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- PDB-7ogs: X-ray Structure of Interferon Regulatory Factor 4 DNA binding dom... -

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基本情報

登録情報
データベース: PDB / ID: 7ogs
タイトルX-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an interferon-stimulated response element
要素
  • DNA (5'-D(P*AP*TP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*TP*GP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*A)-3')
  • Interferon regulatory factor 4
キーワードDNA BINDING PROTEIN / INTERFERON REGULATORY FACTORS / TRANSCRIPTION REGULATION / PROTEIN-DNA INTERACTION / TRANSCRIPTION
機能・相同性
機能・相同性情報


T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / positive regulation of interleukin-13 production / defense response to protozoan / positive regulation of interleukin-4 production / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of interleukin-10 production / immune system process / positive regulation of interleukin-2 production / Nuclear events stimulated by ALK signaling in cancer ...T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / positive regulation of interleukin-13 production / defense response to protozoan / positive regulation of interleukin-4 production / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of interleukin-10 production / immune system process / positive regulation of interleukin-2 production / Nuclear events stimulated by ALK signaling in cancer / T cell activation / Interferon gamma signaling / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / nucleosome / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily ...Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Interferon regulatory factor 4
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.37 Å
データ登録者Agnarelli, A. / El Omari, K. / Alt, A.O. / Mancini, E.J.
資金援助 英国, 1件
組織認可番号国
Wellcome Trust204833/Z/16/Z 英国
引用ジャーナル: To Be Published
タイトル: X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to interferon-stimulated response element
著者: Agnarelli, A. / El Omari, K. / Alt, A.O. / Mancini, E.J.
履歴
登録2021年5月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年6月1日Provider: repository / タイプ: Initial release
改定 1.12022年6月22日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen
改定 1.22024年1月31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: Interferon regulatory factor 4
B: Interferon regulatory factor 4
C: DNA (5'-D(P*TP*GP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*A)-3')
D: DNA (5'-D(P*AP*TP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*C)-3')
E: Interferon regulatory factor 4
F: Interferon regulatory factor 4
G: DNA (5'-D(P*TP*GP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*A)-3')
H: DNA (5'-D(P*AP*TP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*C)-3')


分子量 (理論値)分子数
合計 (水以外)89,7568
ポリマ－89,7568
非ポリマー00
水00
1
A: Interferon regulatory factor 4
B: Interferon regulatory factor 4
C: DNA (5'-D(P*TP*GP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*A)-3')
D: DNA (5'-D(P*AP*TP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*C)-3')


分子量 (理論値)分子数
合計 (水以外)44,8784
ポリマ－44,8784
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: Interferon regulatory factor 4
F: Interferon regulatory factor 4
G: DNA (5'-D(P*TP*GP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*A)-3')
H: DNA (5'-D(P*AP*TP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*C)-3')


分子量 (理論値)分子数
合計 (水以外)44,8784
ポリマ－44,8784
非ポリマー00
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)64.347, 66.082, 202.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細 (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "E"
d_4ens_1chain "F"
d_1ens_2chain "C"
d_2ens_2chain "G"
d_1ens_3chain "D"
d_2ens_3chain "H"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYLYSA1 - 114
d_21ens_1GLYLYSB1 - 114
d_31ens_1GLYLYSE1 - 114
d_41ens_1GLYLYSF1 - 114
d_11ens_2DTDAC
d_21ens_2DTDAG
d_11ens_3DADCD
d_21ens_3DADCH

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.99453475912, -0.103254429535, -0.0154640125405), (-0.0978611635577, -0.870293244491, -0.482714057451), (0.0363841389839, 0.481589235111, -0.87564148089)-18.8087007136, 4.11999216151, 66.793283972
2given(0.997823556697, 0.0574988154849, 0.0322805811198), (0.0606694813989, -0.99231809052, -0.107814754336), (0.0258333839516, 0.109538547752, -0.993646789775)-43.1316420143, -31.6989155292, 50.9149607993
3given(0.99485555124, -0.101121541181, -0.00607174415108), (0.0831999198696, 0.781404319767, 0.618453767378), (-0.0577945109981, -0.615777332288, 0.785797729406)-61.8312274785, -45.8778483404, -14.8208223584
4given(0.999930554592, 0.0103331274992, -0.0056667865785), (0.00958751098265, -0.992882092211, -0.118714913136), (-0.00685314724765, 0.118652338551, -0.992912210082)-42.1425441033, -31.9113635106, 50.4378293184
5given(0.999813651277, 0.0189917629705, 0.00346058663212), (0.019283125693, -0.990958322639, -0.132777120982), (0.000907625514726, 0.132819109062, -0.991139879373)-42.4301638482, -31.2924202864, 50.6793973265

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要素

#1: タンパク質
Interferon regulatory factor 4 / IRF-4 / Lymphocyte-specific interferon regulatory factor / LSIRF / Multiple myeloma oncogene 1 / NF-EM5


分子量: 16306.470 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IRF4, MUM1 / プラスミド: pCDFDUET / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q15306
#2: DNA鎖 DNA (5'-D(P*TP*GP*TP*AP*CP*TP*TP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*A)-3')


分子量: 6120.960 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: DNA鎖 DNA (5'-D(P*AP*TP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*AP*AP*GP*TP*AP*C)-3')


分子量: 6144.034 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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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: 2.39 Å3/Da / 溶媒含有率: 48.64 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5
詳細: 0.1M Bis Tris pH 5.5, 0.2M ammonium acetate, 25% PEG 3350

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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: Diamond / ビームライン: I04-1 / 波長: 0.9119 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2020年1月26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: 0.9119 Å / 相対比: 1
反射解像度: 2.37→64.35 Å / Num. obs: 35957 / % possible obs: 99.99 % / 冗長度: 6.3 % / Biso Wilson estimate: 63.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.074 / Rrim(I) all: 0.189 / Net I/σ(I): 5.8
反射 シェル解像度: 2.37→2.41 Å / 冗長度: 5.5 % / Rmerge(I) obs: 3.086 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 1740 / CC1/2: 0.281 / Rpim(I) all: 1.434 / Rrim(I) all: 3.409 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
xia2データ削減
xia2データスケーリング
PHASER位相決定
PHENIX1.18.2_3874精密化
精密化構造決定の手法: 分子置換
開始モデル: 7O56

7o56


解像度: 2.37→62.81 Å / SU ML: 0.5164 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 34.5193
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2494 1724 4.95 %
Rwork0.2167 33082 -
obs0.2183 34806 96.97 %
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: 76.85 Å2
精密化ステップサイクル: LAST / 解像度: 2.37→62.81 Å
タンパク質核酸リガンド溶媒全体
原子数3792 1640 0 0 5432
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00995732
X-RAY DIFFRACTIONf_angle_d1.25088076
X-RAY DIFFRACTIONf_chiral_restr0.0655832
X-RAY DIFFRACTIONf_plane_restr0.0079764
X-RAY DIFFRACTIONf_dihedral_angle_d30.01122284
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.296299807953
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.25241330114
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.276051849632
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.583357700148
ens_3d_2DX-RAY DIFFRACTIONTorsion NCS0.550695991247
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.440.41291040.43791983X-RAY DIFFRACTION71.55
2.44-2.520.40221250.42392751X-RAY DIFFRACTION98.32
2.52-2.610.40911820.38852752X-RAY DIFFRACTION99.86
2.61-2.710.37971510.37712821X-RAY DIFFRACTION99.83
2.71-2.840.41141550.38892762X-RAY DIFFRACTION99.59
2.84-2.990.36211400.33532821X-RAY DIFFRACTION99.6
2.99-3.170.30081470.27892758X-RAY DIFFRACTION97.84
3.17-3.420.29991230.26212792X-RAY DIFFRACTION97
3.42-3.760.25261400.21722833X-RAY DIFFRACTION99.77
3.76-4.310.20951390.17792866X-RAY DIFFRACTION99.73
4.31-5.420.21321550.15852910X-RAY DIFFRACTION99.97
5.43-62.810.16111630.13013033X-RAY DIFFRACTION99.81
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)
14.14436183020.557245651818-0.2971518564373.09861312174-0.669132370070.8252967943520.1754561940730.380306228390.123914539178-0.6226183951710.09188086125080.692279521997-0.648673467824-0.3735866310930.06429883197660.860883680613-0.0855628297808-0.09244946860470.5037717252880.07155296781530.54076609881-16.186334805510.230689360216.4368273818
22.047922488410.4157042441371.841177547362.723073666571.991387868873.51999052843-0.590305752984-0.1342425656280.286841124802-0.1747697202730.308994203555-0.943672026323-1.306450226150.602490410960.04940112041650.801527937113-0.1998508817260.01110135327950.6389951126180.04128408269070.828373846696-1.856742356497.5515134040624.515731168
32.80206346609-0.1057253377030.3590253614960.581764356006-0.7673329823851.976549778880.117944948486-0.7296092178260.2501435135370.488566027556-0.223784756273-0.0487789022036-0.1052757184780.1478864669630.09143892477880.699920982566-0.1244001953820.01315092250260.503522740098-0.06291336020420.573570409014-12.87590911847.0493648065432.6843642785
44.61587679833-1.1024384197-1.147805461342.72329793111-0.0440187005073.715110874880.3608240234550.86880649386-0.731397226055-0.697202618081-0.178051294405-0.7528007367250.4285086644190.36267616479-0.01431870988810.929366716539-0.07949356695770.08169174732170.684535900332-0.02339478798360.712226438128-8.34579972585-0.46928084283215.6973574014
50.0496056529631-0.146471168693-0.08156338644560.5882302517620.5523554548950.774212024068-0.2696506871940.3749492557570.983280035844-0.6160641062890.0675857751867-0.2028465972980.1813578258790.633237374496-0.1346175189111.02192859478-0.170585681082-0.02156072050061.174662100920.1341755069411.27087523902-25.757913492-1.7306172675813.1159220872
64.30393542885-0.09969172102141.575922366881.88416685574-0.4913862866740.7061238918950.279538451559-0.53770068803-0.05051745372760.114310578949-0.3734542846480.2532949350090.594334069182-0.75179120848-0.06366319698650.605965467167-0.08657871376730.02042572533420.7723483035570.01072294200640.633384734135-36.2191640683-11.123849725456.7725426902
71.95391622716-1.02077142773-1.776243626054.851853784562.94622691362.89733300262-0.320487828746-1.54199817586-0.250652009629-0.1868322116870.580261691612-0.3084062811150.05274667114650.90705142396-0.1926374118680.588816070389-0.00312866614792-0.09708564413320.68994428614-0.01461940299270.532325013781-21.2917803087-11.949374778849.2613590896
89.22449267685-0.206222134823-1.347327533983.02037619014-2.697162817772.918144692480.417904009967-0.701881232579-1.139064684320.136257312768-0.1147446536940.135289803004-0.4868003999050.551352276734-0.3231806490640.628354419297-0.0461910852171-0.09203812063020.607368108769-0.02792883637210.783313671925-23.3626490766-20.973564807847.6701642641
91.85854172374-0.365494413762-0.2805521047591.62982999990.3964027179431.84276412648-0.00582948735113-0.10801901322-0.0773593163299-0.3861843761390.08259044414580.1044676037490.0136763211678-0.132835826871-0.07839205260850.566268181956-0.0642215645108-0.09083401875560.5522882569380.04890797109820.539986404753-32.8313168011-16.52867996441.0724226527
104.495349127790.5203660672461.681459610843.18370481310.6469286896473.32594161052-0.316581797616-0.8572848354110.8895049973390.3532878203360.247330109851-0.231446757615-0.462976181973-0.07414824006440.0006788886161440.639575974447-0.0364731708558-0.03175484607770.612500123101-0.01925189636780.564877430462-27.3214209465-2.2160798797852.5545323358
110.156434747417-0.0453040199562-0.1262357797240.006208511653340.03026173976530.0881969018538-0.205095947584-0.201850471141-0.258403626138-0.5867744859691.08009688858-0.1762430454420.1533351916620.710378948398-0.09355324284230.7419510655970.1132895738860.003350733605631.15681885817-0.2515297803921.42311087145-44.5032008261.9407763996653.4560200414
123.85957065952-0.563959367106-2.537750055299.951459503922.283145902932.90606696272-0.7335585690131.944283624111.703491183370.006817085226570.07728856903571.10923699928-1.10155534778-0.40897590704-0.09194959826430.4377628674-0.0159268394506-0.1593727660381.240735994330.1404706620971.03319540259-49.0137250972-3.2550204358138.1784143177
133.572822139852.98097817596-2.011195870652.70673789466-0.8921246838632.39008554646-0.0867481884201-0.12739784591-0.425353099899-0.0165745844821-0.0523136390419-0.402307953525-0.003846791477920.1969901770290.1094095363670.513437371583-0.0727387192692-0.04628699085850.705430870241-0.001965109718620.685542562556-16.643836174-7.0518588400732.7967225523
141.282653551640.3449243790231.699958250262.663249997173.7528635566.56808094802-0.103901274648-2.0162857395-0.9434651237880.864661506139-0.137513608855-1.14954070778-1.613556093511.555600788920.6147557829750.427666452568-0.244233841448-0.1681794025021.389130687180.3469809299061.21400459983.54940087935-3.794752159337.0380093306
153.160620268821.04601564492-0.4607873199172.9927648139-1.311588293773.17732880511-0.3563264304440.438929752859-0.188607263765-0.334491935350.1706361405750.0452514057858-0.0313942054312-0.3283285055560.1638041052810.433611621315-0.0833166088465-0.08574191097760.523472077909-0.0245022947220.478769177486-28.5953014176-6.5009438354532.9663151603
164.32044507481-0.2581937026521.348705797242.06278335084-0.3530657217811.19943526870.263004036261-0.829872495383-0.8529718427950.006401827466920.2918998307270.3413698311330.837375206495-0.745021214245-0.00176966946080.69123189141-0.113480914312-0.06967497109830.6874702784150.1417564741890.622244144663-58.1609153534-44.593459553835.2896842511
172.40249347941-1.22170650567-1.282680025653.432031313651.722226972153.30373222118-0.415058562644-0.788344637475-1.25075246513-0.309859894445-0.0190303173573-0.5115304092660.8071450717280.933829996972-0.144704343450.7291885198590.03991445819950.03518325838130.7457039180450.07381882888550.852085480974-43.7225739453-41.969186271927.3073346643
182.91008834949-0.428641190833-0.215355919970.538621077611-0.8773089855762.670128633060.2260664304660.79192630898-0.595953349033-0.615494087046-0.334774132006-0.1192129910750.33164383515-0.152187382293-0.05119426079190.705859262203-0.143861592117-0.03234369652850.639849823215-0.1370538230520.647592112967-54.4921700466-42.964254604318.8806659852
194.684845769990.2581169294211.69784805772.9278524021.102519666113.25689647930.33928403108-0.8388760587690.7248840939510.343471694874-0.000612716534102-0.201419696153-0.322509992004-0.05059934062060.02154737071490.648371281428-0.136239612049-0.05540087101220.5931611847520.01163148635860.561055601223-51.0460551945-33.491457271335.0528450528
200.192335319958-0.216192306681-0.2928234680610.5955222527160.4044960832290.4668377526430.377006712873-0.558157079922-0.7334331681320.9995835025110.972901854479-0.442802550401-0.928999002640.533632931203-0.1936195214540.945117701859-0.02042915814390.02671159351471.494672604590.08095806338211.57401232353-68.5238987664-32.886838710237.0600447727
214.413198016990.114774811725-0.5366178395351.4907384792-0.5593256937321.23248523190.08814541992690.8391030172570.224584760037-0.681058903676-0.1712703515860.214019511511-0.0300998236145-0.3764046487440.1199805277121.035806764870.176902854234-0.1833675438190.952100778993-0.04732104593220.533860759911-79.1068914838-29.0434298366-7.27170927759
223.39274232308-0.05567462755451.493165709142.573698984370.3067198007992.608866052170.04229124611650.5944840052890.385809287472-0.419766287019-0.453138314712-0.148187053846-0.4727759818890.348296656917-0.03835724084910.753310227750.0361723778399-0.0458611440820.7032776496390.01182858030460.543591351574-71.3782020744-22.63485385234.47967449909
234.70501407091-0.681263478532-0.7823414565872.970455514170.3296252792193.11484361980.01161090234391.26589076708-1.23911250983-0.512290520303-0.238505069022-0.1904286935450.9490081224470.9071842724640.02938346160471.050768626740.222754027302-0.02289482320510.934814181246-0.2202670650470.783239840428-70.21372171-37.2439566721-1.69493693692
240.0190859536817-0.007679637015570.084977617560.11271183563-0.1076758794420.4138814016530.3551491023471.21125752361-0.848763623112-0.2553774124640.4050837905880.389097591620.8448872153730.962070528683-0.08459137624031.23435647641-0.0272675957287-0.3067121543061.23913446137-0.2124096241231.36751981712-87.4175556598-41.3575861606-1.94504183545
252.768035758781.073167758912.290866281062.16818312880.153069981993.41811333028-0.612339185638-1.25465417429-1.7590353996-0.3854299480610.226920249770.4621782122681.668513753-0.3159544742680.2485942752960.593633806646-0.07675496958460.01620007900981.193722608180.08978476848481.27427217908-91.4068042876-33.291750473412.6286564876
264.10042799857-0.9975348439873.169780515872.33944134419-0.1650893583162.1971727914-0.05562653541840.1700945764540.730299115512-0.0836154839393-0.143067286258-0.481913628892-0.1177137405570.05538783404310.1250736160950.485011987276-0.0818733822643-0.05648594772910.7088935692660.06114373342030.648760960051-59.0334245378-29.089512147517.0997139496
271.388168412080.089004935463-0.1641808006965.777342211524.255204959963.993266389420.06617707050132.505752455051.00358487543-0.79050080913-0.624355254416-1.574097560330.7656088629381.295719910650.3066655966940.5190686817970.1121117530140.08666568096011.444110289930.2807472513540.962049593587-38.6325114992-32.130632133713.5999715788
283.60939409609-2.703406358691.159103661982.624529253990.1551540274352.48542011646-0.228157692115-0.2423657851230.380519349030.2813110096690.02786848832320.3229420023684.77020830125E-5-0.2781122537170.1894233810670.520113727895-0.03761548522770.01358410153480.654039884974-0.03485993827040.576867351093-71.0908483938-29.857451111317.0744375827
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 20 through 48 )AA20 - 481 - 29
22chain 'A' and (resid 49 through 68 )AA49 - 6830 - 49
33chain 'A' and (resid 69 through 103 )AA69 - 10350 - 84
44chain 'A' and (resid 104 through 127 )AA104 - 12785 - 108
55chain 'A' and (resid 128 through 133 )AA128 - 133109 - 114
66chain 'B' and (resid 20 through 48 )BB20 - 481 - 29
77chain 'B' and (resid 49 through 63 )BB49 - 6330 - 44
88chain 'B' and (resid 64 through 68 )BB64 - 6845 - 49
99chain 'B' and (resid 69 through 103 )BB69 - 10350 - 84
1010chain 'B' and (resid 104 through 127 )BB104 - 12785 - 108
1111chain 'B' and (resid 128 through 133 )BB128 - 133109 - 114
1212chain 'C' and (resid 1 through 5 )CC1 - 5
1313chain 'C' and (resid 6 through 20 )CC6 - 20
1414chain 'D' and (resid 1 through 5 )DD1 - 5
1515chain 'D' and (resid 6 through 20 )DD6 - 20
1616chain 'E' and (resid 20 through 48 )EE20 - 481 - 29
1717chain 'E' and (resid 49 through 68 )EE49 - 6830 - 49
1818chain 'E' and (resid 69 through 103 )EE69 - 10350 - 84
1919chain 'E' and (resid 104 through 127 )EE104 - 12785 - 108
2020chain 'E' and (resid 128 through 133 )EE128 - 133109 - 114
2121chain 'F' and (resid 20 through 48 )FF20 - 481 - 29
2222chain 'F' and (resid 49 through 103 )FF49 - 10330 - 84
2323chain 'F' and (resid 104 through 127 )FF104 - 12785 - 108
2424chain 'F' and (resid 128 through 133 )FF128 - 133109 - 114
2525chain 'G' and (resid 1 through 5 )GG1 - 5
2626chain 'G' and (resid 6 through 20 )GG6 - 20
2727chain 'H' and (resid 1 through 5 )HH1 - 5
2828chain 'H' and (resid 6 through 20 )HH6 - 20

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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