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- PDB-7n5v: ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (... -

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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: 7n5v
タイトルZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (Oligo 20)
要素
  • DNA Strand I
  • DNA Strand II
  • Zinc finger and BTB domain-containing protein 7A
キーワードDNA BINDING PROTEIN/DNA / zinc-finger domain / gene expression / DNA BINDING PROTEIN-DNA complex
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 / nuclear androgen receptor binding / histone acetyltransferase binding / negative regulation of Notch signaling pathway / fat cell differentiation ...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 / nuclear androgen receptor binding / histone acetyltransferase binding / negative regulation of Notch signaling pathway / fat cell differentiation / erythrocyte maturation / SMAD binding / regulation of alternative mRNA splicing, via spliceosome / 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 / sequence-specific double-stranded DNA binding / chromatin organization / site of double-strand break / positive regulation of NF-kappaB transcription factor activity / 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 / nucleus / metal ion binding / 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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / 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: 3.08 Å
データ登録者Horton, J.R. / Ren, R. / Cheng, X.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 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2021年6月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年6月8日Provider: repository / タイプ: Initial release
改定 1.12022年9月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.title / _citation_author.name
改定 1.22023年1月25日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
改定 1.32023年2月15日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.42023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Zinc finger and BTB domain-containing protein 7A
F: Zinc finger and BTB domain-containing protein 7A
X: DNA Strand I
Y: DNA Strand II
H: DNA Strand I
I: DNA Strand II
D: DNA Strand I
E: DNA Strand II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)79,82817
ポリマ－79,3059
非ポリマー5238
水181
1
A: Zinc finger and BTB domain-containing protein 7A
X: DNA Strand I
Y: DNA Strand II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,5665
ポリマ－26,4353
非ポリマー1312
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Zinc finger and BTB domain-containing protein 7A
D: DNA Strand I
E: DNA Strand II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,6977
ポリマ－26,4353
非ポリマー2624
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
F: Zinc finger and BTB domain-containing protein 7A
H: DNA Strand I
I: DNA Strand II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,5665
ポリマ－26,4353
非ポリマー1312
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)51.292, 60.067, 133.729
Angle α, β, γ (deg.)90.000, 98.502, 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
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 379 through 401 or (resid 402...
d_2ens_1(chain "F" and ((resid 379 through 381 and (name N...
d_1ens_2chain "D"
d_2ens_2(chain "H" and (resid 1 through 14 or (resid 15...
d_3ens_2(chain "X" and (resid 1 through 14 or (resid 15...
d_1ens_3(chain "E" and (resid 1 through 15 or (resid 16...
d_2ens_3(chain "I" and (resid 1 through 15 or (resid 16...
d_3ens_3(chain "Y" and (resid 1 through 15 or (resid 16...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSGLYA1 - 56
d_21ens_1LYSGLYI1 - 56
d_11ens_2DADCP
d_21ens_2DADCN
d_31ens_2DADCL
d_11ens_3DGDTQ
d_21ens_3DGDTO
d_31ens_3DGDTM

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.130800678349, -0.677114498261, -0.724159608641), (-0.693509207932, -0.584470289353, 0.42123563403), (-0.708474530986, 0.447113449929, -0.546034249691)-15.3940848472, 59.6245027417, -81.5115377629
2given(-0.106827484986, 0.750003058391, -0.652750565573), (0.762067834659, -0.359911884166, -0.538252776132), (-0.638623914232, -0.554940400439, -0.533104725294)-2.32299743829, 32.8985942194, -24.6610116095
3given(-0.146435222703, 0.736617886803, 0.660265714992), (-0.652457845724, -0.573614348955, 0.495242706383), (0.743542524073, -0.358274570008, 0.56460946448)-18.7879822946, 32.333032574, -51.9732457752
4given(-0.0990823439393, 0.771834944826, -0.628055337582), (0.779740026541, -0.331899993572, -0.530893478277), (-0.61821370102, -0.542322055805, -0.568945171047)-2.65869982475, 32.1531015776, -25.225229292
5given(-0.156361589238, 0.723291652482, 0.672607046396), (-0.64901964737, -0.588566690593, 0.482040193398), (0.744529751412, -0.361162617355, 0.561459716353)-18.1236374466, 32.553400974, -51.7314226705

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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: 16638.525 Da / 分子数: 3 / 断片: zinc finger domain (UNP residues 369-500) / 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) / Variant (発現宿主): Gold / 参照: UniProt: O95365
#2: DNA鎖 DNA Strand I


分子量: 4876.194 Da / 分子数: 3 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#3: DNA鎖 DNA Strand II


分子量: 4920.188 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: 8 / 由来タイプ: 合成 / 式: Zn
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1 / 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

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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: 2.57 Å3/Da / 溶媒含有率: 52.12 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 / 詳細: 0.1 M Bis-Tris, pH 6.5, 20% PEG5000 MME

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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: 2021年3月6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: 3.08→43.47 Å / Num. obs: 27875 / % possible obs: 96 % / 冗長度: 5.4 % / Biso Wilson estimate: 88.56 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.067 / Net I/σ(I): 7.8
反射 シェル解像度: 3.08→3.2 Å / 冗長度: 4.3 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2492 / CC1/2: 0.992 / Rpim(I) all: 0.274 / % possible all: 86.7

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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
PHENIX1.19.1_4122精密化
SERGUIデータ収集
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: PDB entry 7N5U

7n5u


解像度: 3.08→43.47 Å / SU ML: 0.5473 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 44.7648
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3136 1391 5.03 %
Rwork0.2598 26251 -
obs0.2627 27642 94.29 %
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: 141.4 Å2
精密化ステップサイクル: LAST / 解像度: 3.08→43.47 Å
タンパク質核酸リガンド溶媒全体
原子数1705 1947 8 1 3661
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00353921
X-RAY DIFFRACTIONf_angle_d0.57565682
X-RAY DIFFRACTIONf_chiral_restr0.0347620
X-RAY DIFFRACTIONf_plane_restr0.004399
X-RAY DIFFRACTIONf_dihedral_angle_d26.27321583
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.669167902998
ens_2d_2XX-RAY DIFFRACTIONTorsion NCS1.65934053102
ens_2d_3XX-RAY DIFFRACTIONTorsion NCS1.01144792603
ens_3d_2YX-RAY DIFFRACTIONTorsion NCS1.45274751178
ens_3d_3YX-RAY DIFFRACTIONTorsion NCS0.957290176408
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.190.47081400.41272268X-RAY DIFFRACTION80
3.19-3.310.38671210.3832605X-RAY DIFFRACTION94.72
3.31-3.470.40721470.37292660X-RAY DIFFRACTION95.57
3.47-3.650.36091410.3692648X-RAY DIFFRACTION96.14
3.65-3.880.37951340.36192745X-RAY DIFFRACTION98.16
3.88-4.180.34841460.28052735X-RAY DIFFRACTION97.66
4.18-4.60.31841420.26172555X-RAY DIFFRACTION91.7
4.6-5.260.35551400.23512654X-RAY DIFFRACTION96.28
5.26-6.620.28371420.21772754X-RAY DIFFRACTION98.27
6.63-43.470.22231380.16962627X-RAY DIFFRACTION94.89
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)
11.91135644570.8877879186711.092025470164.335264040342.853039080812.285762390810.389304370388-0.464366890383-0.1046214488771.01968159378-0.322056462494-0.5403929659510.1089343670630.344628642014-0.03910311485921.39217441363-0.457571964575-0.7875742107581.18546776493-0.3603620643650.839987233486-15.026144747220.5958055781-31.1806665494
27.217578927583.005573787065.902700061453.041073905133.685813436325.671456082060.177225377889-0.453436844221-0.09498707460450.193785456926-0.2439429167570.3423532448780.184240546564-0.908625933856-0.2266399007430.658581465071-0.119063375498-0.8575335404791.67852892778-0.02076838695980.475147793938-19.519589926429.5884596105-37.2311018854
33.40442175016-2.719260516933.936042607952.86622915189-2.086463885236.274799188620.1015318432771.03635046123-0.7538087272810.0440775479771-0.01720836479790.0904171191821.15967801647-0.761352255533-0.2062528506951.86359402224-0.424488760276-0.5353540333621.84207434322-0.006589261280350.958976275535-13.6695468119.6259287278-35.7781047713
42.4793918865-0.191803612638-0.7507401364842.948128972351.279646560531.984637249650.03938110000130.4852230222030.0547809960653-0.3920233321670.02630039522420.0841994161275-0.00205925222057-0.09559986155370.1065962059021.29804713397-0.147908191675-0.7852097108741.46378726417-0.5944704574840.342459037848-12.16261536926.5532563242-42.5351546066
55.77743913291.72379233581-1.642255478252.405343705132.455444558765.051197236090.5813934134420.637227844663-0.638537921779-0.570359119183-0.21777646680.258241074838-0.0330612956312-0.0825020370102-0.2166842795111.93209859609-0.00041047811674-0.6510166585232.217840710410.09134688415060.711745130285-7.0193401337729.81805895-48.893800317
68.549128454380.677696806705-6.654554239172.665394423810.5874100245245.69660679251-0.58699887186-0.2921773601540.180078500642-0.461135745259-3.144749385530.709767707563-1.65648416879-4.845269019743.704628612.45576626379-0.086044619769-0.7807772913052.46517076279-0.3174318498741.680897707052.0004435436322.771980035-54.4890162264
76.610167000210.639759039128-6.182200497490.647651708366-0.03370929644786.336448190190.3835936357380.0514517923765-0.160441200607-1.619176354-0.40664860307-0.412145866389-0.6128192861811.083759099260.006011985446172.746242036490.222268060475-0.1660169167882.070857416-0.07063824345280.593319471093-3.3202181822723.5648263056-53.9317033286
87.25251613216-0.2041744412866.828351289638.4014015623-4.612952244418.75318204088-0.3627904963554.11679714518-1.82018996361-2.99248217873-0.594015420258-0.418189821545-0.9475968153250.664194441930.9815371774062.00217016751-0.0247103986706-0.08276099340462.59322329064-0.4125729172410.99580913567-2.3519319064614.4160540058-54.7701046131
98.844953347854.97378233622-2.983374203093.12858496059-1.213933164089.349101756910.6688579608940.573558911856-0.8135357782030.572880512336-0.375954634266-1.0938102982-0.03161300177171.06730241706-0.0663968870661.031031027810.293517255398-0.1446095839020.72278922530.2826396385340.41519861384515.07457024822.113619772046.47550148842
106.61645818787-1.36915918683-4.936273828233.613366725171.531358262523.76991979260.5031485655431.429933405031.59933677042-0.603322841970.9215535442721.03886768631-0.631461223136-0.413178838596-1.057396946891.10500599696-0.0760830255553-0.5633703028631.358767141480.4163709369111.378406707441.1488745832916.89767989763.02438103939
115.86442544119-6.317711573147.570542806976.82773003688-8.135455378469.79278291491-0.4516584399410.5396038839310.915539348069-1.53833715419-0.423339021577-0.0543962769022-1.27161592484-0.4097321929140.8093662456351.48615072139-0.225443972178-0.6524275878461.429080814940.1562258888311.098353568127.5620490712123.5246830454-1.69508187059
123.981035625610.5397495127652.392301094353.988616647111.149963276234.92181060125-0.3284983893760.156223379840.4017283635130.02655952590320.0998346954966-0.273794624089-0.4694552209060.3161069500440.01603771796730.99014333703-0.29052767476-0.535819866731.51397693889-0.09107609973340.660261679632-1.8091143280231.9298805997-14.723903046
135.57484830265-2.743423328682.651181806233.94587238918-1.457641929653.313092734670.0344848676176-0.04820253680620.451393544405-0.1915135007390.271203069754-0.0274935145038-0.113492579196-0.429976531198-0.1475534133210.558433033860.334491412792-0.7901187796851.80073502812-0.2860068050640.361340946561-11.680759295336.7547681793-24.9843200506
144.579040198752.691631685491.604341886392.495532073432.022820117191.83735389944-1.44170389721.120108551672.20723497037-2.101602892350.7628836170341.35857413774-1.505007966240.3700128244340.9260637384691.56426256767-0.434116035486-0.7347901969761.430476431090.08282036212081.26751439217-8.8999318992545.9084969217-44.2705951055
151.17435580692-0.739409907772-2.061716322550.8860862520751.408121787163.64017783538-0.7710243234360.8225513904640.9355938192-0.349084159981-0.1700572279060.215872328743-0.8736375892540.5339633685940.8526272866721.185779660690.174043619058-0.5594274224521.724585758030.0418671340530.897612769756-7.8079229412941.2849766448-38.5145544618
162.919726147680.983377875388-1.544690899792.22665496526-0.1210400552180.902776410213-0.0755253856730.294246713643-0.197786806278-0.111620651579-0.05595985310340.0993853578323-0.06371421214750.0264569417101-0.2076123683440.850098092206-0.109760944866-1.14224520171.680119770660.3407423621890.741951899479-4.3868882672335.0337479808-37.6866239013
172.13064342780.1445963314050.6615625761090.4862018441790.1332519227470.223605566024-0.363660284312-0.638716195811-1.42192543032-0.3440002582660.6405601458530.465542199373-0.9746767458370.947193882553-0.283831084411.418373507340.396243241968-0.5302450942151.58576475930.02123494199940.9013731175524.559902004623.8811830596-40.1927984712
182.00424850134-1.659089369351.674952844374.435059739-2.424625129488.71164112679-0.090820083870.339453170719-0.248532997359-0.163956905282-0.554054827366-0.9815280150961.42278346122.22219741231-0.1731657987841.72841957090.539597352771-0.6909670511282.25761969450.1605542857820.8419633350037.2838689641225.4613238743-39.1146630323
199.11068652727-2.1954411236.409613388941.48995169384-1.811524791164.597068255240.1194602501531.459907442860.17117812893-0.60743526306-0.349920132206-1.062380274960.3852028356633.821947579610.08593948969131.49313698950.385770212557-0.1829853264413.15738897368-0.01549656135320.8886560372914.319605588129.7130527114-43.5924422347
204.705653676640.9175092887741.026256461394.423951578275.013801812935.68286897590.1351297869281.01822543325-0.548108691279-0.5264030957230.585079738197-0.3801394307360.7715960088530.209064757571-0.8310348122232.39931256027-0.306859090317-0.6409894672252.1643841159-0.3986338890171.17517690525-18.196383001211.957315284-52.5050388531
219.70770421497-0.178322285957-0.3426919698147.418425501227.494591664118.135093381850.1264298929531.07599897546-0.8504753492130.20791323807-0.8555861477830.1658468736530.3603441279781.228649066070.5889561357512.47940189550.360715368855-0.4125791469222.133408143570.02353425657830.770872129716-3.7138102585113.6775503224-40.5162398847
227.231279778952.20023224497.628137585140.7565399986082.057489407978.75929137463-0.371725267249-0.7210353132050.1041758315231.582859493740.669908849043-1.03035362312-1.01765131220.51521104125-0.1440536172182.54185501228-0.072661819606-0.6853113638892.26282812445-0.2647151564681.32742833932-21.605544662112.5623225006-60.1098211386
238.470406728042.30056435154.871937746037.171518868033.819225587928.796980448610.4454427779311.0751479137-0.397432829777-0.2217431805980.608493448536-0.429809373884-0.6493306997270.724945190464-1.165075805081.02777215045-0.0694992114681-0.3702804506251.89317197266-0.04468081065811.1357723925412.665086754843.7447429067-33.1662748759
242.22626894087-3.698779275540.2150656887426.497533004891.646136895582.00005447023-0.4743990509131.10739376020.204913252454-0.396832506252-0.802605196645-1.579296097980.2555831072515.443324530981.46767080291.33090729670.75028445507-0.203870703862.944475909010.5662076248291.006036535125.6151178491441.3792259703-58.0371448374
255.036118934591.718364873254.879698271245.427029309141.402451397484.761526959390.4996041954392.021760958540.426456553814-0.8935976768320.0818957165896-0.06870345660050.769547285770.805508579442-0.389497058531.848922855090.129187476744-0.401839635152.480094928430.2947397416130.9613314014514.3520488898837.1469836552-50.3939618336
267.714974607671.253384092716.005379067567.099806628680.2618393628.493040141310.5095038346270.144309210271-1.12118167996-0.2483751959220.4720362942430.674463806602-0.390027203029-0.553188364938-1.163324415660.766041356862-0.17524483201-0.07824802692121.91693459017-0.2020688003770.92739457422316.722436341742.5090347755-26.6588888279
274.62491596185.311508569534.636322976386.082871452085.314199757474.64339792602-1.367941662882.12777066449-0.48470346173-2.832845494881.244699521781.219268823181.292580836030.4693664324440.05500069380012.16327474644-0.147939929803-0.3093758264071.5545817305-0.0856160376851.356586337095.7561089615811.250722958-26.8694947162
289.00965744859-0.9718823149836.161770324524.83465175458-2.943108288635.39133551048-0.6155593973291.268465816260.668743449664-1.301058713390.171940198073-0.119365061302-1.258623238030.418614931230.421182411571.559172187860.105343359644-0.1611111174251.576650520240.09509475936360.77531725544216.105575484913.1921077156-2.52732127211
291.421395576682.890935927641.622034990238.730761005767.531491186078.12269423947-1.00326473460.7778395822760.110997771428-2.45870086353-0.1468126278920.235979891946-2.062945892530.7737300221091.019408775161.6220637291-0.0149785345745-0.3660889328581.5055806230.1960833193010.90492174341416.821428821113.8052432088-2.13417742167
307.60957461689-6.478199458055.977680943495.52112735232-5.09042200094.69164690589-1.518622063170.288466856652-0.1557110513652.788362153591.35252806570.637429522043-3.34160081915-1.318610690180.02043383740742.251924581550.35484724001-0.6235723448371.807466659910.1227568625561.4156352910.71593890615114.1032574436-21.2389407882
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 379 through 383 )AA379 - 3831 - 5
22chain 'A' and (resid 384 through 389 )AA384 - 3896 - 11
33chain 'A' and (resid 390 through 396 )AA390 - 39612 - 18
44chain 'A' and (resid 397 through 404 )AA397 - 40419 - 26
55chain 'A' and (resid 405 through 409 )AA405 - 40927 - 31
66chain 'A' and (resid 410 through 414 )AA410 - 41432 - 36
77chain 'A' and (resid 415 through 421 )AA415 - 42137 - 43
88chain 'A' and (resid 422 through 434 )AA422 - 43444 - 56
99chain 'B' and (resid 379 through 404 )BD379 - 4041 - 26
1010chain 'B' and (resid 405 through 421 )BD405 - 42127 - 43
1111chain 'B' and (resid 422 through 433 )BD422 - 43344 - 55
1212chain 'B' and (resid 434 through 450 )BD434 - 45056 - 72
1313chain 'B' and (resid 451 through 491 )BD451 - 49173 - 113
1414chain 'F' and (resid 379 through 383 )FI379 - 3831 - 5
1515chain 'F' and (resid 384 through 396 )FI384 - 3966 - 18
1616chain 'F' and (resid 397 through 404 )FI397 - 40419 - 26
1717chain 'F' and (resid 405 through 414 )FI405 - 41427 - 36
1818chain 'F' and (resid 415 through 421 )FI415 - 42137 - 43
1919chain 'F' and (resid 422 through 434 )FI422 - 43444 - 56
2020chain 'X' and (resid 2 through 15 )XL2 - 15
2121chain 'Y' and (resid 1 through 5 )YM1 - 5
2222chain 'Y' and (resid 6 through 16 )YM6 - 16
2323chain 'H' and (resid 1 through 15 )HN1 - 15
2424chain 'H' and (resid 16 through 16 )HN16
2525chain 'I' and (resid 1 through 5 )IO1 - 5
2626chain 'I' and (resid 6 through 16 )IO6 - 16
2727chain 'D' and (resid 1 through 5 )DP1 - 5
2828chain 'D' and (resid 6 through 16 )DP6 - 16
2929chain 'E' and (resid 1 through 10 )EQ1 - 10
3030chain 'E' and (resid 11 through 16 )EQ11 - 16

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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://pdbjlvh1.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