBFLPCGMQDHNRUZejVafkXchm

#1: タンパク質
Histone H3.2


分子量: 15435.126 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P84233
#2: タンパク質
Histone H4 / ヒストンH4


分子量: 11394.426 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62799
#3: タンパク質
Histone H2A type 1


分子量: 14109.436 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P06897
#4: タンパク質
Histone H2B 1.1 / H2B1.1


分子量: 13655.948 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus laevis (アフリカツメガエル)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02281
#7: タンパク質
Ubiquitin carboxyl-terminal hydrolase 8 / Deubiquitinating enzyme 8 / Ubiquitin thioesterase 8 / Ubiquitin-specific-processing protease 8


分子量: 53731.281 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: UBP8, YMR223W, YM9959.05 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P50102, ubiquitinyl hydrolase 1
#8: タンパク質
Transcription and mRNA export factor SUS1


分子量: 11094.497 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: SUS1, YBR111W-A / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q6WNK7
#10: タンパク質
Polyubiquitin-B


分子量: 8576.831 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG47

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DNA鎖 , 2種, 4分子 ISJT

#5: DNA鎖 DNA (145-MER)


分子量: 44520.383 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)
#6: DNA鎖 DNA (145-MER)


分子量: 44991.660 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)

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SAGA-associated factor ... , 2種, 8分子 WbglYdin

#9: タンパク質
SAGA-associated factor 11


分子量: 11297.625 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain YJM789) (パン酵母)
株: YJM789 / 遺伝子: SGF11, SCY_5678 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A6ZWK1, UniProt: Q03067*PLUS
#11: タンパク質
SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


分子量: 11538.081 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: SGF73, YGL066W / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P53165

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非ポリマー , 1種, 32分子

#12: 化合物...
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 32 / 由来タイプ: 合成 / 式: Zn

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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: 3.65 Å3/Da / 溶媒含有率: 66.28 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol

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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: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2014年10月14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: 1.0332 Å / 相対比: 1
反射解像度: 3.693→49.5 Å / Num. obs: 121413 / % possible obs: 99.28 % / 冗長度: 7.12 % / Rmerge(I) obs: 0.1053 / Net I/σ(I): 7.12

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
XDSデータ削減
Aimlessデータスケーリング
Cootモデル構築
精密化解像度: 3.82→49.498 Å / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 49.29 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2559 3456 1.64 %
Rwork0.2338 --
obs0.2369 210557 98.93 %
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: 3.82→49.498 Å
タンパク質核酸リガンド溶媒全体
原子数37169 11878 32 0 49079
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00551211
X-RAY DIFFRACTIONf_angle_d1.02371446
X-RAY DIFFRACTIONf_dihedral_angle_d24.33420103
X-RAY DIFFRACTIONf_chiral_restr0.0458075
X-RAY DIFFRACTIONf_plane_restr0.0057104
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8672-3.93220.41361930.40659800X-RAY DIFFRACTION97
3.9322-4.00170.37961930.37389735X-RAY DIFFRACTION98
4.0017-4.07640.34681930.35359819X-RAY DIFFRACTION98
4.0764-4.15710.39281910.34939738X-RAY DIFFRACTION97
4.1571-4.24450.35651900.33879620X-RAY DIFFRACTION97
4.2445-4.33980.3162700.33099855X-RAY DIFFRACTION98
4.3398-4.44420.34341230.32179885X-RAY DIFFRACTION98
4.4442-4.55950.29971920.32219711X-RAY DIFFRACTION98
4.5595-4.68780.27651990.31769836X-RAY DIFFRACTION98
4.6878-4.83190.30411980.3149808X-RAY DIFFRACTION98
4.8319-4.99550.33051940.3119678X-RAY DIFFRACTION97
4.9955-5.18370.29032000.29959733X-RAY DIFFRACTION97
5.1837-5.404000.29839867X-RAY DIFFRACTION99
5.404-5.66720.29931850.31139554X-RAY DIFFRACTION96
5.6672-5.99060.33541900.29619691X-RAY DIFFRACTION97
5.9906-6.40320.34811930.2769741X-RAY DIFFRACTION97
6.4032-6.95970.31021810.25819665X-RAY DIFFRACTION97
6.9597-7.77970.28111770.22629584X-RAY DIFFRACTION96
7.7797-9.20730.15451820.18579436X-RAY DIFFRACTION94
9.2073-13.16170.17521840.14249735X-RAY DIFFRACTION97
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)
11.16522.24130.09545.35851.4111.0458-0.0485-0.2944-0.3506-0.59170.6885-0.2841-0.2834-0.29840.00061.1446-0.0649-0.02932.05940.12111.505-72.454-42.3122-14.532
23.7717-3.69251.35663.3713-1.02544.6788-0.2891-1.1222-0.2306-1.26620.8829-0.99270.2613-0.3597-0.00111.1416-0.2787-0.04391.6581-0.1871.3383-77.009-34.1066-11.9282
31.7848-1.82420.49252.2540.05192.49860.1143-0.34180.3002-0.03250.1881-0.48660.32120.0197-0.00021.26550.2187-0.08921.5877-0.05731.4645-74.9706-23.164116.6247
43.5422-1.9044-1.25266.2922-1.7832.95760.00290.7943-0.3530.63441.2156-0.7282-0.593-1.57980.08571.13-0.0284-0.38631.4682-0.06471.4415-76.0752-14.80612.48
54.54012.2265-0.46763.96631.65352.77010.17470.5778-0.84651.32210.5586-0.98520.1026-0.19040.01481.11570.0956-0.47932.0449-0.27921.6685-55.2092-42.090216.3679
65.16560.4875-1.25924.92941.75722.7628-0.11190.92950.32681.69920.83252.05270.68220.49350.08311.32170.4468-0.61761.75760.12471.3996-51.7818-33.902713.5968
70.42971.2242-0.22223.0519-0.41551.07430.07450.0260.2677-0.18460.2333-0.9378-0.0422-0.066901.3201-0.22890.03251.8066-0.2461.9654-52.5869-23.2082-15.6361
82.43640.110.19144.28021.0272.2332-0.0613-0.8861-0.804-0.35541.23730.41810.03311.3116-0.00051.28090.1202-0.26121.7606-0.03981.8213-51.2637-15.5976-10.8624
91.0556-0.099-0.08022.12760.27881.29720.04910.052-0.10690.07540.013-0.3259-0.0396-0.078501.5301-0.0468-0.15071.9945-0.03291.8305-64.1244-28.87711.2039
101.09540.3483-0.03851.99860.13331.51610.02260.0206-0.0005-0.01760.0152-0.4758-0.0957-0.0445-01.50410.1233-0.24451.96790.07551.8035-63.5443-29.08020.8369
112.2061-0.95260.42614.1283-0.2883-0.05910.28970.35860.9055-0.58160.52170.20860.04990.80150.00122.02930.01940.11431.6190.14291.627.9674-10.407677.5316
121.4446-0.283-1.14523.58640.13974.9114-0.2590.55570.94230.9596-0.47870.82040.6660.52710.00011.30540.00180.13741.2560.2831.66310.4523-14.862973.7653
130.9766-0.16941.58311.8220.43232.5226-0.0477-0.2705-0.3993-0.2546-0.17740.6779-0.32480.0406-0.00031.6996-0.1144-0.13761.5114-0.01441.7871-27.0797-12.948186.5148
143.6108-0.77460.2144.7963-1.60113.1331-0.5581-0.39190.0191-0.59270.1467-0.79430.8398-0.3849-0.00061.58590.1622-0.08680.9176-0.19981.8302-30.2555-14.315378.0929
155.1122-2.16221.82683.73341.94013.17550.4073-0.49870.40080.0765-0.31870.19420.6-0.67650.00011.6897-0.09630.12111.3051-0.11081.7793-13.89836.909598.9786
165.61880.9526-2.30084.6034-2.23621.55940.6738-1.7230.8508-1.6489-0.5226-0.65842.5357-2.2349-0.11882.1927-0.7036-0.11921.7562-0.12451.1658-17.25139.965891.7308
172.2782-0.6368-1.13531.00311.17491.5370.19590.55250.0144-0.8212-0.0764-0.0173-0.12380.192702.0962-0.0489-0.10051.4790.22491.5304-5.17129.544863.3425
183.761.08440.30341.6299-1.040.83311.50.57481.17070.0267-0.83970.3347-0.0737-0.24490.02542.22040.2612-0.21891.2806-0.1971.4202-13.607110.348861.1754
190.77190.01690.47661.4708-0.29890.98750.12980.16540.0716-0.1225-0.15050.0784-0.1086-0.0275-01.85460.0779-0.05022.11760.01121.7401-12.32-2.249779.3405
200.96560.01310.55471.1752-0.21211.33290.0420.10980.0945-0.0977-0.02740.0748-0.289-0.068801.9896-0.05220.05381.9826-0.15871.8168-11.9315-1.687379.1528
213.0241-0.3462-0.8561.8849-1.45692.1142-0.1347-0.36530.3091-0.0533-0.06060.0833-0.13650.12560.00011.38440.09180.03791.57960.15351.7894-121.3942-5.378315.6115
223.5142-0.1808-2.12263.1223-1.31023.34790.1835-0.09071.4262-1.3550.0643-0.73240.4871-0.17960.00031.7455-0.03650.44351.33370.35862.4697-134.928416.958316.0906
231.74470.3315-0.59254.5313-0.286-0.1414-0.2638-0.87430.43541.07670.0493-0.03920.26890.9436-0.11951.5467-0.2-0.04522.2534-0.20361.4153-110.8583-0.17725.6854
242.08260.4338-0.23342.2192-0.5452.48811.10452.396-1.09350.0890.2825-0.02140.4365-1.84380.14131.50340.31320.27832.4730.13691.7563-110.8878-20.6314-8.1776
251.82352.277-1.00723.1157-2.21673.22-0.2924-0.09361.2285-0.7514-0.34510.1170.9643-0.6027-0.0871.1783-0.04340.15852.3642-0.25331.9564-136.7874-5.508622.3862
260.91920.2704-0.37742.06670.88443.0829-0.10660.36990.3408-0.1858-0.0330.0692-0.1406-0.060801.4253-0.10490.18581.7828-0.14212.3754-5.6793-5.8061-16.5308
273.4467-0.4964-3.03360.52861.35543.84970.78330.5072.66671.3317-0.24621.18620.77260.19820.00182.10270.01610.3291.34540.02162.7847.583316.9524-18.9223
280.22720.7756-0.38211.3016-1.10610.5613-0.23890.4302-0.1628-1.8172-0.596-0.50270.0518-0.6543-0.01522.0320.16710.11122.2751-0.00672.3388-17.3852-1.2844-26.7244
290.90330.4823-0.63131.43340.18742.53151.3711-0.8814-0.5041-0.10740.2992-0.06632.0216-0.23230.08261.3649-0.36880.03611.8614-0.25442.428-15.3016-19.79698.7924
300.09690.31390.6512.3748-0.10322.8814-0.54191.20741.2814-0.041-0.0917-0.57131.23381.3147-0.26261.1729-0.27910.31122.1251-0.06632.832610.359-4.1798-22.9857
311.18110.83860.18933.6404-0.79852.1533-0.01340.24970.1029-0.1250.07130.6953-0.3194-0.2112-0.00021.59460.021-0.41151.6636-0.13091.6126-39.5447-60.120972.6962
323.6668-0.10311.12451.73921.11222.3086-1.5027-0.17520.4010.08640.31370.5531-0.24542.1963-0.0182.2792-0.1016-0.77862.30340.03482.0327-56.7027-72.916457.2458
332.3607-0.88870.86761.721-0.93520.6160.80390.3189-0.97520.45040.52840.9732-1.6605-0.7230.80131.4563-0.0055-0.19882.12890.28162.4109-50.4147-49.424177.1521
341.96251.38740.97671.72080.61220.516-0.01590.08771.4293-0.7477-0.2927-1.4127-0.25910.70210.0011.94290.0864-0.41092.1624-0.02432.1839-12.2342-48.952265.724
352.6330.1727-0.77190.0346-0.52432.6144-0.3445-0.5442-0.8386-0.07760.13742.03241.081.1742-0.17141.8658-0.1561-0.49411.13540.0292.8541-45.149-76.335275.0431
361.3880.54490.22261.35680.1080.7978-0.2810.06870.1944-0.45380.1980.54960.0751-0.07610.00011.79610.1173-0.28881.66040.40221.9203-16.645855.534849.879
374.4518-0.1160.78652.172-1.51191.75051.3242-1.6209-0.0046-0.8573-0.36610.24350.9921-1.01940.00171.9076-0.2825-0.56362.3990.56652.1224-30.44667.079931.7764
381.03090.77380.25461.2592-1.51662.2731-0.18730.901-0.2409-0.6969-0.28370.06890.30120.4993-0.00072.3916-0.2086-0.06571.85610.01521.5534-13.7345.448939.0107
392.81991.3046-0.0791.68730.43630.6958-0.3618-1.74380.90251.1760.76090.34240.49610.56880.01812.01240.1755-0.43311.340.29452.1877-24.934346.442877.8844
401.75911.0441-1.04630.4589-0.52861.28530.1880.94351.547-0.89060.2980.64140.48130.41120.68822.5065-0.0966-0.31561.02260.57132.5254-13.617471.082343.8789
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 38 through 134)
2X-RAY DIFFRACTION2(chain 'B' and resid 20 through 102)
3X-RAY DIFFRACTION3(chain 'C' and resid 16 through 118)
4X-RAY DIFFRACTION4(chain 'D' and resid 28 through 122)
5X-RAY DIFFRACTION5(chain 'E' and resid 39 through 135)
6X-RAY DIFFRACTION6(chain 'F' and resid 25 through 102)
7X-RAY DIFFRACTION7(chain 'G' and resid 14 through 118)
8X-RAY DIFFRACTION8(chain 'H' and resid 29 through 121)
9X-RAY DIFFRACTION9(chain 'I' and resid -72 through 72)
10X-RAY DIFFRACTION10(chain 'J' and resid -72 through 72)
11X-RAY DIFFRACTION11(chain 'K' and resid 38 through 134)
12X-RAY DIFFRACTION12(chain 'L' and resid 20 through 102)
13X-RAY DIFFRACTION13(chain 'M' and resid 16 through 118)
14X-RAY DIFFRACTION14(chain 'N' and resid 28 through 122)
15X-RAY DIFFRACTION15(chain 'O' and resid 39 through 135)
16X-RAY DIFFRACTION16(chain 'P' and resid 25 through 102)
17X-RAY DIFFRACTION17(chain 'Q' and resid 14 through 118)
18X-RAY DIFFRACTION18(chain 'R' and resid 29 through 121)
19X-RAY DIFFRACTION19(chain 'S' and resid -72 through 72)
20X-RAY DIFFRACTION20(chain 'T' and resid -72 through 72)
21X-RAY DIFFRACTION21(chain 'U' and resid 0 through 471)
22X-RAY DIFFRACTION22(chain 'V' and resid 5 through 93)
23X-RAY DIFFRACTION23(chain 'W' and resid 6 through 95)
24X-RAY DIFFRACTION24(chain 'X' and resid 1 through 76)
25X-RAY DIFFRACTION25(chain 'Y' and resid 11 through 98)
26X-RAY DIFFRACTION26(chain 'Z' and resid 0 through 471)
27X-RAY DIFFRACTION27(chain 'a' and resid 5 through 95)
28X-RAY DIFFRACTION28(chain 'b' and resid 7 through 95)
29X-RAY DIFFRACTION29(chain 'c' and resid 1 through 76)
30X-RAY DIFFRACTION30(chain 'd' and resid 5 through 98)
31X-RAY DIFFRACTION31(chain 'e' and resid 0 through 471)
32X-RAY DIFFRACTION32(chain 'f' and resid 10 through 95)
33X-RAY DIFFRACTION33(chain 'g' and resid 6 through 95)
34X-RAY DIFFRACTION34(chain 'h' and resid 1 through 76)
35X-RAY DIFFRACTION35(chain 'i' and resid 5 through 98)
36X-RAY DIFFRACTION36(chain 'j' and resid 0 through 471)
37X-RAY DIFFRACTION37(chain 'k' and resid 5 through 90)
38X-RAY DIFFRACTION38(chain 'l' and resid 3 through 95)
39X-RAY DIFFRACTION39(chain 'm' and resid 1 through 76)
40X-RAY DIFFRACTION40(chain 'n' and resid 5 through 98)

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る