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- PDB-8g66: Structure with SJ3149 -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 8g66
タイトルStructure with SJ3149
要素
  • Casein kinase I isoform alpha
  • DNA damage-binding protein 1
  • Protein cereblon
キーワードLIGASE / molecular glue
機能・相同性
機能・相同性情報


negative regulation of monoatomic ion transmembrane transport / Activation of SMO / intermediate filament cytoskeleton organization / negative regulation of NLRP3 inflammasome complex assembly / cellular response to nutrient / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation by virus of viral protein levels in host cell ...negative regulation of monoatomic ion transmembrane transport / Activation of SMO / intermediate filament cytoskeleton organization / negative regulation of NLRP3 inflammasome complex assembly / cellular response to nutrient / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / Disassembly of the destruction complex and recruitment of AXIN to the membrane / biological process involved in interaction with symbiont / Maturation of nucleoprotein / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / positive regulation of Rho protein signal transduction / Golgi organization / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / positive regulation of TORC1 signaling / Recognition of DNA damage by PCNA-containing replication complex / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / DNA Damage Recognition in GG-NER / nucleotide-excision repair / Degradation of beta-catenin by the destruction complex / positive regulation of protein-containing complex assembly / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / negative regulation of canonical Wnt signaling pathway / Formation of Incision Complex in GG-NER / regulation of circadian rhythm / kinetochore / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / spindle / Wnt signaling pathway / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / chromosome, telomeric region / cell surface receptor signaling pathway / protein phosphorylation / non-specific serine/threonine protein kinase / protein ubiquitination / protein kinase activity / viral protein processing / nuclear speck / cilium / ciliary basal body / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / apoptotic process / centrosome / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / signal transduction / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / ATP binding
類似検索 - 分子機能
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / : / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / : / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / PUA-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Chem-YOT / Casein kinase I isoform alpha / DNA damage-binding protein 1 / Protein cereblon
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.45 Å
データ登録者Miller, D.J. / Young, S.M. / Fischer, M.
資金援助 米国, 1件
組織認可番号国
Alexs Lemonade Stand Foundation for Cancer 米国
引用ジャーナル: To Be Published
タイトル: Structure of ternary complex with molecular glue targeting CK1A for degradation by the CRL4CRBN ubiquitin ligase
著者: Miller, D.J. / Young, S.M. / Fischer, M.
履歴
登録2023年2月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年12月13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

ダウンロードとリンク

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集合体

登録構造単位
A: DNA damage-binding protein 1
B: Protein cereblon
C: Casein kinase I isoform alpha
D: DNA damage-binding protein 1
E: Protein cereblon
F: Casein kinase I isoform alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)369,1329
ポリマ－368,6256
非ポリマー5073
水00
1
A: DNA damage-binding protein 1
B: Protein cereblon
C: Casein kinase I isoform alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)184,7545
ポリマ－184,3123
非ポリマー4422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: DNA damage-binding protein 1
E: Protein cereblon
F: Casein kinase I isoform alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)184,3784
ポリマ－184,3123
非ポリマー651
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)86.660, 109.710, 112.340
Angle α, β, γ (deg.)105.490, 94.410, 100.030
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

#1: タンパク質 DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


分子量: 96033.945 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DDB1, XAP1 / 細胞株 (発現宿主): High Five / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q16531
#2: タンパク質 Protein cereblon


分子量: 48976.117 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CRBN, AD-006 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q96SW2
#3: タンパク質 Casein kinase I isoform alpha / CKI-alpha / CK1


分子量: 39302.238 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CSNK1A1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ)
参照: UniProt: P48729, non-specific serine/threonine protein kinase
#4: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#5: 化合物 ChemComp-YOT / (3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione


分子量: 376.365 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C20H16N4O4 / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY

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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: 2.74 Å3/Da / 溶媒含有率: 55.14 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年9月29日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.45→50 Å / Num. obs: 49793 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / 冗長度: 4.5 % / Biso Wilson estimate: 107.24 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.204 / Net I/σ(I): 8.56
反射 シェル解像度: 3.45→3.54 Å / 冗長度: 3.4 % / Mean I/σ(I) obs: 1.75 / Num. unique obs: 3410 / CC1/2: 0.708 / Rrim(I) all: 0.902 / Rsym value: 1.514 / % possible all: 90.2

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
XDS0.7.3データスケーリング
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.45→48.25 Å / SU ML: 0.5124 / 交差検証法: FREE R-VALUE / σ(F): 1.93 / 位相誤差: 30.526
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2721 1998 4.02 %
Rwork0.213 47746 -
obs0.2153 49744 97.09 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 122.92 Å2
精密化ステップサイクル: LAST / 解像度: 3.45→48.25 Å
タンパク質核酸リガンド溶媒全体
原子数21267 0 30 0 21297
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.008821739
X-RAY DIFFRACTIONf_angle_d1.007729581
X-RAY DIFFRACTIONf_chiral_restr0.05373412
X-RAY DIFFRACTIONf_plane_restr0.00753803
X-RAY DIFFRACTIONf_dihedral_angle_d16.00917577
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.540.38451230.30583157X-RAY DIFFRACTION90.01
3.54-3.630.34571460.28093445X-RAY DIFFRACTION96.69
3.63-3.740.34841580.29533441X-RAY DIFFRACTION98.96
3.74-3.860.3471240.26533447X-RAY DIFFRACTION98.81
3.86-40.32151520.23633475X-RAY DIFFRACTION98.53
4-4.160.25091590.21683430X-RAY DIFFRACTION98.57
4.16-4.350.26531370.21363481X-RAY DIFFRACTION98.1
4.35-4.570.25521510.20953441X-RAY DIFFRACTION97.95
4.58-4.860.2531310.17823425X-RAY DIFFRACTION97.4
4.86-5.240.2721460.19343305X-RAY DIFFRACTION94.6
5.24-5.760.28571450.21133494X-RAY DIFFRACTION98.67
5.76-6.590.31261480.21683456X-RAY DIFFRACTION99.09
6.59-8.30.24581420.1993438X-RAY DIFFRACTION97.97
8.3-48.250.21671360.1863311X-RAY DIFFRACTION93.97
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)
10.621422830809-0.2368277402380.1527432338050.886857535585-0.4399366516950.879082611365-0.0305158160055-0.158920605431-0.174948428288-0.119241605967-0.229221991572-0.11155576490.476711295422-0.270385576188-1.344458160990.917136500462-0.1122904259840.1184243065240.9181386617160.1266446890790.95499862643561.924-17.831-37.967
2-0.381417579454-0.389640994925-0.8195543961080.0110665109289-0.1024250199580.9322505273610.0275414609305-0.06518219488050.00654980318604-0.195711165861-0.186727166290.020484591643-0.0636329805843-0.1308538703-2.92564919888E-70.9026286063580.017911806180.04329808464940.8725614302920.03256260862680.84840883974764.1826.012-54.042
30.3269721772340.237536882194-0.1236079667310.409682711152-0.4023648862470.9471514769210.341714353561-0.207211159576-0.03257331069790.285497146281-0.202760292102-0.00593343908019-0.446216434743-0.342700755553-5.219448227370.9576873152650.1153862177980.1102649347440.936625173801-0.06757708872170.67678020711454.00523.525-37.062
40.155060337258-0.426582063416-0.2249727273850.3286246691610.1666545435380.2978441715850.153677071125-0.189153350237-0.160582634768-0.300797208579-0.09266243072840.145639351810.161705116054-0.07557063917924.15824581259E-60.746151959824-0.287544226248-0.05956704098531.67403222223-0.0005611781637030.97077319654133.48-1.242-41.73
50.484132201351-0.145950789160.2133784675480.2122230045820.0620262179161-0.2201686257550.13134733075-0.168383022266-0.140894052423-0.0546880276760.147090730715-0.04611096200610.215051314347-0.222539002844-7.7262407628E-60.9556226572840.0265510184128-0.02950964392990.9244361660250.09108485423710.87611479915252.4769.318.667
60.03573230974550.2052832822230.107306003542-0.1390458048950.1192863666840.0820042808623-0.503088761908-0.3162766712530.136395293305-0.2883398649040.31102286559-0.317223727653-0.1507131098710.6581800213050.0004289865719371.56677314439-0.313690996703-0.05746353430321.313543628180.1048535444451.3817881883765.7412.74-27.236
70.551740826114-0.3187721068250.2669132032870.0772294617150.1434122792310.136837371314-0.1647640852460.607465662392-0.07520443948860.2293085934140.4269175863130.03298485090750.1030809505060.125160375087-1.24221673201E-51.09760544871-0.0844113985876-0.01156460607481.15525512804-0.08198798865480.90323401231264.42714.188-15.87
80.4162331620470.659604628893-0.1278426101730.103256758464-0.8184324524580.000290418691647-0.34399811033-0.073645209059-0.155316832854-0.2621043687680.3848898405260.0617263439026-0.1789260375740.209581106512-1.37101713421E-51.05806276536-0.012741827511-0.03203620990790.9632883272430.01427497375630.95842401824970.20725.9476.271
90.003238508002820.08174826069920.02121713024640.008865399599490.00472212072524-0.022751978799-0.366136214433-0.0126373188855-0.156484818233-0.075301484392-0.1905304073690.1587245130160.7021998758590.309726344581-1.46363347217E-51.097148330730.2852783457080.0239966340090.9949497180960.01626749113740.96118594901260.77531.94728.056
100.05981886353310.287758423905-0.1356138156430.02116035204690.1054415437410.0801013303745-0.0379922192077-0.07896267626460.0065830702289-0.180661202530.121928970780.4340751577560.3185835155590.2770482803050.001892924324030.8726032364730.001666824571390.06313772693540.700059333530.04691703743620.98470706763557.36842.29124.912
110.19390731445-0.284339834693-0.3525936822440.0731433010812-0.5353947405060.2096681095150.090590310218-0.25393217040.198039317738-0.04233652132360.002365515065340.3456262667310.2104975467280.1560121503525.81475222625E-70.7159423747190.223818966006-0.04751487148790.957834586635-0.01987535739630.91819693966475.39850.37827.355
120.0969285070009-0.0104121543458-0.0210025496651-0.0365976252246-0.0366605741955-0.0149375968390.345941815759-0.3171443419030.4834368937920.192308259759-0.1908130180030.1005814282560.0899538591041-0.003550244657740.5812404820010.7535938735140.3129157777240.05669362545340.913930946636-0.05346083293451.5956197194859.46964.2424.418
13-0.06562965634470.02540043463050.00199742049670.0181000284175-0.0801866676806-0.02536088326560.495178599201-0.6170718211560.02675682066070.276575881464-0.466833033593-0.0652692144509-0.642201815336-0.07337016753095.007165846791.011993691410.2810999880020.1415580173261.305103468060.05438155598960.97740380424864.39964.69438.823
140.533345076387-0.316886196110.2420862423410.575840589706-0.7861413536820.03646935612380.0952648377106-0.3349428738660.2197845856320.1442207274040.1624103222780.105116922048-0.04588113496120.1891965776861.76315326272E-60.962804369480.0533191136874-0.03456515110571.26907661133-0.09546204450160.95980942487679.99161.10633.042
151.81220546076-0.005475236542130.3719857349571.07801119732-0.519875529151-0.0557400677348-0.145246009105-0.3562749589920.119413560928-0.2854331821220.0226122842384-0.107479147388-0.0383662027430.149804161380.001869098373050.6676697612180.0089369196317-0.02275886592320.721714279617-0.0004553613541650.8445381231348.116-37.4821.622
16-0.2851162650480.0656271273158-0.821591827911-0.154284580315-0.3510724867350.7954792550720.0414908145888-0.2662030847540.153591471132-0.0550753413908-0.002709001505180.3281441452920.1477006858510.334342211626-0.005042240712340.3525022282640.0640819853894-0.09785645953870.556364164529-0.0517110309220.64020148510818.501-43.6337.232
170.7939218221370.205077386608-0.2146211500890.641352746801-0.227788949770.824079109874-0.2156349857780.2384452033210.0414880744624-0.05128174842470.2478374416830.1363803733920.257791809942-0.09228286135837.23344561172E-60.717564223851-0.0847278890036-0.1627425124140.8491985882850.02922883750780.8337048828764.468-50.2-10.9
180.5368214406870.0148668856744-1.010147045870.2219647152790.8190148795210.1562517410490.01907723654670.1610071818760.276790773804-0.3718254500260.244674214463-0.179515513330.0881952587597-0.04317626655680.3080213428771.09295268258-0.22087731389-0.1557779565470.7010281976720.1508930514030.95220498539919.805-24.424-15.873
190.0325143541755-0.03933564785630.08540529474570.09385761437090.06094276059270.1101685150840.54078141621-0.6844916138730.823818889741-0.4426958653770.0524467794101-0.237732918198-0.2324161917060.9876297174591.03595944741E-51.56708329972-0.2460274236940.3461360560931.72313542356-0.1643432605191.2390341026936.729-50.36-49.638
20-0.2937214340680.2552281129550.2823585498410.303419428390.5017876117010.09137926383530.420603595574-0.420531755148-0.14968459447-0.1205774227230.6703911319820.5571052055570.865157109120.225422895714-0.006430721296051.381688699740.0433097767008-0.02333685425921.535206135720.01269841958741.4930968076733.066-48.248-21.211
210.1806496689710.1182075434970.2281673611920.07682249478090.0191196905650.0560274422205-0.409851136938-0.04002894461850.1723308591890.1513475486340.497601172290.276279339370.1060472482750.893076874111-1.96179657673E-51.15405402928-0.00536807414247-0.01819476094160.98743226635-0.07750409845320.90126121884126.843-54.877-17.324
220.108081732733-0.889192052367-0.1226218860850.3345173221630.92842870038-0.111805779313-0.3763828812870.057258806040.167027892514-0.3660445375670.6723907333470.0931831260583-0.06168777616860.341758343865-98.32034249231.18761263373-0.3153786447050.02601019555741.13634953565-0.1767489562280.89783692791526.421-62.107-39.206
230.1565653484350.09525698249640.04879106849580.136690346291-0.174547248792-0.069287127078-0.1558391372510.443290744133-0.06357462391080.08363026487960.2804828587580.39423950224-0.786327431860.945550213214-1.51155839329E-51.39650613473-0.3949390813870.04955672180891.51703437352-0.2245019845190.99387087669326.833-73.825-49.704
240.11549362414-0.143548644576-0.05346205098350.242734469435-0.0503799494030.02821479647750.3742636893930.3347129704680.01757368894160.750046961264-0.258465979080.244272618543-0.765077945560.499840921475-3.77593013902E-61.45269168768-0.135964687096-0.008860733202491.2692448741-0.1871967600420.80611074529725.916-71.593-71.886
250.058650526135-0.163720116016-0.1639065735310.05609229508410.04586972736210.04757426167130.3210214646510.04762749563680.1976828787170.1901000795860.02545209240060.0553033198203-0.4714137810160.281719495401-1.7279001572E-61.35544822866-0.105146770160.1355189112970.8156753608020.06263600180090.96774983809513.698-71.454-75.225
260.248883797251-0.0365215006419-0.002800093472910.358377805745-0.6409981575890.3981230999410.172558646489-0.162435468101-0.09127796711660.326401994858-0.103070578935-0.205224125317-0.3499464289980.0729623555594-16.53182049820.8538458182130.07936160741110.008347014927760.705073287314-0.05742166157380.82841323474213.708-88.636-71.678
270.510755929989-0.1070991362720.1658148433760.37864638776-0.08761425938630.815144662649-0.2687755710840.497584011314-0.0972518978121-0.1103858649480.2691895093990.1239061971850.000359919161816-0.255117581164-16.47591141550.8094184040150.01864651846260.04639657258070.784187089572-0.02369731745530.824493349044.261-92.498-85.711
280.2013116015880.0902585691453-0.6252197787930.203816651623-0.1161136796080.529648467528-0.398402420931-0.147712506808-0.164404792002-0.00281057718780.2039455512060.233954995880.180845688502-0.3589092384525.55109542676E-60.8469821677310.1221546617240.06794488024490.778482272598-0.00727565952490.9053115994835.258-100.41-69.689
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:299 )A2 - 299
2X-RAY DIFFRACTION2( CHAIN A AND RESID 300:784 )A300 - 784
3X-RAY DIFFRACTION3( CHAIN A AND RESID 785:1009 )A785 - 1009
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1010:1140 )A1010 - 1140
5X-RAY DIFFRACTION5( CHAIN B AND RESID 47:184 )B47 - 184
6X-RAY DIFFRACTION6( CHAIN B AND RESID 185:231 )B185 - 231
7X-RAY DIFFRACTION7( CHAIN B AND RESID 232:323 )B232 - 323
8X-RAY DIFFRACTION8( CHAIN B AND RESID 324:428 )B324 - 428
9X-RAY DIFFRACTION9( CHAIN C AND RESID 11:36 )C11 - 36
10X-RAY DIFFRACTION10( CHAIN C AND RESID 37:90 )C37 - 90
11X-RAY DIFFRACTION11( CHAIN C AND RESID 91:155 )C91 - 155
12X-RAY DIFFRACTION12( CHAIN C AND RESID 156:175 )C156 - 175
13X-RAY DIFFRACTION13( CHAIN C AND RESID 176:199 )C176 - 199
14X-RAY DIFFRACTION14( CHAIN C AND RESID 200:303 )C200 - 303
15X-RAY DIFFRACTION15( CHAIN D AND RESID 2:307 )D2 - 307
16X-RAY DIFFRACTION16( CHAIN D AND RESID 308:795 )D308 - 795
17X-RAY DIFFRACTION17( CHAIN D AND RESID 796:928 )D796 - 928
18X-RAY DIFFRACTION18( CHAIN D AND RESID 929:1140 )D929 - 1140
19X-RAY DIFFRACTION19( CHAIN E AND RESID 86:161 )E86 - 161
20X-RAY DIFFRACTION20( CHAIN E AND RESID 162:231 )E162 - 231
21X-RAY DIFFRACTION21( CHAIN E AND RESID 232:264 )E232 - 264
22X-RAY DIFFRACTION22( CHAIN E AND RESID 265:371 )E265 - 371
23X-RAY DIFFRACTION23( CHAIN E AND RESID 372:427 )E372 - 427
24X-RAY DIFFRACTION24( CHAIN F AND RESID 11:41 )F11 - 41
25X-RAY DIFFRACTION25( CHAIN F AND RESID 42:84 )F42 - 84
26X-RAY DIFFRACTION26( CHAIN F AND RESID 85:155 )F85 - 155
27X-RAY DIFFRACTION27( CHAIN F AND RESID 156:253 )F156 - 253
28X-RAY DIFFRACTION28( CHAIN F AND RESID 254:303 )F254 - 303

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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