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- PDB-8e3e: ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing CAST seq... -

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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: 8e3e
タイトルZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing CAST sequence (#10)
要素
  • DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3')
  • DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3')
  • Zinc finger and BTB domain-containing protein 7A
キーワードDNA BINDING PROTEIN/DNA / gene expression / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN
機能・相同性
機能・相同性情報


regulation of transcription regulatory region DNA binding / negative regulation of androgen receptor signaling pathway / DNA-dependent protein kinase complex / double-strand break repair via classical nonhomologous end joining / regulation of DNA-binding transcription factor activity / regulation of glycolytic process / regulation of alternative mRNA splicing, via spliceosome / nuclear androgen receptor binding / histone acetyltransferase binding / erythrocyte maturation ...regulation of transcription regulatory region DNA binding / negative regulation of androgen receptor signaling pathway / DNA-dependent protein kinase complex / double-strand break repair via classical nonhomologous end joining / regulation of DNA-binding transcription factor activity / regulation of glycolytic process / regulation of alternative mRNA splicing, via spliceosome / nuclear androgen receptor binding / histone acetyltransferase binding / erythrocyte maturation / SMAD binding / fat cell differentiation / negative regulation of Notch signaling pathway / protein localization to nucleus / B cell differentiation / transcription corepressor binding / negative regulation of transforming growth factor beta receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of NF-kappaB transcription factor activity / sequence-specific double-stranded DNA binding / chromatin organization / site of double-strand break / regulation of apoptotic process / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytoplasm
類似検索 - 分子機能
: / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...: / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Zinc finger and BTB domain-containing protein 7A
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: 2.99 Å
データ登録者Horton, J.R. / Ren, R. / Cheng, X.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 米国
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 米国
引用ジャーナル: J.Biol.Chem. / 年: 2023
タイトル: Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia.
著者: Ren, R. / Horton, J.R. / Chen, Q. / Yang, J. / Liu, B. / Huang, Y. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
履歴
登録2022年8月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年2月8日Provider: repository / タイプ: Initial release
改定 1.12023年2月15日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.22023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.32024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Zinc finger and BTB domain-containing protein 7A
X: DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3')
Y: DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3')
B: Zinc finger and BTB domain-containing protein 7A
D: DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3')
E: DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3')
F: Zinc finger and BTB domain-containing protein 7A
H: DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3')
I: DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,00921
ポリマ－96,2249
非ポリマー78512
水1629
1
A: Zinc finger and BTB domain-containing protein 7A
X: DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3')
Y: DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,3367
ポリマ－32,0753
非ポリマー2624
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-43 kcal/mol
Surface area13020 Å2
手法PISA
2
B: Zinc finger and BTB domain-containing protein 7A
D: DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3')
E: DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,3367
ポリマ－32,0753
非ポリマー2624
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-42 kcal/mol
Surface area13070 Å2
手法PISA
3
F: Zinc finger and BTB domain-containing protein 7A
H: DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3')
I: DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)32,3367
ポリマ－32,0753
非ポリマー2624
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-38 kcal/mol
Surface area13830 Å2
手法PISA
単位格子
Length a, b, c (Å)67.519, 147.175, 68.064
Angle α, β, γ (deg.)90.000, 96.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

#1: タンパク質 Zinc finger and BTB domain-containing protein 7A / Factor binding IST protein 1 / FBI-1 / Factor that binds to inducer of short transcripts protein 1 ...Factor binding IST protein 1 / FBI-1 / Factor that binds to inducer of short transcripts protein 1 / HIV-1 1st-binding protein 1 / Leukemia/lymphoma-related factor / POZ and Krueppel erythroid myeloid ontogenic factor / POK erythroid myeloid ontogenic factor / Pokemon / Pokemon 1 / TTF-I-interacting peptide 21 / TIP21 / Zinc finger protein 857A


分子量: 19188.326 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ZBTB7A, FBI1, LRF, ZBTB7, ZNF857A / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): Gold / 参照: UniProt: O95365
#2: DNA鎖 DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3')


分子量: 6516.189 Da / 分子数: 3 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#3: DNA鎖 DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3')


分子量: 6370.154 Da / 分子数: 3 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#4: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Zn
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 9 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN
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: 3.49 Å3/Da / 溶媒含有率: 64.78 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: 12% PEG3350, 0.1M Sodium malonate pH7.0

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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: 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6月9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: 2.99→49.8 Å / Num. obs: 26193 / % possible obs: 98.7 % / 冗長度: 7.1 % / Biso Wilson estimate: 58.8 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.044 / Net I/σ(I): 15.7
反射 シェル解像度: 2.99→3.1 Å / 冗長度: 6.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2577 / CC1/2: 0.945 / Rpim(I) all: 0.331 / % possible all: 97.6

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解析

ソフトウェア
名称バージョン分類
SERGUIデータ収集
PHENIX1.20.1_4487精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7N5U

7n5u


解像度: 2.99→49.8 Å / SU ML: 0.3106 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 31.0861
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2354 1284 4.99 %
Rwork0.2031 24441 -
obs0.2047 25725 96.69 %
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: 119.28 Å2
精密化ステップサイクル: LAST / 解像度: 2.99→49.8 Å
タンパク質核酸リガンド溶媒全体
原子数2703 2565 12 9 5289
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00315642
X-RAY DIFFRACTIONf_angle_d0.51438138
X-RAY DIFFRACTIONf_chiral_restr0.0317883
X-RAY DIFFRACTIONf_plane_restr0.0036609
X-RAY DIFFRACTIONf_dihedral_angle_d24.91872285
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.110.36571360.32512597X-RAY DIFFRACTION92.77
3.11-3.260.32251390.31172591X-RAY DIFFRACTION92.95
3.26-3.430.30151420.2612692X-RAY DIFFRACTION96.26
3.43-3.640.29921360.24162674X-RAY DIFFRACTION95.71
3.64-3.920.28331430.23712729X-RAY DIFFRACTION96.86
3.92-4.320.2431460.212772X-RAY DIFFRACTION99.29
4.32-4.940.23431470.19482799X-RAY DIFFRACTION99.39
4.94-6.220.21871490.19442814X-RAY DIFFRACTION99.63
6.23-49.80.18181460.1562773X-RAY DIFFRACTION97.33
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)
12.81890834306-0.1875940860973.569380265159.181941446652.396462830075.34480261207-0.577214660757-0.36295087397-0.0798560899675-0.704831874629-0.122150229050.50958877478-0.2426532017720.3857935965280.5603144644650.7021504124060.2130764507550.05533587407710.6668437717260.08674011169670.418973199693-23.274722799520.883679182-34.2003216689
21.584000944330.970789792332.137765106182.57333682216-0.639828027864.626824377481.108388812160.1855318698830.09152492346560.260654588519-0.624330023215-0.1205493626710.202076355633-0.0118959385431-0.4210895165390.457257299123-0.0370592038850.1091319715011.01659307581-0.0618484858190.368643359928-21.2386966913-1.47976077423-23.1884874132
36.06251409399-3.710268013810.1332143245375.5340412607-2.829680252262.43366306965-0.199920033079-1.297357244550.8871521890071.628944477750.318685048352-0.477436724321-1.24956710742-0.120076059931-0.1282424209361.138249511260.08145953739530.1244301262441.46350127960.0363328766228-0.352540820598-9.2235406934812.9813839023-7.48494041196
42.03396159885-0.934604308544-3.92511510510.4069875021731.791814727047.54927666048-0.287883254488-0.8237622450970.601648082589-0.4315566562451.09612196308-0.0165416395212-2.32248593958-0.229287063562-0.201409868621.667313286050.245657794240.3763615658381.681862585060.1473487717070.419277613226-19.770029154512.12644150390.33221347961
52.45430021346-1.549252607710.8615392626893.26381750208-1.675223343242.72293152050.3337228074470.4343533068580.217683371377-0.3992611446070.3241825788460.1083606557110.513723906185-1.50282138714-0.6336177187070.978870020807-0.08541120536890.06353150855871.401300720830.1987966814690.563169555173-18.62550533959.90809283695-32.6835807995
66.16015805779-1.81558950167-3.546745888591.379496513932.250995423617.342081399711.09230686139-0.05878598588240.39531520463-0.8757914603770.493043717209-0.387528739363-0.9176425128741.20569499743-0.9870931295821.872861654060.4165787471280.2916876079372.059569193040.0507638009980.560109233398-11.685517510113.0229578406-54.0823877626
71.03576416143-1.4387304506-0.5297760460552.213384755691.824490693095.150131882110.524356542621-0.06527324495690.5306809998430.2420571698680.5370433055510.0130177921549-0.586163511813-0.496239675065-0.4566600936191.122288195960.1670739568280.3299834670441.354110054520.2492248089420.543572676636-17.06496739399.86642725548-29.8474304792
81.787776726290.0493617575126-0.6957137348891.85692677279-3.246746970437.534511178680.0993389836959-0.573314432386-0.2221403334670.549596524757-0.07994512346460.615207567516-0.325701637694-1.07729836583-0.1589148488461.53022548480.2490996803630.529378502052.160992112310.4700026964750.421577722421-27.403780635610.4459856217-6.19648202733
92.23590101831-3.9030686404-1.428682283758.008105863312.46323635790.921863856899-0.1804219341220.209917393417-0.2531181432930.6649158066-0.597517435088-0.316339672851.104146050850.5462420858330.5789614347681.89732250659-0.103128121434-0.01041398946852.599216194340.2533041337350.80799575992-21.47647947284.422222277852.79685511949
105.919145745125.906477956872.160675070556.021681084662.234824360381.970406763071.57903689242-0.151858254175-2.746718636151.23661782481-0.617145585512-1.249423599322.73000250267-0.220129017448-1.012438696311.0605559076-0.019577016762-0.1339256892520.888445401428-0.07722339585651.34321874602-30.4797415224-51.7718505138-21.2097747152
118.315674419592.816558309953.41498658037.38941484734-0.4337083134929.090889562450.8833342175070.499030346496-1.056666736860.796060699380.298922002099-0.2302804300640.649593095115-0.0231006709254-0.9471917809970.724018632336-0.3273867234060.01192860465960.874354255591-0.2700980525590.887768719579-31.0675463649-43.2318112298-23.9837443766
125.335533864843.73428935934-4.231189984483.96342810105-4.735532245785.684501324350.2266571273321.11927406914-0.361974132611-1.04181841829-0.0633751209753-0.475342552798-0.0881318735901-0.8786406803460.7037756337841.00639963743-0.4450535596560.6202574321721.64905908112-0.06485065706460.643648171803-24.2470931429-31.12733772-37.0428705849
133.639279460920.7877734327714.296377365636.49095394792-0.1568309449055.25978339136-1.429666879940.0953899317170.0710670407158-1.007513406830.421813239249-0.895204254355-0.4469444404050.05236154415060.6455231938810.93828188503-0.3525419630190.1791644826821.25987125618-0.1389856086130.533508671877-23.5542121732-26.8589477084-31.0182361472
147.872452665594.395404182995.888415432438.17688275074.841030160167.41332057549-0.173093579711-0.1935557805610.105162918428-0.493009744482-0.3303722191130.914035260777-0.130857687123-0.06644927695470.522807506780.606558319221-0.241624994032-0.02161694535020.678894754056-0.005869251926480.453629767815-18.4890324496-15.3994955751-13.9293324082
157.772478332-1.73858717539-3.125299210667.222169295853.229583001333.219668041670.808829299657-2.10953331722-0.2761463867862.528502707740.888793984158-1.807536829871.391286414331.94485868923-1.391329725941.44306373898-0.21374097507-0.3818129173031.50530258084-0.1093508665471.0674887725-9.03806757008-25.3216738489-3.92628675874
162.38227226703-3.068089288923.90127876574.11269975749-4.77997968086.761871776630.253712825152-0.382042716223-0.1197589761231.53806904564-0.632843965113-1.07806464825-0.9413830274940.7187758076260.4368818807230.79755496327-0.765488630875-0.2385985598721.795843663090.4365610571741.19335310185-7.40738073685-26.690259179-10.4075214623
173.808650543721.15672248067-0.07637425693369.532479945836.742552087974.989086907910.418592535458-1.15302562719-1.655011541141.465611237160.453078792975-3.031527403721.039808924822.40363319511-0.715988041470.6636482153140.0495446344782-0.1446829999671.927631302930.2419331319581.83749988858-7.80211016997-35.3837112024-9.59706116013
189.39217853633-5.951929483642.877045706467.84773401193-3.708235948067.2798617513-0.39408111332-0.163100063478-1.428312957470.4511776095230.263315248037-1.18471165697-0.009550131556271.20146877780.278750304590.6814836812790.06247010834130.06768465386181.81513432722-0.3265231799411.998305582760.183763347083-33.6361120189-17.7857368392
198.335950560880.2688552959560.9093698145529.10917314804-0.6069934741045.63840385374-1.23150522355-0.6753324435911.25264268881-0.6400725151060.721406573324-0.457808299826-0.0242475939199-0.1067541719540.5191174830940.69101257959-0.1208422273340.1106152222281.309834811-0.1801615560690.971186291796-16.2518440305-33.1513170595-25.1049897353
203.31383063037-4.59620486683-3.885111013328.499030896122.108699286559.563904862990.0562505235128-0.1115137160670.7738862864251.385636057810.6619573868770.790025641570.29000264556-0.128788119705-0.6523308925930.89072543639-0.2320319989650.207422264971.37166503398-0.2551062782180.980813729269-31.3419650103-34.7188056202-15.0952742978
217.379295918054.253177885950.1541478000816.48614967948-1.590936753596.87163106059-1.297378346091.13819918574-0.0169966339842-0.2940011248280.6166611107722.393122659510.495856476331-1.628376131740.3942408715390.8164134615650.04622456958830.2846018229812.41343888851-0.3894074083241.91826669456-48.3438632184-33.3676077792-23.4813957134
223.753590133981.489015809291.50041345615.022977676580.9889975020550.617704060091-2.00897721711-0.178036855548-1.56648044568-0.3191235904210.8669719466231.752234029720.502791382108-1.372393418760.4394754992930.734168134994-0.1924594269940.340246368812.21873865044-0.3466149755921.71363537521-45.697301135-34.1241684939-19.9665764026
238.96229366314-0.9856560901380.1483427339868.567908120840.7690944077644.795867900490.1403280178681.44729766831-0.937832863303-0.780771496836-0.431693527241-1.18378554204-0.03212411182580.9795567052040.28826351990.664004134163-0.1508084007820.08457472814731.39889764576-0.1540268489241.15243610248-11.5264469725-33.4554146737-21.2055612925
243.70768755617-0.4769567546620.3246810298344.857987244090.500965931425.73557742339-0.0478223917113-0.6282466884860.385814554993-0.0446883645523-0.0595654386449-0.749899145142-0.4164938738360.7751807515870.07208528959330.751639823548-0.15999555597-0.02093890708841.32320784644-0.02734270183750.355439665713.591417747351.24262511915-1.13150677958
254.20249607968-3.037148214715.665296591682.65367494674-3.785411901998.614363144671.37066034118-0.947619300863-2.474822746070.727188437829-1.23502653604-0.5662496760221.65390215914-0.00390680257803-0.2301984096832.162541202550.0418045666405-0.5038814702631.974627992570.3388630166971.401836809663.44023916438-23.33127678366.81570288001
269.127161164833.442426157786.586494576692.066478399843.29653898977.901287181861.12093809098-1.30908126662-1.37248174161-0.334976202993-0.004360591701490.1657143828551.690014302390.434063359742-1.174639213831.45251940140.0606604516414-0.380986807111.756634357220.276198275441.0841478868614.8574940274-17.622715449216.9813631143
273.30964982044-5.304142515212.32316016448.52153428439-4.015259144655.31978339715-0.2420252164070.1640497674630.9333529394421.53625275898-0.243063168294-1.004420364270.4421001702270.9708921720860.4000363525220.99861366495-0.251547938146-0.06176330748812.419192413620.02350934063020.43938934889218.93854139-7.4224291040225.6166267321
280.889303077282-0.49416290527-0.6671639997743.81081306917-2.475937294458.026426445030.746125729788-0.05282030060660.1569980687420.1262130222210.4754730898460.418563618538-0.0437993840834-0.385388045762-0.9583512799081.15750441346-0.2787397751080.06382392637332.648706528490.1803418229730.7358845740057.03456809132-6.4906200450122.1420847016
294.53902642254-2.243802136120.1136300911452.951267085523.339100211446.485248007460.1369871991250.7854328796150.662719594944-1.13054507290.803790925984-0.4143851707280.7608680804040.650199653963-0.5219499278541.39469057085-0.3127628192770.1899641849252.451417291640.05227872585460.60867945368412.7793852371-5.15713537453-9.46111629258
301.71660496398-1.680472487490.1626700054993.132613653992.443715759334.602891292970.6371458777140.1076095261310.260503483764-0.7928904989080.866468786351-0.6768104148920.2408605607081.376305465450.4194705252791.64771177766-0.3298706226920.2242148709663.18492402676-0.2267076645050.63822062711918.2777106261-5.33488786676-22.7933143657
313.64490699579-0.1582799596230.4864158631973.197430203112.355295275447.21844130650.530146424907-0.04044638675260.30371069861-0.3124930225910.554723863913-0.2453715506670.4672306354091.25700463571-1.014025163481.14074340192-0.05049648472880.07928031918752.20504713490.0405047288110.61845002302510.9007677988-6.237943235130.401628032624
327.04217059788-1.104680501451.340304243462.299913245431.408868472423.910937579451.60258262108-1.047341423930.3341168925271.312882161760.6744231901031.01135222114-0.267193816501-0.584577721246-1.634344454141.75376393921-0.1807139527910.2444030076272.876358246560.2678348322350.8398219960852.5405837974-4.501606305425.268889704
336.59628616733-4.485458117040.3697413971878.40939676881-5.367287536864.90390332939-0.309505307918-1.01188746584-0.7122398293890.4150751760231.736003981190.597069079971-0.661187497355-2.54133196626-1.168686471822.32849566187-0.754189193446-0.1498735079482.436048621030.1527638014310.9198246518835.78798992447-12.574224776734.0161124757
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 381 through 411 )AA381 - 4111 - 31
22chain 'A' and (resid 412 through 461 )AA412 - 46132 - 81
33chain 'A' and (resid 462 through 491 )AA462 - 49182 - 111
44chain 'X' and (resid 1 through 5 )XF1 - 5
55chain 'X' and (resid 6 through 21 )XF6 - 21
66chain 'Y' and (resid 1 through 5 )YG1 - 5
77chain 'Y' and (resid 6 through 15 )YG6 - 15
88chain 'Y' and (resid 16 through 20 )YG16 - 20
99chain 'Y' and (resid 21 through 21 )YG21
1010chain 'B' and (resid 381 through 390 )BH381 - 3901 - 10
1111chain 'B' and (resid 391 through 405 )BH391 - 40511 - 25
1212chain 'B' and (resid 406 through 415 )BH406 - 41526 - 35
1313chain 'B' and (resid 416 through 433 )BH416 - 43336 - 53
1414chain 'B' and (resid 434 through 461 )BH434 - 46154 - 81
1515chain 'B' and (resid 462 through 471 )BH462 - 47182 - 91
1616chain 'B' and (resid 472 through 477 )BH472 - 47792 - 97
1717chain 'B' and (resid 478 through 491 )BH478 - 49198 - 111
1818chain 'D' and (resid 1 through 5 )DM1 - 5
1919chain 'D' and (resid 6 through 10 )DM6 - 10
2020chain 'D' and (resid 11 through 15 )DM11 - 15
2121chain 'D' and (resid 16 through 21 )DM16 - 21
2222chain 'E' and (resid 1 through 10 )EN1 - 10
2323chain 'E' and (resid 11 through 21 )EN11 - 21
2424chain 'F' and (resid 381 through 433 )FO381 - 4331 - 53
2525chain 'F' and (resid 434 through 449 )FO434 - 44954 - 69
2626chain 'F' and (resid 450 through 471 )FO450 - 47170 - 91
2727chain 'F' and (resid 472 through 501 )FO472 - 50192 - 121
2828chain 'H' and (resid 1 through 10 )HT1 - 10
2929chain 'H' and (resid 11 through 21 )HT11 - 21
3030chain 'I' and (resid 1 through 5 )IU1 - 5
3131chain 'I' and (resid 6 through 15 )IU6 - 15
3232chain 'I' and (resid 16 through 20 )IU16 - 20
3333chain 'I' and (resid 21 through 21 )IU21

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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