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- PDB-9isz: Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 meth... -

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基本情報

登録情報
データベース: PDB / ID: 9isz
タイトルStructure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation
要素
  • Histone H3.1/H3.2
  • Histone-lysine N-methyltransferase, H3 lysine-9 specific
  • Ubiquitin
キーワードGENE REGULATION / Epigenetics / Methylation / Ubiquitination / Crosstalk
機能・相同性
機能・相同性情報


Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / CLRC complex / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / positive regulation of pericentric heterochromatin formation / co-transcriptional gene silencing by RNA interference machinery / Estrogen-dependent gene expression ...Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / CLRC complex / Oxidative Stress Induced Senescence / Factors involved in megakaryocyte development and platelet production / positive regulation of pericentric heterochromatin formation / co-transcriptional gene silencing by RNA interference machinery / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / siRNA-independent facultative heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / nucleolar peripheral inclusion body / subtelomeric heterochromatin / Transcriptional regulation by small RNAs / mating-type region heterochromatin / heterochromatin boundary formation / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 trimethyltransferase activity / mitotic sister chromatid biorientation / histone H3K9 monomethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / siRNA-mediated pericentric heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / ubiquitin-modified histone reader activity / chromatin-protein adaptor activity / pericentric heterochromatin formation / protein-lysine N-methyltransferase activity / spindle pole body / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / silent mating-type cassette heterochromatin formation / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / histone methyltransferase activity / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / subtelomeric heterochromatin formation / heterochromatin / pericentric heterochromatin / energy homeostasis / regulation of neuron apoptotic process / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / 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 / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / 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
類似検索 - 分子機能
Histone H3-K9 methyltransferase / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain ...Histone H3-K9 methyltransferase / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Ubiquitin conserved site / Core histone H2A/H2B/H3/H4 / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
類似検索 - ドメイン・相同性
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-9 specific / Histone H3.1/H3.2 / Polyubiquitin-B
類似検索 - 構成要素
生物種Schizosaccharomyces pombe 972h- (分裂酵母)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å
データ登録者Du, Y.X. / Liu, L.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)22137005 中国
引用ジャーナル: To Be Published
タイトル: Mechanism of Histone H3K9 Methyltransferase Clr4 Regulation by Proximal H3K14 Ubiquitination in-cis
著者: Du, Y.X. / Liu, L.
履歴
登録2024年7月19日登録サイト: PDBJ / 処理サイト: PDBC
改定 1.02025年4月30日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific
C: Ubiquitin
D: Ubiquitin
E: Histone H3.1/H3.2
F: Histone H3.1/H3.2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)90,33616
ポリマ－89,0166
非ポリマー1,32010
水95553
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-42 kcal/mol
Surface area32510 Å2
手法PISA
2
A: Histone-lysine N-methyltransferase, H3 lysine-9 specific
C: Ubiquitin
E: Histone H3.1/H3.2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1688
ポリマ－44,5083
非ポリマー6605
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-20 kcal/mol
Surface area17580 Å2
手法PISA
3
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific
D: Ubiquitin
F: Histone H3.1/H3.2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1688
ポリマ－44,5083
非ポリマー6605
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-18 kcal/mol
Surface area17900 Å2
手法PISA
単位格子
Length a, b, c (Å)53.175, 105.977, 131.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

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タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 Histone-lysine N-methyltransferase, H3 lysine-9 specific / Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / H3-K9-HMTase / HKMT / Lysine N- ...Cryptic loci regulator 4 / Histone H3-K9 methyltransferase / H3-K9-HMTase / HKMT / Lysine N-methyltransferase 1 / Protein lysine methyltransferase clr4 / PKMT


分子量: 34078.062 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Schizosaccharomyces pombe 972h- (分裂酵母)
株: 972 / ATCC 24843 / 遺伝子: clr4, kmt1, SPBC428.08c / プラスミド: pGEX-6p-1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: O60016, [histone H3]-lysine9 N-trimethyltransferase, [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase, [histone H3]-lysine9 N-methyltransferase
#2: タンパク質 Ubiquitin


分子量: 8622.922 Da / 分子数: 2 / Mutation: G76C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / プラスミド: pGEX-6p-1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0CG47

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タンパク質・ペプチド , 1種, 2分子 EF

#3: タンパク質・ペプチド Histone H3.1/H3.2


分子量: 1807.084 Da / 分子数: 2 / Mutation: K10L,K15C / 由来タイプ: 合成
由来: (合成) Schizosaccharomyces pombe 972h- (分裂酵母)
参照: UniProt: P09988

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非ポリマー , 3種, 63分子

#4: 化合物 ChemComp-SAM / S-ADENOSYLMETHIONINE


分子量: 398.437 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C15H22N6O5S / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 53 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.1 Å3/Da / 溶媒含有率: 41.44 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL02U1 / 波長: 0.979176 Å
検出器タイプ: DECTRIS EIGER2 S 9M / 検出器: PIXEL / 日付: 2023年5月22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: 0.979176 Å / 相対比: 1
反射解像度: 2.44→82.62 Å / Num. obs: 28662 / % possible obs: 99.9 % / 冗長度: 11.6 % / Biso Wilson estimate: 49.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.058 / Rrim(I) all: 0.196 / Net I/σ(I): 8.8
反射 シェル解像度: 2.44→2.57 Å / 冗長度: 12.2 % / Num. unique obs: 4108 / CC1/2: 0.884 / % 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
PHENIX1.19.2_4158精密化
autoPROCデータ削減
Aimless0.7.4データスケーリング
PHENIX1.19.2_4158位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6BP4,1UBQ

6bp4

1ubq


解像度: 2.6→37.53 Å / SU ML: 0.2729 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 34.896
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2739 1175 4.98 %
Rwork0.2309 22420 -
obs0.2332 23595 99.75 %
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 mean: 71.59 Å2
精密化ステップサイクル: LAST / 解像度: 2.6→37.53 Å
タンパク質核酸リガンド溶媒全体
原子数5880 0 62 53 5995
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00326049
X-RAY DIFFRACTIONf_angle_d0.6058165
X-RAY DIFFRACTIONf_chiral_restr0.0431884
X-RAY DIFFRACTIONf_plane_restr0.00441076
X-RAY DIFFRACTIONf_dihedral_angle_d14.70342272
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.35421480.33442742X-RAY DIFFRACTION99.86
2.72-2.860.34421430.30832767X-RAY DIFFRACTION99.86
2.86-3.040.35881510.28892740X-RAY DIFFRACTION99.62
3.04-3.280.31591250.27142807X-RAY DIFFRACTION99.97
3.28-3.60.25591490.23282766X-RAY DIFFRACTION99.76
3.6-4.130.31481470.22652817X-RAY DIFFRACTION99.8
4.13-5.20.23361620.19252821X-RAY DIFFRACTION99.93
5.2-37.530.23021500.19842960X-RAY DIFFRACTION99.2
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)
10.7683141696640.083606805298-1.227662241241.37233955891-0.4858326868462.0497333950.09622616044970.2008128251420.0607718900692-0.182562732506-0.1644628644720.296690356410.147130577811-0.7736449226640.04572081116180.319058401069-0.01942490004390.0415543475480.953857133987-0.08102632703980.3686324923744.3775467112-0.7811922449136.89426846299
25.833798932791.309900343172.942126295771.860643984250.8220579925416.03186287262-0.0544752759111-0.469209706131-0.5426252221570.156739425647-0.244246821909-0.246122773881.005445849950.7641067933890.1049532709160.2994382138710.1340739576840.01122386532961.012837380360.1185065304980.43197534947217.0703660335-10.017986162821.011506168
35.42714073722-1.48790399523-0.2216508201524.889189570770.57050277882.995670284710.3347831921930.18882623142-0.493654508556-0.0288956490822-0.1953662074750.5199224021980.742943005865-0.929378164223-0.05587256079830.430186484589-0.07250183371780.06603094458480.914081384626-0.0500721873860.289922856931-0.328551092842-10.97435395414.2668451364
40.871726593027-1.28503488773-0.8495947101073.280544175010.03493129478147.826775227160.0251113256704-0.12847825185-0.623251210352-0.4909553787990.1214682922710.4766041988081.84924542581-0.2055718151330.09665024703350.52460405334-0.06331223674890.1008900218940.819859972132-0.02021553132120.3316380601866.72101093619-18.55208058412.0475470038
54.828630294463.10519353826-1.97074805827.200374844120.8187589623955.108568191860.128324789379-0.216054509643-0.380161721598-0.1955357451770.13093295729-0.780692890860.07266694266350.301675452787-0.1996958806760.315640935277-0.1180324616850.02269377877810.9885523763380.07065575974550.32874578787725.92240122711.74176372485.03292724028
61.498315418930.510582268112-1.980521796593.24451635798-0.8981173130622.63845034585-0.238338053822-0.256852293024-0.247588528022-0.1955383385340.0885718009337-0.6286378991530.5438677946180.5429687057470.147350763680.234499282534-0.117304945859-0.05554266423191.008802887780.1629325937230.330319547519.143971945810.025464746519.2701374706
74.194129518370.1600438902052.538201773252.65156937202-2.221587853613.5706355312-0.0116202853559-0.3090892490180.213477012434-0.07873057813230.2972809341390.562164923672-0.356717870854-0.670357746799-0.23223244650.2531734398450.09083250963620.01797197769941.154296102040.02009253853530.45811000326-11.361245431314.993185090122.000072856
83.745354548650.4345387107930.4608414850131.0854738890.5600861120471.21478706485-0.2326928547190.3420400247370.241159766663-0.2301769942320.07074607423350.0856667179651-0.350528201752-0.445972534788-0.02893361580490.1598062773190.0526142103242-0.05235848658760.9603440625120.1106815865470.2822896026134.2700095234318.346150853912.5452873483
91.34714754302-3.02825173762-0.1780660928676.871315552240.07730202863192.03151890684-0.0437416205628-0.08322309625970.203833533937-0.156031651416-0.0278766904454-1.64106039354-0.7748149614411.11226925003-0.03000985537630.331071303136-0.234412127951-0.03712663016661.25010784673-0.03722257860820.45181293597222.351027929517.79985119429.7053239085
103.29598235232-0.7233185090522.363881809563.04090782451-1.66864357223.58093542884-0.000980157170008-0.6066497609370.2835889761870.281317552004-0.108529903151-0.0850698406131-0.2101293955320.06886903154490.07808656596760.248513354805-0.0348277942786-0.02316239129810.6226903840340.02332082146040.2735582248218.9065751363219.606049409623.5768054423
113.24848643172-0.1358607339631.457183095995.57061622722-0.02970260423432.427980032080.2538831329740.6351412758171.30917853249-0.300869046057-0.3094098504971.07568440135-0.334103053074-1.257844122140.1217562823670.0454020307861-0.0348134793352-0.03065392697480.7478175371530.07058276860290.6080275144769.5425579688530.613574123314.1720826202
121.008030792050.960720606052-0.1855706038411.11176580773-0.8382400297773.00211702749-0.215288989459-0.6612204250520.6442043105910.920901484745-0.508884016663-0.367500176169-0.4562337060320.04273325936170.7387222338231.00883787081-0.448981285871-0.09796570324571.063843725030.09204445542170.8196754237518.375590878737.020546714323.1295507406
130.423566237839-0.2289316913560.3464862271711.96469892723-0.1203293262936.97646403787-0.579063245509-0.2468085358860.250407191794-0.151074799946-0.4239942472720.4709492872030.670999178997-0.7721409967990.8242867210160.347630369816-0.02803822380830.07198907142561.28622979972-0.04477427881560.46110845747-2.66529239708-3.0050959897248.8317137818
142.724649056621.30931383974-0.7820229091026.60799861789-1.456611441359.17785955391-0.242918545056-0.829343405766-0.5362215544570.0254925112653-0.367613920811-0.1288303266661.47898114154-0.6060405908320.5837257328180.4570221945380.03650209143550.07172768023741.151043556090.2052874565380.5103185965715.60772493668-8.8620435393852.2901486875
150.4604957278211.260242377531.333283505033.481041698583.318053811928.65717322261-0.05545941601090.242076665845-0.1940219952630.004325848658250.560337429815-0.6502082615771.01958857761.86131521907-0.2380241753790.327724670637-0.028722658962-0.04671511911091.142910019130.03269516860830.21578340479312.8397821933-1.9821826116747.5128012538
165.50033818471-0.963296909203-3.325136291362.321940663081.058721377832.894374822580.284800643530.8770830934950.193701755664-0.128243436301-0.436646029686-0.1057716936-1.681863007560.3646513399930.2008791079540.692801530358-0.0603360853363-0.1542561636411.104825075480.1113235553740.3382677865867.45156676435.611677176351.6647838806
173.82022285141-1.38058657647-3.296951820751.868526041762.467671593496.34398089536-0.2610014484260.605953966358-0.3166889203850.0780841703867-0.04953231550890.1329864753350.449528764943-0.08512146233920.4194563290390.216653893798-0.0946726153350.07027384577791.102363028820.02565994033660.1735718066652.88526940643-5.00080108843.3477654213
182.015869034361.482353507881.389508001297.050145709484.536816668227.70146095542-0.165303290136-1.96179668579-1.22671571782-0.6601893231060.484725758514-1.55095655494-0.452881349762.95013465923-0.3591527799261.06354967944-0.03810319081230.1904916178011.65743982575-0.07133507428470.9122007348727.95831098116-17.865127296837.190491983
191.182309268660.4896083899580.01304285078060.519023798022-0.3529888458090.875611453451-0.012123412303-0.124742294021-0.05594447434060.156701902825-0.1294298346380.009568004801510.331423405282-0.05862965204540.1049378549360.385871970485-0.09902852807320.1158894880811.348282458450.05350330705560.211997781309-11.78855419492.229046579546.465229074
206.357518946463.443973863051.299419748817.24044382726-2.800850386142.00021953583-0.182746585202-0.8529138668040.2963770834240.543813168274-0.3186585803760.223478532623-0.73163643436-1.286729077670.5758555002430.486784681427-0.113358888653-0.03784153187531.5264492421-0.2343706424560.36937440241-1.26307565810.709950316543.7035815059
211.373710627270.8717501783-0.5123995154420.606646622475-0.3136425290090.1962280374320.0591508042747-0.2559220524210.08228556354050.09250859916470.04098953389820.4870590920570.134711369866-0.261628491537-0.01117307633970.196352817984-0.1040145586770.07207639630081.835612276890.03420695193890.531035956358-17.79078754934.8872783946447.5903132678
220.5313959048861.88515660391.130376077919.155069769830.0903091185938.654508079450.6969276137091.488373863660.3983371159790.276165562365-0.04383566557910.322627897824-0.288836745921-0.0795714272326-0.6237180135180.4458200278760.1850989943540.06157203261211.41729778502-0.06297361143850.624567499437-16.349346747613.343997345246.8315274877
237.76947978481-1.91342077024-0.7370076295456.99103908882-0.003020959005411.99847900539-0.150037095606-1.840936208361.524567849270.593912528160.822341359639-0.51322203767-1.021084566910.0760065188043-1.074124009240.2556915990490.03200371942070.04198817865691.01632055559-0.05205705523360.492810129131-12.413067198716.348096875740.1420332611
244.40567408492.51134132496-0.9581439835351.44939186421-0.6394311315220.6714870958420.159230077283-0.1927148546450.872858986210.04032854229790.4039571847410.7383459509770.128177092802-0.326153733474-0.01328543299220.179137848145-0.0404407106931-0.1223941301381.297194592730.00525915886530.740885829888-18.24124469487.5273413750934.1748469162
259.73680814342-1.08488459738-3.930329241283.113973118931.108341055551.73611859811-0.38520007035-1.37593141024-0.7269938385410.4073127136440.6292459582260.2087498712870.1382319251080.532646562527-0.1454409330480.267401282346-0.0506416621810.1154397619711.4040472051-0.02227162285780.590796297454-18.5770652369-0.84509259930540.0354100886
263.76571942497-0.7652854844282.046208819974.903250738022.717878544324.51066625109-0.1322950140290.9494588704230.184276458716-0.362059040135-0.137532072546-0.326632803092-1.457176503110.09514697114580.02208317267810.4922231950570.01772528011120.09617703561361.026778486860.09040574892370.254112848382-8.522127435598.7843022386839.3933087023
272.30000242084-2.491872041330.4638982889772.74311310388-0.3574905840342.139969189561.467482191282.470830730132.61136401603-0.510045899880.730278204059-1.230027132870.2532853543433.27912867686-2.094643036640.8026998638930.06771114991790.08475699308052.02361564201-0.191497155031.60220607328-7.6148971142823.625727929433.2140898385
284.57477250447-5.45070280343-0.2625916327387.873575088861.357596640121.16492273629-1.25704312541-1.4760133135-1.93719130550.6054346187490.9982663129270.4538588033161.62571898931-0.7610890872710.08640385323941.15446490951-0.2418640501690.332601510190.9129562786610.1789766777750.7768535983713.70339812016-21.553990431719.6099372964
293.596942828432.47534283952-4.755145990795.51247795819-4.165580776018.498413751210.3922793392340.2318347728641.0783491570.2789716784270.4439028252120.512103688859-0.986586181901-0.91852516993-0.6752200990180.60927083741-0.0560105511445-0.05782246195221.422371769310.005150155831230.5360393249447.817422074628.813705157126.5198631599
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 195 through 266 )AA195 - 2661 - 72
22chain 'A' and (resid 267 through 344 )AA267 - 34473 - 150
33chain 'A' and (resid 345 through 403 )AA345 - 403151 - 207
44chain 'A' and (resid 404 through 490 )AA404 - 490208 - 279
55chain 'B' and (resid 197 through 229 )BH197 - 2294 - 36
66chain 'B' and (resid 230 through 249 )BH230 - 24937 - 56
77chain 'B' and (resid 250 through 294 )BH250 - 29457 - 101
88chain 'B' and (resid 295 through 359 )BH295 - 359102 - 166
99chain 'B' and (resid 360 through 381 )BH360 - 381167 - 186
1010chain 'B' and (resid 382 through 437 )BH382 - 437187 - 242
1111chain 'B' and (resid 438 through 457 )BH438 - 457243 - 262
1212chain 'B' and (resid 458 through 490 )BH458 - 490263 - 286
1313chain 'C' and (resid 1 through 16 )CO1 - 161 - 16
1414chain 'C' and (resid 17 through 44 )CO17 - 4417 - 44
1515chain 'C' and (resid 45 through 56 )CO45 - 5645 - 56
1616chain 'C' and (resid 57 through 65 )CO57 - 6557 - 65
1717chain 'C' and (resid 66 through 71 )CO66 - 7166 - 71
1818chain 'C' and (resid 72 through 76 )CO72 - 7672 - 76
1919chain 'D' and (resid 1 through 6 )DQ1 - 61 - 6
2020chain 'D' and (resid 7 through 11 )DQ7 - 117 - 11
2121chain 'D' and (resid 12 through 22 )DQ12 - 2212 - 22
2222chain 'D' and (resid 23 through 34 )DQ23 - 3423 - 34
2323chain 'D' and (resid 35 through 44 )DQ35 - 4435 - 44
2424chain 'D' and (resid 45 through 55 )DQ45 - 5545 - 55
2525chain 'D' and (resid 56 through 65 )DQ56 - 6556 - 65
2626chain 'D' and (resid 66 through 71 )DQ66 - 7166 - 71
2727chain 'D' and (resid 72 through 76 )DQ72 - 7672 - 76
2828chain 'E' and (resid 6 through 19 )ES6 - 191 - 14
2929chain 'F' and (resid 5 through 19 )FT5 - 191 - 15

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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