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- PDB-5wqd: Crystal structure of TRF2 TRFH in complex with an NBS1 peptide -

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基本情報

登録情報
データベース: PDB / ID: 5wqd
タイトルCrystal structure of TRF2 TRFH in complex with an NBS1 peptide
要素
  • Nibrin
  • Telomeric repeat-binding factor 2
キーワードCELL CYCLE / Telomere / shelterin complex / DNA damage response
機能・相同性
機能・相同性情報


telomere maintenance via telomere trimming / chromosomal region / telomeric 3' overhang formation / axonal transport of messenger ribonucleoprotein complex / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / Mre11 complex / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of telomeric D-loop disassembly ...telomere maintenance via telomere trimming / chromosomal region / telomeric 3' overhang formation / axonal transport of messenger ribonucleoprotein complex / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / Mre11 complex / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of telomeric D-loop disassembly / blastocyst growth / negative regulation of telomere capping / BRCA1-C complex / Sensing of DNA Double Strand Breaks / protection from non-homologous end joining at telomere / R-loop processing / RNA-templated DNA biosynthetic process / t-circle formation / telomeric D-loop disassembly / negative regulation of telomere maintenance / negative regulation of t-circle formation / shelterin complex / phosphorylation-dependent protein binding / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / double-stranded telomeric DNA binding / DNA strand resection involved in replication fork processing / homologous recombination / nuclear inclusion body / DNA double-strand break processing / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / Impaired BRCA2 binding to PALB2 / double-strand break repair via alternative nonhomologous end joining / G-rich strand telomeric DNA binding / chromatin-protein adaptor activity / protein localization to site of double-strand break / telomere capping / isotype switching / HDR through MMEJ (alt-NHEJ) / mitotic G2/M transition checkpoint / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / regulation of telomere maintenance / regulation of DNA-templated DNA replication initiation / negative regulation of telomere maintenance via telomere lengthening / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / protein localization to chromosome, telomeric region / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / neuromuscular process controlling balance / positive regulation of double-strand break repair / Impaired BRCA2 binding to RAD51 / telomeric DNA binding / mitotic G2 DNA damage checkpoint signaling / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / telomere maintenance in response to DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cellular senescence / Telomere Extension By Telomerase / protein K63-linked ubiquitination / neuroblast proliferation / positive regulation of double-strand break repair via homologous recombination / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / intrinsic apoptotic signaling pathway / DNA damage checkpoint signaling / protein serine/threonine kinase activator activity / replication fork / meiotic cell cycle / double-strand break repair via homologous recombination / male germ cell nucleus / DNA damage response, signal transduction by p53 class mediator / Nonhomologous End-Joining (NHEJ) / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / PML body / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / cellular senescence / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / double-strand break repair / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / histone binding / damaged DNA binding / DNA-binding transcription factor binding
類似検索 - 分子機能
Nibrin, C-terminal / Nibrin / DNA damage repair protein Nbs1 / DNA damage repair protein Nbs1 / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / Telomere repeat-binding factor, dimerisation domain / Nibrin-related / Telomeric repeat-binding factor 2, Rap1-binding domain ...Nibrin, C-terminal / Nibrin / DNA damage repair protein Nbs1 / DNA damage repair protein Nbs1 / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / Telomere repeat-binding factor, dimerisation domain / Nibrin-related / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Myb domain / Myb-like DNA-binding domain / SMAD/FHA domain superfamily / BRCA1 C Terminus (BRCT) domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
類似検索 - ドメイン・相同性
Nibrin / Telomeric repeat-binding factor 2
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 Å
データ登録者Hu, C. / Chen, Y. / Lei, M.
引用ジャーナル: Mol. Cell / 年: 2017
タイトル: NBS1 Phosphorylation Status Dictates Repair Choice of Dysfunctional Telomeres
著者: Rai, R. / Hu, C. / Broton, C. / Chen, Y. / Lei, M. / Chang, S.
履歴
登録2016年11月26日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02017年3月8日Provider: repository / タイプ: Initial release
改定 1.12017年3月15日Group: Database references
改定 1.22023年11月8日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2
C: Telomeric repeat-binding factor 2
D: Telomeric repeat-binding factor 2
E: Telomeric repeat-binding factor 2
F: Telomeric repeat-binding factor 2
G: Telomeric repeat-binding factor 2
H: Nibrin
I: Nibrin
J: Nibrin
K: Nibrin
L: Nibrin
M: Nibrin
N: Nibrin


分子量 (理論値)分子数
合計 (水以外)179,20614
ポリマ－179,20614
非ポリマー00
水00
1
A: Telomeric repeat-binding factor 2
H: Nibrin


分子量 (理論値)分子数
合計 (水以外)25,6012
ポリマ－25,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Telomeric repeat-binding factor 2
I: Nibrin


分子量 (理論値)分子数
合計 (水以外)25,6012
ポリマ－25,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Telomeric repeat-binding factor 2
J: Nibrin


分子量 (理論値)分子数
合計 (水以外)25,6012
ポリマ－25,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Telomeric repeat-binding factor 2
K: Nibrin


分子量 (理論値)分子数
合計 (水以外)25,6012
ポリマ－25,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Telomeric repeat-binding factor 2
L: Nibrin


分子量 (理論値)分子数
合計 (水以外)25,6012
ポリマ－25,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Telomeric repeat-binding factor 2
M: Nibrin


分子量 (理論値)分子数
合計 (水以外)25,6012
ポリマ－25,6012
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Telomeric repeat-binding factor 2
N: Nibrin


分子量 (理論値)分子数
合計 (水以外)25,6012
ポリマ－25,6012
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)144.616, 153.267, 108.029
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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要素

#1: タンパク質
Telomeric repeat-binding factor 2 / TRF2


分子量: 23724.646 Da / 分子数: 7 / 断片: UNP residues 84-287 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TERF2, TRBF2, TRF2 / プラスミド: PETSumo / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q15554
#2: タンパク質・ペプチド
Nibrin / NBS1


分子量: 1876.247 Da / 分子数: 7 / 断片: UNP residues 423-438 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: O60934

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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: 3.41 Å3/Da / 溶媒含有率: 63.88 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: 0.1M MES, 20% PEG8000, 2mM DTT

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 21-ID-F / 波長: 0.9787 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2007年3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: 0.9787 Å / 相対比: 1
反射解像度: 3→50 Å / Num. obs: 47897 / % possible obs: 96.4 % / 冗長度: 7.5 % / Biso Wilson estimate: 69.1 Å2 / Rmerge(I) obs: 0.08 / Net I/av σ(I): 19.833 / Net I/σ(I): 8.7
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3-3.053.40.4370.938179.9
3.05-3.1140.4560.869184.9
3.11-3.174.60.4710.892187.2
3.17-3.235.40.3920.915189.2
3.23-3.36.10.3510.943193.2
3.3-3.386.70.2840.964196.1
3.38-3.467.10.2490.977198
3.46-3.567.40.2330.981199.1
3.56-3.667.60.1970.986199.5
3.66-3.787.80.1530.991199.8
3.78-3.9180.1250.994199.6
3.91-4.078.10.1070.9961100
4.07-4.268.40.0820.9971100
4.26-4.488.60.0670.9981100
4.48-4.768.90.0660.9981100
4.76-5.1390.0740.9971100
5.13-5.6490.0820.9971100
5.64-6.4690.0830.9971100
6.46-8.1390.0440.9991100
8.13-508.50.0241199.9

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位相決定

位相決定手法: 分子置換
Phasing MRModel details: Phaser MODE: MR_AUTO
最高解像度最低解像度
Rotation7.37 Å48.17 Å
Translation7.37 Å48.17 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
HKL-2000データ収集
HKL-2000data processing
PHASER2.5.6位相決定
PDB_EXTRACT3.2データ抽出
HKL-2000データ削減
HKL-2000データスケーリング
HKLデータ削減
HKLデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 3BUA

3bua


解像度: 3→48.171 Å / SU ML: 0.4 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 31.17
Rfactor反射数%反射
Rfree0.2844 2267 4.81 %
Rwork0.2326 --
obs0.2351 47155 96.71 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 210.19 Å2 / Biso mean: 87.734 Å2 / Biso min: 23.9 Å2
精密化ステップサイクル: final / 解像度: 3→48.171 Å
タンパク質核酸リガンド溶媒全体
原子数11619 0 0 0 11619
残基数----1470
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00311798
X-RAY DIFFRACTIONf_angle_d0.55115913
X-RAY DIFFRACTIONf_chiral_restr0.0351855
X-RAY DIFFRACTIONf_plane_restr0.0042033
X-RAY DIFFRACTIONf_dihedral_angle_d2.3467300
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.06530.40321000.33362369246982
3.0653-3.13660.39061390.31142434257386
3.1366-3.2150.34341450.29892552269789
3.215-3.30190.31811580.28652659281794
3.3019-3.3990.29831480.26792802295097
3.399-3.50870.32381340.25832825295999
3.5087-3.63410.32241360.24752882301899
3.6341-3.77950.32871360.240528643000100
3.7795-3.95150.30251240.236429073031100
3.9515-4.15970.31691270.227828973024100
4.1597-4.42010.23271320.192529113043100
4.4201-4.76110.25731860.194128563042100
4.7611-5.23970.28841620.217729113073100
5.2397-5.99670.27771530.258929283081100
5.9967-7.55060.29621220.255230093131100
7.5506-48.17760.22941650.196430823247100
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)
12.5146-0.11530.48286.5883-0.85592.77140.16550.1639-0.2397-1.21950.2996-0.14370.4418-0.0149-0.27560.26810.00430.08880.3171-0.04680.419514.347222.4235143.6432
22.07430.22180.41742.5789-1.72772.2375-0.293-0.03560.20590.02310.2481-0.45450.13-0.0614-0.02010.23510.0130.04960.27020.03010.470315.719931.6596146.9679
33.9691-3.2582-0.46984.88071.67681.0069-0.6659-0.88310.69750.87981.3844-1.76540.76760.556-0.05920.35620.02690.02050.7643-0.11950.655318.318745.6595155.461
41.3735-1.02351.03554.54-1.81331.76930.01380.08491.0305-0.3471-0.3037-1.3222-0.4320.4360.04830.3621-0.09050.140.46390.10221.186320.552752.4731142.2794
53.69431.9922-0.81978.6841.16174.0968-0.13781.8484-0.2078-0.97380.3313-0.01380.7618-0.46790.15140.92620.0919-0.04930.8862-0.02640.5848.963220.6237134.5303
60.8426-0.6579-0.27333.2021-0.49833.8496-0.0552-0.042-0.0171-0.2607-0.04690.10590.53-0.11040.04190.2165-0.0612-0.02160.2554-0.00210.42677.234717.9612153.9229
73.38840.37651.67854.1782-0.72453.0325-0.1279-0.4150.25950.56390.09330.5548-0.2819-0.428-0.00550.29480.05150.13390.36490.01760.47511.971816.2761175.5476
80.54640.3197-0.12432.2589-1.87432.551-0.0893-0.1891-0.05460.2313-0.04480.2870.1576-0.30750.14850.32680.06390.06180.39980.03140.49848.86738.6337174.4393
91.3573-0.39350.03314.2134-2.79063.5720.2246-0.63510.07980.21130.0693-0.77631.7329-0.0137-0.16361.01410.3574-0.09590.518-0.01650.605732.1497-6.7963196.5025
101.76531.30160.611.14550.16833.29830.1185-0.00340.2090.0773-0.1823-0.19750.63450.4906-0.01760.60370.2063-0.03590.4550.02260.450732.5471.6557191.2751
113.93230.485-0.075.0106-1.86313.17150.218-0.4278-0.30720.5172-0.1015-0.70390.09141.2745-0.16250.37580.1125-0.05450.7078-0.05210.524238.000211.5135183.3715
125.1172-0.972-0.06170.81730.92081.3163-0.72290.04640.55-0.5909-0.2029-1.61050.91670.3931-0.09940.99470.3420.22691.0658-0.02460.900342.1546-0.5477171.3789
130.75190.02940.73434.5772-1.04574.8255-0.1443-0.03950.1342-0.6710.0002-0.37530.32290.575-0.00150.22140.0460.09810.51630.0480.463433.032615.2921170.3842
147.61972.2929-2.08424.9133-2.75484.4684-0.08490.4144-0.3971-0.3830.5462-0.58530.3151-0.6866-0.37231.49610.1829-0.05940.4943-0.13720.529525.113-15.25192.7086
150.89590.2992-0.18583.28942.54354.339-0.09210.25780.26440.4572-0.14890.34420.78730.16840.20551.0539-0.0224-0.03440.48560.07660.515924.7928-6.2502206.2933
161.6477-1.33630.76691.0019-0.68982.9366-0.4308-0.18270.34070.33950.0464-0.1452-0.17280.4577-0.04630.60030.13870.02140.60580.00260.327532.63623.3985210.2122
170.2597-0.14680.03170.3110.13610.0832-0.09920.258-0.8806-0.0777-0.02810.64670.0263-0.8526-0.0940.9313-0.080.17350.66180.05740.531816.0893-1.2255202.6972
183.2796-0.50761.13291.9572-0.293.83680.2246-0.37180.01170.04260.02220.21160.4037-0.6426-0.03120.67090.07830.07160.69410.01580.359221.10567.9441218.6191
192.71960.79590.66543.067-0.38112.9532-0.3244-0.47310.41450.0313-0.01550.088-0.0156-0.1091-0.00630.60940.16950.14210.6557-0.13360.45923.871216.0921229.9709
201.6883-1.06180.77751.1285-0.54061.7972-0.2842-0.45510.15540.51580.0760.40890.08170.03620.06230.84260.04730.13670.795-0.1630.527428.411619.4234238.0042
210.2282-0.8614-1.10015.56543.57093.4087-0.073-0.1749-0.24150.09990.14570.4531.27620.2518-0.05881.330.20510.01110.6510.06480.615129.4769-7.1017217.9972
221.8621-0.13020.89471.6591.37972.44620.11030.0489-0.0540.10330.0139-0.22360.58510.9364-0.12480.64570.1347-0.06111.0829-0.01080.518654.396212.2905136.9695
230.5327-0.0608-1.10313.34520.90953.21940.11470.2957-0.0645-0.36970.0466-0.6498-0.0230.9907-0.14610.58330.10270.0710.9834-0.11740.586754.38419.1362116.9024
240.735-0.19050.1364.91141.03822.83870.14760.04670.34650.646-0.30560.365-0.32210.90.10460.7211-0.1734-0.04030.9460.05710.45848.603727.6396147.0652
251.2326-1.54080.46623.05931.6132.1739-0.3369-0.03480.28040.7610.018-0.13480.01110.2170.20160.9417-0.1933-0.12050.79690.0540.671550.058244.099153.4416
261.0549-1.1766-0.01812.334-1.40611.728-1.0078-0.61680.02932.44670.6037-0.0954-0.7621-0.080.32411.58040.4930.3621-0.2169-0.46230.146467.58933.6948198.0035
272.1835-0.1960.25456.8065-0.66860.8916-0.22810.5269-0.04880.63630.32660.99820.1911-0.3333-0.10540.401-0.08220.11960.49560.01080.697364.441511.8112185.3163
281.06040.47730.51130.42020.12860.2949-0.425-0.3737-0.65240.5969-0.34281.64750.2005-1.04360.77460.85620.57031.00230.6617-0.63612.416353.313124.8072192.1227
293.75431.02280.06966.40210.55285.5044-0.18780.98650.5627-0.2240.61931.2547-0.4588-0.4156-0.35730.512-0.0589-0.16230.5850.23160.799164.885630.1742176.5841
300.10730.0797-0.11470.0863-0.25010.48130.3349-0.28650.54860.726-0.02470.2337-0.0207-0.21880.71472.92130.14880.78950.3051-0.61320.365669.91611.1338205.2383
311.88640.94860.23982.3154-0.38714.6846-0.409-0.789-0.42921.5869-0.063-0.90340.09061.65840.01610.60730.06810.02090.72780.00190.908220.561234.7311154.9028
322.2381-1.5064-0.94943.0575-0.87971.5083-0.042-0.12230.54160.0706-0.00930.9852-0.1774-1.51230.03520.42920.0646-0.05390.66940.030.7394-0.693625.7758164.5116
333.2528-0.5058-0.05673.9911-0.16584.38230.35541.24450.10950.3281-0.8904-0.8566-0.07780.26080.16080.7564-0.0833-0.1080.71390.22280.652936.857510.8798192.5247
344.31850.51080.23096.5112-0.37416.0405-0.39770.16440.70561.78340.80650.9212-1.09180.17560.17270.70870.00250.09410.6922-0.08760.47422.27511.6577209.9904
351.15960.35370.7724.72991.43992.6602-0.42420.5030.3371-0.4497-0.40730.2231-0.55950.96660.59760.40290.2789-0.37252.14190.2230.385357.911121.6758127.8962
361.7378-1.41230.85431.3588-1.50373.2666-1.42080.37450.15610.6072-1.37531.06660.4834-0.20490.5580.996-0.1520.40550.99890.04340.948845.704732.9562140.301
372.45661.00811.62585.560.06471.23740.4034-0.2923-0.8184-0.8709-0.53731.31750.2899-0.63670.07081.13530.28220.34720.92990.13070.880662.51586.5021181.6692
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 69 )A44 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 111 )A70 - 111
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 127 )A112 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 227 )A128 - 227
5X-RAY DIFFRACTION5chain 'A' and (resid 228 through 245 )A228 - 245
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 95 )B43 - 95
7X-RAY DIFFRACTION7chain 'B' and (resid 96 through 185 )B96 - 185
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 244 )B186 - 244
9X-RAY DIFFRACTION9chain 'C' and (resid 42 through 69 )C42 - 69
10X-RAY DIFFRACTION10chain 'C' and (resid 70 through 111 )C70 - 111
11X-RAY DIFFRACTION11chain 'C' and (resid 112 through 143 )C112 - 143
12X-RAY DIFFRACTION12chain 'C' and (resid 144 through 153 )C144 - 153
13X-RAY DIFFRACTION13chain 'C' and (resid 154 through 228 )C154 - 228
14X-RAY DIFFRACTION14chain 'C' and (resid 229 through 245 )C229 - 245
15X-RAY DIFFRACTION15chain 'D' and (resid 43 through 69 )D43 - 69
16X-RAY DIFFRACTION16chain 'D' and (resid 70 through 86 )D70 - 86
17X-RAY DIFFRACTION17chain 'D' and (resid 87 through 94 )D87 - 94
18X-RAY DIFFRACTION18chain 'D' and (resid 95 through 146 )D95 - 146
19X-RAY DIFFRACTION19chain 'D' and (resid 147 through 182 )D147 - 182
20X-RAY DIFFRACTION20chain 'D' and (resid 183 through 213 )D183 - 213
21X-RAY DIFFRACTION21chain 'D' and (resid 214 through 245 )D214 - 245
22X-RAY DIFFRACTION22chain 'E' and (resid 46 through 111 )E46 - 111
23X-RAY DIFFRACTION23chain 'E' and (resid 112 through 243 )E112 - 243
24X-RAY DIFFRACTION24chain 'F' and (resid 43 through 127 )F43 - 127
25X-RAY DIFFRACTION25chain 'F' and (resid 128 through 244 )F128 - 244
26X-RAY DIFFRACTION26chain 'G' and (resid 43 through 69 )G43 - 69
27X-RAY DIFFRACTION27chain 'G' and (resid 70 through 142 )G70 - 142
28X-RAY DIFFRACTION28chain 'G' and (resid 143 through 153 )G143 - 153
29X-RAY DIFFRACTION29chain 'G' and (resid 154 through 227 )G154 - 227
30X-RAY DIFFRACTION30chain 'G' and (resid 228 through 241 )G228 - 241
31X-RAY DIFFRACTION31chain 'H' and (resid 425 through 436 )H425 - 436
32X-RAY DIFFRACTION32chain 'I' and (resid 424 through 436 )I424 - 436
33X-RAY DIFFRACTION33chain 'J' and (resid 427 through 436 )J427 - 436
34X-RAY DIFFRACTION34chain 'K' and (resid 427 through 436 )K427 - 436
35X-RAY DIFFRACTION35chain 'L' and (resid 427 through 436 )L427 - 436
36X-RAY DIFFRACTION36chain 'M' and (resid 429 through 435 )M429 - 435
37X-RAY DIFFRACTION37chain 'N' and (resid 427 through 435 )N427 - 435

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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