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- PDB-6u4y: Crystal Structure of an EZH2-EED Complex in an Oligomeric State -

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基本情報

登録情報
データベース: PDB / ID: 6u4y
タイトルCrystal Structure of an EZH2-EED Complex in an Oligomeric State
要素
  • Histone-lysine N-methyltransferase EZH2
  • Polycomb protein EED
キーワードTRANSFERASE / TRANSCRIPTION / Methyltransferase
機能・相同性
機能・相同性情報


hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway ...hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development / primary miRNA binding / regulatory ncRNA-mediated heterochromatin formation / regulation of adaxial/abaxial pattern formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / histone H3K27 methyltransferase activity / sex chromatin / positive regulation of cell cycle G1/S phase transition / facultative heterochromatin formation / genomic imprinting / ESC/E(Z) complex / negative regulation of stem cell differentiation / protein-lysine N-methyltransferase activity / cardiac muscle hypertrophy in response to stress / chromatin silencing complex / pronucleus / G1 to G0 transition / positive regulation of dendrite development / histone H3 methyltransferase activity / histone methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / lncRNA binding / negative regulation of gene expression, epigenetic / synaptic transmission, GABAergic / Transcriptional Regulation by E2F6 / : / positive regulation of MAP kinase activity / pericentric heterochromatin / oligodendrocyte differentiation / negative regulation of transcription elongation by RNA polymerase II / positive regulation of GTPase activity / positive regulation of protein serine/threonine kinase activity / positive regulation of epithelial to mesenchymal transition / subtelomeric heterochromatin formation / ribonucleoprotein complex binding / RNA polymerase II core promoter sequence-specific DNA binding / nucleosome binding / keratinocyte differentiation / protein localization to chromatin / negative regulation of cytokine production involved in inflammatory response / liver regeneration / cellular response to leukemia inhibitory factor / B cell differentiation / Regulation of PTEN gene transcription / transcription corepressor binding / PRC2 methylates histones and DNA / Defective pyroptosis / stem cell differentiation / hippocampus development / enzyme activator activity / promoter-specific chromatin binding / chromatin DNA binding / G1/S transition of mitotic cell cycle / regulation of circadian rhythm / PKMTs methylate histone lysines / protein modification process / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / HCMV Early Events / rhythmic process / transcription corepressor activity / heterochromatin formation / response to estradiol / chromosome / chromatin organization / Oxidative Stress Induced Senescence / histone binding / methylation / chromosome, telomeric region / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / synapse / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
類似検索 - 分子機能
EZH2, SET domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain ...EZH2, SET domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
類似検索 - ドメイン・相同性
Polycomb protein EED / Histone-lysine N-methyltransferase EZH2
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: 2.91 Å
データ登録者Jiao, L. / Liu, X.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2020
タイトル: A partially disordered region connects gene repression and activation functions of EZH2.
著者: Jiao, L. / Shubbar, M. / Yang, X. / Zhang, Q. / Chen, S. / Wu, Q. / Chen, Z. / Rizo, J. / Liu, X.
履歴
登録2019年8月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月8日Provider: repository / タイプ: Initial release
改定 1.12020年7月22日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22020年8月12日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年3月13日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-lysine N-methyltransferase EZH2
B: Histone-lysine N-methyltransferase EZH2
C: Histone-lysine N-methyltransferase EZH2
D: Polycomb protein EED
E: Polycomb protein EED
F: Polycomb protein EED


分子量 (理論値)分子数
合計 (水以外)203,6586
ポリマ－203,6586
非ポリマー00
水00
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 area25640 Å2
ΔGint-135 kcal/mol
Surface area69420 Å2
手法PISA
単位格子
Length a, b, c (Å)181.632, 114.721, 131.524
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2

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要素

#1: タンパク質 Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


分子量: 25701.156 Da / 分子数: 3 / 断片: UNP residues 2-182, linker, UNP residues 220-257 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EZH2, KMT6 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15910, histone-lysine N-methyltransferase
#2: タンパク質 Polycomb protein EED / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


分子量: 42184.965 Da / 分子数: 3 / 断片: UNP residues 78-441 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EED / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O75530

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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: 3.36 Å3/Da / 溶媒含有率: 67.38 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 1 M sodium/potassium tartrate, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 7.0

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データ収集

回折平均測定温度: 93 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.97927 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2015年12月12日
放射モノクロメーター: double crystal 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: 0.97927 Å / 相対比: 1
反射解像度: 2.9→50 Å / Num. obs: 54528 / % possible obs: 99.8 % / 冗長度: 13.7 % / Biso Wilson estimate: 53.78 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.052 / Net I/σ(I): 15.1
反射 シェル解像度: 2.9→2.95 Å / Rmerge(I) obs: 1.329 / Mean I/σ(I) obs: 1 / Num. unique obs: 2382 / CC1/2: 0.561 / Rpim(I) all: 0.579

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
BUSTER2.10.3精密化
PHENIX1.16_3549精密化
HKL-2000データスケーリング
PHASER位相決定
PDB_EXTRACT3.25データ抽出
HKL-2000データ削減
精密化構造決定の手法: 分子置換 / 解像度: 2.91→48.5 Å / SU ML: 0.2878 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.1215
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2243 2576 4.73 %RANDOM
Rwork0.182 51939 --
obs0.184 54515 89.08 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 57.03 Å2
精密化ステップサイクル: LAST / 解像度: 2.91→48.5 Å
タンパク質核酸リガンド溶媒全体
原子数12736 0 0 0 12736
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004213021
X-RAY DIFFRACTIONf_angle_d0.700317573
X-RAY DIFFRACTIONf_chiral_restr0.04731895
X-RAY DIFFRACTIONf_plane_restr0.00342236
X-RAY DIFFRACTIONf_dihedral_angle_d7.50127814
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-2.960.3423490.29441140X-RAY DIFFRACTION35.4
2.96-3.020.4157730.27041429X-RAY DIFFRACTION44.73
3.02-3.090.2871780.24671801X-RAY DIFFRACTION56.31
3.09-3.160.31351180.23392436X-RAY DIFFRACTION76.42
3.16-3.240.2641460.24032931X-RAY DIFFRACTION91.41
3.24-3.330.26431480.22853129X-RAY DIFFRACTION97.82
3.33-3.430.29651490.21673228X-RAY DIFFRACTION99.53
3.43-3.540.22391460.19073216X-RAY DIFFRACTION99.97
3.54-3.660.25441420.1783211X-RAY DIFFRACTION100
3.66-3.810.2251600.1743244X-RAY DIFFRACTION100
3.81-3.980.22561560.16423224X-RAY DIFFRACTION99.97
3.98-4.190.2231680.1553214X-RAY DIFFRACTION99.97
4.19-4.450.17081510.14273237X-RAY DIFFRACTION99.97
4.45-4.80.18111880.13563229X-RAY DIFFRACTION100
4.8-5.280.16141680.13933252X-RAY DIFFRACTION100
5.28-6.040.23641700.18383289X-RAY DIFFRACTION100
6.04-7.610.21421740.19633307X-RAY DIFFRACTION100
7.61-48.50.22841920.21123422X-RAY DIFFRACTION99.37
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)
11.03804194734-1.866783799140.1700164912165.69203905699-0.395105145570.8042787921740.167250249366-0.3036293486820.1427225368650.292020245323-0.192525382302-0.3618782279910.09598869264420.201694186585-0.1249485375110.34733865375-0.068158251441-0.0593473587780.728988085482-0.1067850860380.49045383033393.92226325153.26855219782286.57473824
22.919013026620.197597800206-0.6219246013822.00782585994-0.3297279442841.646027479920.247604536959-0.1108415392660.8192450587050.0659776216254-0.05909285474340.242103003682-0.2392079381410.0160841995378-0.06133456994520.5569204688750.04107374362370.1044472382030.388623154854-0.1423276782770.48245661809858.76786636135.4141481942280.874467509
31.18709316908-0.547060720149-0.645486024071.505717203770.5250846326030.361755193164-0.1284521085290.1868624591770.588801424775-0.2742599289890.43411009696-0.0815862540259-0.8232580735480.339623229349-0.03323577983631.21807034907-0.06821515894720.2297754448250.793669510608-0.004335077895781.042582052549.379808388947.6394418976242.09519514
46.07196451191-0.1600026861461.932876275130.2743968137230.3016230468751.42027944570.31574162292-0.587414106373-0.5031296912260.351523401806-0.3178577786860.2448546662080.152630007273-0.1637925893880.06650198124080.431307754082-0.1021403509950.04000052043030.5659036776540.3208981359240.48386902721419.6881105194-21.9826674826298.784007676
51.792451534720.02384113858320.1094572583572.5168015605-0.7029962760181.07286267546-0.05471798753-0.250546218284-0.08204685330290.2023191020520.082780276429-0.6006714940470.3303473493660.0574849059267-0.007830690586320.327745671686-0.0255072624046-0.08607065999620.5046102400360.01711848510290.347482448165.4972908732-8.95390722208297.679299162
63.173244309161.409355749421.385460279171.736111338681.331209291971.989272261830.0762107472222-0.3852619598-0.3078452799750.116004754269-0.0407439405691-0.03330061251180.311712019831-0.140310801576-0.1977638328680.544417044715-0.0286935489362-0.1703625221290.569418204483-0.003483176362780.47715665613295.66480916-23.0658437193277.221312307
71.433926386560.3989408774290.01234662434490.8594047827460.1455520561921.041279164070.0347847506196-0.2331270162060.344511625164-0.135502616725-0.02300954089350.261977785485-0.214793251812-0.2186404057540.04543741249880.4835374179970.166324687524-0.03678033177270.367836946441-0.1047545193340.42376693183524.442631046726.9943233512274.318031395
83.315775040080.477043839652-0.7145406873241.88928947195-0.3594710330932.77482001623-0.3145735033290.464417245257-0.586429324018-0.2876135915030.3202613579910.00376453038720.110246908743-0.241336381760.2720378935920.461610977735-0.05491554645520.1608511913270.672472073948-0.08204471724670.5934238096982.94244381972-26.5222238386281.276030251
93.331418772030.313542483492-0.7200975536553.2986146930.01805131923283.062104248030.332038816622-0.5082145239880.7218046290580.1757700156130.2801002247780.181564257841-0.813359496277-0.07007681252810.02158649844640.337690038373-0.05373492037820.09553263254260.239887285738-0.1956805880140.30210650401864.850598996327.9304134902283.116406739
102.503375951981.06347586022-0.6019541333144.192741898731.637241255543.303195908050.0118407162490.3864901912221.15131459684-0.4832315508470.1576602057120.243647067802-1.280431326080.0817027267023-0.1483403556520.607572215775-0.02117996372730.1015164303810.220062549411-0.003364985720970.59984722249868.742162886936.9657466587270.528960732
115.779490110460.637563151538-0.1597848943094.32464362809-0.03977068955134.055793995560.2529293698930.4802705525680.674907412658-0.402903825181-0.0648597631027-0.151387822262-0.512213490290.215063714985-0.2698539778550.356000007422-0.07769854776530.1150516341330.261814876494-0.003178865721770.28386545718876.221303554126.9925882255267.802359937
124.795334436170.525809168373-0.4513433183132.99461114208-0.5061990910212.561423984660.0789770592570.7731915866971.05252666038-0.809228852298-0.1300559841-0.00205241753661-0.433646879850.0909237078156-0.3079504318210.518878407426-0.08039729050990.1370195168490.3759605049220.02015449597310.34321404226277.750634443828.1124995935261.222124732
134.05457047688-0.175065568684-0.943088316841.60811327418-0.8011705892443.50493547723-0.1643849837960.41735882216-0.0385985244728-0.5078345631830.273862254932-0.5283945941070.1041800609420.423225112678-0.1081605545220.305446241681-0.08610776968160.1290171122490.36776332396-0.08718567270750.32892186550982.581367517516.6771578867266.403702697
143.82553099792-0.007151059990330.07611397781523.083926290390.2500063248293.29157204522-0.04202585329310.6851681088140.604583297964-0.812246701996-0.0649560010641-0.828324165763-0.7847949099510.22724262519-0.3277845248960.596652018091-0.154130931760.2270737206760.655572723743-0.001681839145310.50655921868586.938325825429.1789971523258.570578433
154.395871334410.62485203657-1.472247620692.62483948462-0.1297358194973.73945229267-0.001336192154420.172572298913-0.54638645082-0.1202986369410.0642024231439-0.6133991116580.2522879142740.6669594510130.02724914841410.3162955762940.02860571499460.02263669777060.360674893227-0.1557846590640.38323780148785.56139946868.2715157146274.313496766
163.678211160390.164922051037-1.740190938122.70706854203-0.8462812530722.855326339280.128186616087-0.2360008869690.18645431676-0.118477378813-0.154095159542-0.141158700246-0.1650936854240.504294062118-0.05462945187370.241614730150.008799155552510.03921847891370.276253805108-0.07883723472060.19787617404873.978646190814.2372837229282.403610358
176.267469285791.58769502187-0.69734874452.420575371750.6285428177253.033416735350.181503878465-1.50346861264-0.6536967997580.523207022713-0.176464302881-0.5154023315050.4126054715630.409477395546-0.00887036381950.3369047580060.0424346150057-0.1015050230630.498469718382-0.0004965751900720.14847819902576.37484868879.31881538969290.284715847
183.265559936530.653958628082-0.2271851991252.80683609075-0.1572958675753.060929729080.249470441027-0.4367985102650.2360432287470.507387285190.0213505373888-0.211417928688-0.2008309880570.350559051337-0.1173894064080.263548433505-0.02039604201890.01452460915880.265433341091-0.1368356138640.24490679176966.815182135818.6689725302288.309263892
194.706276721650.624517496225-0.4115450282894.311621897420.838424067124.160354819020.332710985156-0.926995811422-0.05889190222630.440332350132-0.118492599792-0.405125129516-0.130706525368-0.117355132439-0.02959909815790.274705593375-0.08046371194290.06976318788630.414876107579-0.2305047721260.13260889465165.532668888320.798429465290.554175592
203.16493018312-0.2756179157590.1938826555433.34014001789-0.1337966448442.265241702580.0885006692019-0.517041091944-0.08570024896740.3173354366490.0243174116961-0.323748849776-0.01098818750280.136194638742-0.02250332652740.229701024114-0.0630732438448-0.1482952376680.4522319718710.1145900952130.24646367409156.4846334311-8.16216194462300.089723509
212.821855578110.9677767486942.41973064272.672690725912.243470480136.718225611220.4872970428480.325177757061-0.4889820891260.266862162153-0.00812737670389-0.7801389644320.2622048339160.91546765641-0.1685425709910.238830703054-0.0160156394686-0.1098043878490.5146150331110.03128441708920.5284499615766.4037781096-17.9871800384294.128358552
222.74783953570.007694575161530.3183638564273.15745720739-0.430388462293.034295790670.352104114064-0.0326784144278-0.7003682349760.007109326010550.1041610898420.006002796827860.3895462241450.379966014381-0.2085764161580.3696409088860.0237856389643-0.1610939088910.3860856839440.1011916629180.39985480706754.5584026942-24.1862781342292.670523374
236.51665066888-0.6681724667310.9817400226852.80331709422-2.097140525354.18981129695-0.0836744613092-0.539291471046-1.10597624775-0.347606189567-0.235801565452-0.3431802197490.1937466672160.640811606951-0.7664185354150.4761212054740.0755444412266-0.1872981803830.3514441813470.02055033913160.5162282704457.0304182915-29.5381919711289.099007338
242.7161280723-0.186291707717-0.2171109219833.455059705680.02443847777242.957447528470.237262944793-0.13272937131-0.900343364419-0.282469648881-0.07496352338520.2455175726190.949928336110.35925917438-0.2678334457150.5675321919960.0176794920354-0.1868938863670.3475469270610.1727688763550.59116241759248.5578461225-32.5721058137289.872420053
253.730897319990.387747976808-0.4099594116964.45667424982-0.4732052800715.494368660410.122726925801-0.0223181671314-0.485341363864-0.5056586934630.04159662935980.5520231722770.665296687283-0.359799619654-0.2166649105630.348027023716-0.0710808288924-0.1483758650530.3862084244040.1334164891250.41019435650336.6740328843-20.5384526643289.167258473
261.887041770550.9239625145820.4099246385074.224983022240.4133574040021.911440794580.0233093553691-0.43944169296-0.1288780486010.00474289428380.04299600181410.6296954347290.120309945124-0.433376507591-0.1129406644160.255257912924-0.0371740101369-0.09662687868440.5119754400240.164591828670.32187484712737.7264285638-11.7444963149296.500293518
273.217028233270.2183849058320.8141486433241.80463163682-0.2653164625633.192212121350.0278700934878-0.273612277368-0.06004837627750.0633955889514-0.04403709382650.3541127418140.0825404066456-0.7680924510730.001543758657240.22261487290.07004544083760.01389757201720.340823146307-0.03394514038470.32687518718920.71073477318.0780192689278.222444952
283.30453768686-0.549588766096-1.071065609612.62351990637-0.01370818560834.12857768551-0.3896911959650.918935039188-0.2247606098960.025959529490.0776384644841.024079759940.463695483463-1.52989737213-0.07557355307110.4880718314320.140684987167-0.1478769395351.03790032443-0.06780125585480.6119711404086.3068006752121.43150325262.566973373
294.33690890993-0.4376282760991.150712691572.59361418497-0.1922057413634.207995723-0.07863614630060.4859024750050.634895813562-0.334558498502-0.1474998492510.0791768842768-0.624948497524-0.3955778461570.2222264230110.512344809510.125971269244-0.05674457516590.3265906661260.009233306266960.38063718314328.473179805634.0021383184262.756306271
303.274688853110.2793032491321.20050377441.82547216284-0.9384398937143.07998585477-0.10264161171-0.3125895945840.5438759919960.139063870689-0.02928443608330.100781554615-0.563056496496-0.1130071032180.1650972168950.3418684909410.0411584795328-0.003744053145560.234754262159-0.08665538031590.26417056841535.29934066628.6502823612281.408674134
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 12 THROUGH 62 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 63 THROUGH 107 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 108 THROUGH 249 )A0
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 12 THROUGH 60 )B0
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 61 THROUGH 112 )B0
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 113 THROUGH 249 )B0
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 16 THROUGH 144 )C0
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 145 THROUGH 249 )C0
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 76 THROUGH 154 )D0
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 155 THROUGH 186 )D0
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 187 THROUGH 210 )D0
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 211 THROUGH 229 )D0
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 230 THROUGH 267 )D0
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 268 THROUGH 301 )D0
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 302 THROUGH 357 )D0
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 358 THROUGH 380 )D0
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 381 THROUGH 404 )D0
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 405 THROUGH 423 )D0
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 424 THROUGH 441 )D0
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESID 76 THROUGH 167 )E0
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 168 THROUGH 186 )E0
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 187 THROUGH 210 )E0
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESID 211 THROUGH 229 )E0
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESID 230 THROUGH 301 )E0
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESID 302 THROUGH 322 )E0
26X-RAY DIFFRACTION26CHAIN 'E' AND (RESID 323 THROUGH 440 )E0
27X-RAY DIFFRACTION27CHAIN 'F' AND (RESID 77 THROUGH 267 )F0
28X-RAY DIFFRACTION28CHAIN 'F' AND (RESID 268 THROUGH 301 )F0
29X-RAY DIFFRACTION29CHAIN 'F' AND (RESID 302 THROUGH 357 )F0
30X-RAY DIFFRACTION30CHAIN 'F' AND (RESID 358 THROUGH 440 )F0

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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