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- PDB-7cux: Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N... -

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基本情報

登録情報
データベース: PDB / ID: 7cux
タイトルCrystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA cleaving and DNA binding
要素Schlafen family member 5
キーワードDNA BINDING PROTEIN / pseudo-dimeric architecture / CCCH-type zinc finger / RNase / DNA binding
機能・相同性
機能・相同性情報


cell differentiation / ATP binding / nucleus
類似検索 - 分子機能
: / Schlafen, GTPase-like domain / Schlafen family / Orthopoxvirus B3 protein / Poxviridae B3 protein / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2 / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Schlafen family member 5
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: 3.29477066393 Å
データ登録者Yang, J.Y. / Luo, M. / Ou, J.Y. / Wang, Z.W. / Gao, S.
資金援助 中国, 3件
組織認可番号国
National Natural Science Foundation of China (NSFC)81772977 中国
National Natural Science Foundation of China (NSFC)81902841 中国
Chinese Academy of Sciences2018M640852 中国
引用ジャーナル: To Be Published
タイトル: Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA cleaving and DNA binding
著者: Yang, J.Y. / Luo, M. / Ou, J.Y. / Wang, Z.W. / Gao, S.
履歴
登録2020年8月25日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年8月25日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Schlafen family member 5
B: Schlafen family member 5
C: Schlafen family member 5
D: Schlafen family member 5
E: Schlafen family member 5
F: Schlafen family member 5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)221,21112
ポリマ－220,8196
非ポリマー3926
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint4 kcal/mol
Surface area87220 Å2
単位格子
Length a, b, c (Å)211.860, 156.442, 131.459
Angle α, β, γ (deg.)90.000, 110.382, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUARGARG(chain 'A' and (resid 13 through 71 or (resid 76...AA13 - 712 - 60
12LEULEUGLNGLN(chain 'A' and (resid 13 through 71 or (resid 76...AA76 - 14265 - 131
13ASNASNMETMET(chain 'A' and (resid 13 through 71 or (resid 76...AA169 - 333158 - 322
24GLUGLUARGARG(chain 'B' and (resid 13 through 71 or resid 76...BB13 - 712 - 60
25LEULEUGLNGLN(chain 'B' and (resid 13 through 71 or resid 76...BB76 - 14265 - 131
26ASNASNMETMET(chain 'B' and (resid 13 through 71 or resid 76...BB169 - 333158 - 322
37GLUGLUARGARG(chain 'C' and (resid 13 through 22 or (resid 23...CC13 - 712 - 60
38LEULEUGLNGLN(chain 'C' and (resid 13 through 22 or (resid 23...CC76 - 14265 - 131
39ASNASNMETMET(chain 'C' and (resid 13 through 22 or (resid 23...CC169 - 333158 - 322
410GLUGLUARGARG(chain 'D' and (resid 13 through 22 or (resid 23...DD13 - 712 - 60
411LEULEUGLNGLN(chain 'D' and (resid 13 through 22 or (resid 23...DD76 - 14265 - 131
412ASNASNMETMET(chain 'D' and (resid 13 through 22 or (resid 23...DD169 - 333158 - 322
513GLUGLUARGARG(chain 'E' and (resid 13 through 22 or (resid 23...EE13 - 712 - 60
514LEULEUGLNGLN(chain 'E' and (resid 13 through 22 or (resid 23...EE76 - 14265 - 131
515ASNASNMETMET(chain 'E' and (resid 13 through 22 or (resid 23...EE169 - 333158 - 322
616GLUGLUARGARG(chain 'F' and (resid 13 through 22 or (resid 23...FF13 - 712 - 60
617LEULEUGLNGLN(chain 'F' and (resid 13 through 22 or (resid 23...FF76 - 14265 - 131
618ASNASNMETMET(chain 'F' and (resid 13 through 22 or (resid 23...FF169 - 333158 - 322

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要素

#1: タンパク質
Schlafen family member 5


分子量: 36803.141 Da / 分子数: 6 / 断片: N'-terminal domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SLFN5
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: Q08AF3
#2: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn
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: 4.55 Å3/Da / 溶媒含有率: 72.95 %
結晶化温度: 277.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 100 mM Tris, pH 7.5, 80 mM magnesium chloride, 1.6 M ammonium sulfate
PH範囲: 6.5-8.5

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データ収集

回折平均測定温度: 87.15 K / Serial crystal experiment: Y
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL19U1 / 波長: 0.9785 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2019年6月27日
放射プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9785 Å / 相対比: 1
反射解像度: 3.294→50 Å / Num. obs: 43847 / % possible obs: 90.2 % / 冗長度: 6.8 % / Biso Wilson estimate: 80 Å2 / CC1/2: 1 / Net I/σ(I): 13.5
反射 シェル解像度: 3.3→3.61 Å / Num. unique obs: 2193 / CC1/2: 0.731
Serial crystallography sample delivery手法: fixed target

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解析

ソフトウェア
名称バージョン分類
PHENIX1.11.1-2575精密化
REFMAC7.0.077精密化
XDSデータ削減
STARANISO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
開始モデル: 5YD0

5yd0


解像度: 3.29477066393→41.0761808916 Å / SU ML: 0.357439767352 / 交差検証法: FREE R-VALUE / σ(F): 1.34999900373 / 位相誤差: 34.7159202908
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.247153773675 2162 4.95439754343 %
Rwork0.201355733206 41476 -
obs0.203555713424 43638 71.9161489148 %
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: 70 Å2
精密化ステップサイクル: LAST / 解像度: 3.29477066393→41.0761808916 Å
タンパク質核酸リガンド溶媒全体
原子数14069 0 6 0 14075
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002892971336314347
X-RAY DIFFRACTIONf_angle_d0.75854551138619339
X-RAY DIFFRACTIONf_chiral_restr0.04627531048052137
X-RAY DIFFRACTIONf_plane_restr0.003988059014822487
X-RAY DIFFRACTIONf_dihedral_angle_d3.231559033858713
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2948-3.37140.34956253119870.34122778378110X-RAY DIFFRACTION20
3.3714-3.45560.31548546971380.308762183914208X-RAY DIFFRACTION20
3.4556-3.5490.332664790032590.323707485602878X-RAY DIFFRACTION23.2448523939
3.549-3.65340.399056442846790.343955551451431X-RAY DIFFRACTION40.9880564604
3.6534-3.77120.3635567751461190.3211199143511962X-RAY DIFFRACTION66.4856230032
3.7712-3.90590.3346789166161380.2902146741252580X-RAY DIFFRACTION78.8054508553
3.9059-4.06220.3046268278681800.266043601513584X-RAY DIFFRACTION94.335839599
4.0622-4.24690.260031264412010.2203607314863878X-RAY DIFFRACTION99.902032819
4.2469-4.47050.219815553622110.1889279504383784X-RAY DIFFRACTION99.8250874563
4.4705-4.75020.2394979557071530.1808551031073886X-RAY DIFFRACTION99.8269896194
4.7502-5.11640.2074308659852230.1797355505493806X-RAY DIFFRACTION99.8265609514
5.1164-5.63010.2358196719382050.1829030715633852X-RAY DIFFRACTION99.9015020931
5.6301-6.44210.2386759944572000.1978938193673848X-RAY DIFFRACTION99.9753025438
6.4421-8.10610.2307269904991930.2109023287313902X-RAY DIFFRACTION99.951183793
8-100.2448036259051860.1772981133863767X-RAY DIFFRACTION95.5523326082
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)
15.21836089503-1.87612981241.325231156453.59486560135-0.382602106453.704578906880.5501762470980.9498968398760.299216518367-0.8053867358070.3993418397350.03616218350431.49857785582-0.248256607558-0.6217703641881.4300799316-0.286073957266-0.08396353151411.50087193973-0.03526397897082.27593667333-88.2489037957-0.94434533601327.2796870855
23.30608192816-1.253874276062.06399955653.07807969319-1.488486653883.72833317013-0.0346137588588-0.398047127266-1.67925933040.8707566759610.5767437387480.3170237282390.5234686533060.139693115608-0.8301747423341.4584852027-0.490259183358-0.1134449562131.886526891930.02683661547032.5101822882-91.4338274863-5.308631733634.4513898122
35.710366298861.539737950531.041839725932.30827426228-1.990367000861.818309184560.444179952334-1.9084877739-0.4461375270930.16443081267-0.3505965340390.855874962787-0.270043392442-1.18668852419-0.1397438878441.05328660965-0.277873358314-0.02121938826691.695432626710.1618670380262.09252698101-88.225915882820.591538039532.4882782811
47.852825111391.25441663837-0.17230796695.112327115960.4555027717445.10557263930.01754295143440.836580759249-0.21330729549-0.639360678380.09378036613060.9911833351470.221868016024-0.631326738139-0.07766153641560.922266661163-0.0241450293648-0.2424635640761.073374566750.1253698058751.07987880426-70.051909615628.285839172519.4696757688
53.163360206962.79234889764-2.887104886112.47481616289-2.628422414872.79747584795-0.2162638054911.068222465242.28727105747-0.3299841226620.8979135625722.86520545251-1.09708355483-0.641135985898-0.3381847333011.00396569180.260587541415-0.281522606061.944841713760.2217705157222.86745267456-93.396314430233.267037814320.2636606509
66.91535968881.75033619699-0.3579843718252.46546090304-0.04890331234654.192011694820.5626138749040.229920694221-0.164622964968-0.0154786531405-0.1503983754021.094676000070.314254052729-1.09054770062-0.168578576980.924263200666-0.108066351535-0.3783040417671.450628301190.1011579926991.57599400858-84.659924676124.398939783120.0090718723
77.33165504807-0.1235304239724.030725481923.57415552959-3.210926625036.171865350330.754752399794-1.17425018658-2.578744676810.8177439207581.304584940140.2042206321023.54323502439-1.37458129925-0.4917608498251.20609276561.04349368532-0.2279432637050.956912592589-0.2004868203272.637043439-12.6589687204-0.88878019738537.4953651225
82.835719802162.76170060709-0.9442095247433.192986035690.3751185866464.08310181673-0.478423227614-0.98201805522-0.5698524486870.7277537109620.5109751491040.7357449502251.285801204150.16065406205-0.2511254824211.258284586130.204397182212-0.4384877021481.32664651378-0.4089414781122.89792920208-10.9977074915-10.445249974533.0936798245
94.78267630137-3.274880093530.07800737990723.256462017120.6805583024043.854986163130.9067502841920.982504361935-1.67072088183-1.49801528693-0.4805671538360.3407073805220.2821997067891.40702423579-0.2309412903711.207434141050.713048118833-0.0599278251941.93633323974-0.343302602811.34180958441-9.2711243959711.662266470929.6838952549
105.2906545732.001710819990.3699640510990.8583789548611.136571623088.426797868380.06703909583020.433421077310.00268667816517-0.255369149852-0.21771005708-0.2535809323490.3453626644520.007339433412430.1477756635150.751825578650.142223522709-0.04029113389890.3922887723020.15101531810.699380482474-31.388685201830.211094628141.9186576539
119.86060173284-3.42116478566-4.193794510061.981551713823.043767532916.521448247720.0702124897475-1.397287227271.07111103830.1110147106020.315628575209-0.644727648541-0.7451364388170.462871715311-0.3927451104420.8292610202150.0642715893484-0.201787851840.7477766043880.09165567583260.709094139837-24.963685790431.426022563850.8082540828
127.53025653189-1.98701761371-2.412296186716.34890457780.537050152596.279360860730.4147232366390.748434695877-0.2611579499620.12048735326-0.11153641961-0.6822580213581.245272965581.7949255466-0.3559679031720.7872662109130.402505814176-0.1725253793081.39145184697-0.1094736298941.23076935799-4.5953287774919.038052992441.0178577085
137.336322264031.53757411862-1.118128918936.99532719237-4.57780793686.686847977410.8488944075970.4073676047310.3146227414983.00334346783-0.693208479925-0.0301232746566-1.200131833571.06490327112-0.1709063139932.40006243989-0.4985734007430.06749215935221.54568826623-0.1971608507252.40769391278-12.614784523166.733643184839.46172145
140.137792551635-0.3521177165170.5774442517983.8434964959-4.179571993375.16360302592-1.153010002880.9119328029581.027625410280.6431444330140.230947378148-0.820142372573-1.11368791228-1.00793399201-0.07484456012541.71361513797-0.887005082011-0.4164344241251.229166018810.0408606344072.18434302515-15.620537668264.378640541731.0020067517
152.36916566422-3.01186046665-0.8086221044783.62360724360.1356632665344.89754254638-1.78848147908-0.68305717462-0.9227744454191.02936395380.1296506879420.494790735365-0.2177551177651.636009085331.447080959642.10395652908-1.04718165535-0.0747200433382.473910905450.4999108920522.16246592015-7.3017451426265.72473296639.8928060488
165.63145545952-0.2003673436023.153206925263.042313993180.2144159124243.09553100702-0.1571927447830.2153680106870.9988712369070.461716915159-0.124356450517-0.686689122516-0.2674140103421.240889759130.09926894311971.3919216821-0.388496155790.02613173434271.947907125690.493825983172.31099112161-11.704412175154.028181427723.6776484999
178.64528105315-0.457454178221-2.684582437015.73452730214-1.591718089764.39038291485-0.6214470534030.6060826955580.501616162906-0.1458721260750.523820280716-0.00877761809216-0.3380820375980.1095596363240.1084177754440.88320020775-0.0494043976638-0.1779882589080.6376378971280.1509702848940.809053756242-41.60818633346.605112993620.0775527958
189.063206073111.268067087712.474611892293.93964363401-1.271874152751.58069405557-0.1671098144141.801973080421.57182885255-0.5274513060150.333075144278-0.0894654951589-1.024559663470.99967795131-0.005260565440531.65553190229-0.42466876629-0.06842879985281.479945824230.475250102761.44017710361-32.512951534357.62622938913.4198541653
195.59546729802-1.863196099050.6305172369584.71187867339-0.141580820463.801192940110.02568645003791.03131468771.32171450571-0.94343969508-0.307589738728-1.02314932486-0.392912707609-1.850797028690.1740874879961.562677410390.827587957938-0.1106941049921.52573619067-0.0800570470791.75095016228-86.815914213565.728766875729.514802025
202.81685331201-0.8510361217841.60175499055.56309910274-0.9656060493371.52070706734-0.587360301720.3844210880840.916647316076-1.334398155881.8070721398-0.411920723337-0.90259465088-0.6050703316280.4872398928591.090525160651.2069100242-0.1498565664271.61161338513-0.6253488025941.9519252126-93.944490504564.908458737824.8257323599
214.87697946727-2.984886703740.8729343152611.63640536903-0.9436161043470.661780600650.102637827555-0.265644202897-0.5099564154330.360423619067-0.1997502074381.015383600130.174173929201-0.6235358960510.116726327721.095890056720.416453751083-0.1216678167981.4056504671-0.3210910245181.87799069899-82.535185145451.864818025343.1549730521
227.28565573566-2.236061438731.875322699852.820338603840.1471252624873.10804576722-0.494812374306-1.144099081210.595796010060.3607365249480.3753305382560.0283592932171-0.844921927317-0.966572225265-0.03914208490671.259897254470.594480328146-0.07207305103050.973357775849-0.1610777409931.14425996526-65.397927642853.829965379847.8705214659
235.51580709544-0.2792050271640.2326394616964.649813885350.04123990350944.35342632199-1.79388266702-0.1553081062690.399946234932-2.03623114457-0.6245741765062.373509629921.05088761343-2.286405020220.9734620893792.121836980970.6660063198230.4229098957912.712894138650.1083967732210.242119465054-38.840248468629.8242489994-16.2595861657
242.227621502030.7445484282273.174164292483.5922571211-3.044773131687.11998172730.2441360185820.9453435517920.222320594193-0.0831867182444-0.336519923217-0.0970999457203-0.6896983823011.072592639160.2973736663761.725063139390.2407624708860.5386918689611.74747334197-0.08688491428261.14601517966-29.537739064630.5004894315-10.4412139437
257.86037690927-1.30784577312-0.5894638509875.343595853351.307689240824.166225476190.01243948938120.496522272711-0.0142931236241-0.493299942147-0.1058927677040.108127785340.2110166280720.395528836685-0.03040020602861.20067161870.108289131917-0.01761811657790.870949562147-0.0090494262730.657113469078-43.687833066617.050337298217.6853001587
262.380261137080.868519394273-4.134818464183.13423914092-1.091724088416.41329318595-0.2782018116790.534771254641-0.757939163352-0.932885052027-0.364471611834-0.5044153337761.439831028460.1478087036430.5710468650471.789115768060.3128626221470.09120942264161.26439185535-0.2214299865540.95495068444-35.011056924810.36571806424.92562582352
276.173299348923.93814856195-2.674596211184.73773854693-1.168100468995.908165701990.410879539003-0.4357730950630.542362542371.13627856369-0.3850983766450.06782707329340.4051004067740.2744360408240.1008073971961.444484113080.2073925630620.2194176743911.77363798549-0.1041234740650.82455713642-61.917988334932.169183959783.2805938953
282.02857696724-0.600862808594-2.278245865541.80430824961.217031353492.661259012381.58887171727-0.2297886125431.499439160221.650945586120.8322342602250.990217840254-1.09114224624-1.12322232207-0.5432164142832.154992331310.8281785180140.7519568459332.227894384150.2209245534211.00372344591-69.53353253235.546605722383.67187455
293.17971047275-1.14438426446-0.9027092212683.224934973080.3798346097744.768882112780.41899413317-0.3993312742050.17368296859-0.0107316146859-0.1069193544360.902111604501-1.14305177317-1.2046702581-0.7171809544531.164580285080.07342580559430.1532457175781.881276434170.07132421534961.26206188775-76.616919339223.773131581863.1697805436
307.64523670025-0.565944641703-2.481101993126.442406748630.5439301238425.629138970.00984544820842-0.101632597931-0.2666017855-0.097982275217-0.4236131099780.04193164317071.39857114529-0.6961056767490.3400333283641.15470044256-0.162295646563-0.05759603048230.6863300921190.05208751367520.593985020349-58.405754368613.332142092748.6314798586
313.6202696632-1.76976585201-0.7870066199564.997058283250.8709005702076.55938187968-0.0427461462638-0.692571699195-0.7376553941091.897840418060.4190444145070.369056768447-0.347168205738-2.58579114160.2994045606711.98871525327-0.3925634904980.3214717982491.985940828230.3109857065451.08161611149-74.058790421714.316315978170.8682388111
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 178 )
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 260 )
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 275 )
6X-RAY DIFFRACTION6chain 'A' and (resid 276 through 333 )
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 53 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 72 )
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 140 )
10X-RAY DIFFRACTION10chain 'B' and (resid 141 through 242 )
11X-RAY DIFFRACTION11chain 'B' and (resid 243 through 298 )
12X-RAY DIFFRACTION12chain 'B' and (resid 299 through 333 )
13X-RAY DIFFRACTION13chain 'C' and (resid 13 through 32 )
14X-RAY DIFFRACTION14chain 'C' and (resid 33 through 52 )
15X-RAY DIFFRACTION15chain 'C' and (resid 53 through 79 )
16X-RAY DIFFRACTION16chain 'C' and (resid 80 through 140 )
17X-RAY DIFFRACTION17chain 'C' and (resid 141 through 242 )
18X-RAY DIFFRACTION18chain 'C' and (resid 243 through 333 )
19X-RAY DIFFRACTION19chain 'D' and (resid 13 through 52 )
20X-RAY DIFFRACTION20chain 'D' and (resid 53 through 79 )
21X-RAY DIFFRACTION21chain 'D' and (resid 80 through 182 )
22X-RAY DIFFRACTION22chain 'D' and (resid 183 through 333 )
23X-RAY DIFFRACTION23chain 'E' and (resid 13 through 53 )
24X-RAY DIFFRACTION24chain 'E' and (resid 54 through 140 )
25X-RAY DIFFRACTION25chain 'E' and (resid 141 through 247 )
26X-RAY DIFFRACTION26chain 'E' and (resid 248 through 333 )
27X-RAY DIFFRACTION27chain 'F' and (resid 13 through 72 )
28X-RAY DIFFRACTION28chain 'F' and (resid 73 through 99 )
29X-RAY DIFFRACTION29chain 'F' and (resid 100 through 140 )
30X-RAY DIFFRACTION30chain 'F' and (resid 141 through 298 )
31X-RAY DIFFRACTION31chain 'F' and (resid 299 through 334 )

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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