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- PDB-6erp: Structure of the human mitochondrial transcription initiation com... -

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基本情報

登録情報
データベース: PDB / ID: 6erp
タイトルStructure of the human mitochondrial transcription initiation complex at the LSP promoter
要素
  • DNA-directed RNA polymerase, mitochondrial
  • Dimethyladenosine transferase 2, mitochondrial
  • Non-Template DNA
  • Template DNA
  • Transcription factor A, mitochondrial
キーワードTRANSCRIPTION / Mitochondria / Initiation / Polymerase
機能・相同性
機能・相同性情報


rRNA (adenine-N6-)-methyltransferase activity / Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription factor activity / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial transcription ...rRNA (adenine-N6-)-methyltransferase activity / Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription factor activity / mitochondrial respiratory chain complex assembly / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial transcription / : / rRNA methylation / DNA binding, bending / mitochondrial nucleoid / : / heat shock protein binding / response to nutrient / Mitochondrial protein degradation / DNA-directed RNA polymerase activity / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / : / : / : / : / : / : / DNA-directed RNA polymerase / 3'-5'-RNA exonuclease activity / sequence-specific DNA binding / response to hypoxia / transcription cis-regulatory region binding / mitochondrial matrix / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / mitochondrion / RNA binding / nucleus / cytosol
類似検索 - 分子機能
DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / : / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. ...DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / : / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Tetratricopeptide-like helical domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / DNA-directed RNA polymerase, mitochondrial / Transcription factor A, mitochondrial / Dimethyladenosine transferase 2, mitochondrial
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: 4.502 Å
データ登録者Hillen, H.S. / Morozov, Y.I. / Sarfallah, A. / Temiakov, D. / Cramer, P.
資金援助 ドイツ, 米国, 6件
組織認可番号国
German Research FoundationSFB860 ドイツ
German Research FoundationSPP1935 ドイツ
European Research Council693023 ドイツ
Volkswagen Foundation ドイツ
National Institutes of HealthRO1 GM104231 米国
Boehringer Ingelheim FondsPhD Student Fellowship ドイツ
引用ジャーナル: Cell / 年: 2017
タイトル: Structural Basis of Mitochondrial Transcription Initiation.
著者: Hillen, H.S. / Morozov, Y.I. / Sarfallah, A. / Temiakov, D. / Cramer, P.
履歴
登録2017年10月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年11月15日Provider: repository / タイプ: Initial release
改定 1.12017年11月29日Group: Database references / カテゴリ: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22018年1月24日Group: Source and taxonomy / カテゴリ: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
改定 1.32018年1月31日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42024年5月1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

ダウンロードとリンク

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集合体

登録構造単位
C: Transcription factor A, mitochondrial
D: Non-Template DNA
E: Template DNA
G: Transcription factor A, mitochondrial
H: Non-Template DNA
I: Template DNA
A: DNA-directed RNA polymerase, mitochondrial
B: DNA-directed RNA polymerase, mitochondrial
F: Dimethyladenosine transferase 2, mitochondrial
J: Dimethyladenosine transferase 2, mitochondrial


分子量 (理論値)分子数
合計 (水以外)453,05010
ポリマ－453,05010
非ポリマー00
水00
1
C: Transcription factor A, mitochondrial
D: Non-Template DNA
E: Template DNA
A: DNA-directed RNA polymerase, mitochondrial
F: Dimethyladenosine transferase 2, mitochondrial


分子量 (理論値)分子数
合計 (水以外)226,5255
ポリマ－226,5255
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint-74 kcal/mol
Surface area84880 Å2
手法PISA
2
G: Transcription factor A, mitochondrial
H: Non-Template DNA
I: Template DNA
B: DNA-directed RNA polymerase, mitochondrial
J: Dimethyladenosine transferase 2, mitochondrial


分子量 (理論値)分子数
合計 (水以外)226,5255
ポリマ－226,5255
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area14660 Å2
ΔGint-73 kcal/mol
Surface area84070 Å2
手法PISA
単位格子
Length a, b, c (Å)103.910, 197.030, 137.210
Angle α, β, γ (deg.)90.00, 99.87, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質 Transcription factor A, mitochondrial / mtTFA / Mitochondrial transcription factor 1 / MtTF1 / Transcription factor 6 / TCF-6 / ...mtTFA / Mitochondrial transcription factor 1 / MtTF1 / Transcription factor 6 / TCF-6 / Transcription factor 6-like 2


分子量: 24516.166 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TFAM, TCF6, TCF6L2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Rosetta2 pLysS / 参照: UniProt: Q00059
#2: DNA鎖 Non-Template DNA


分子量: 15488.921 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#3: DNA鎖 Template DNA


分子量: 15232.778 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
#4: タンパク質 DNA-directed RNA polymerase, mitochondrial / MtRPOL


分子量: 127904.055 Da / 分子数: 2 / Mutation: E555A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: POLRMT / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): RIL / 参照: UniProt: O00411, DNA-directed RNA polymerase
#5: タンパク質 Dimethyladenosine transferase 2, mitochondrial / Hepatitis C virus NS5A-transactivated protein 5 / HCV NS5A-transactivated protein 5 / Mitochondrial ...Hepatitis C virus NS5A-transactivated protein 5 / HCV NS5A-transactivated protein 5 / Mitochondrial 12S rRNA dimethylase 2 / Mitochondrial transcription factor B2 / mtTFB2 / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase 2


分子量: 43383.301 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TFB2M, NS5ATP5 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): RIL
参照: UniProt: Q9H5Q4, 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの
配列の詳細The region of mtRNAP corresponding to the specificity loop (residues 1086-1107) showed fragmented ...The region of mtRNAP corresponding to the specificity loop (residues 1086-1107) showed fragmented density and was modelled based on the structure of the T7 RNAP initiation complex (Cheetham et al., 1999). The density allowed for modelling the main chain trace of this element lacking only three residues (1094-1096) at the tip, yet the sequence register could not be assigned unambiguously and it was therefore modelled as poly-alanine.

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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: 3.05 Å3/Da / 溶媒含有率: 59.74 %
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 / 詳細: L-Proline, PEG8000, BIS-TRIS

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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: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2016年12月2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: 4.5→49.6 Å / Num. obs: 31884 / % possible obs: 98.7 % / 冗長度: 7.1 % / CC1/2: 0.998 / Rrim(I) all: 0.061 / Net I/σ(I): 14.46
反射 シェル解像度: 4.5→4.61 Å / 冗長度: 7 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 2283 / CC1/2: 0.54 / Rrim(I) all: 1.857 / % possible all: 96.1

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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
XDSデータ削減
XDSデータスケーリング
PHENIX位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: Model of the human mitochondrial IC on LSP promoter

解像度: 4.502→49.583 Å / SU ML: 0.65 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 40.32
Rfactor反射数%反射
Rfree0.3101 1595 5.01 %
Rwork0.2701 --
obs0.2721 31840 98.66 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 4.502→49.583 Å
タンパク質核酸リガンド溶媒全体
原子数23890 3718 0 0 27608
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00228592
X-RAY DIFFRACTIONf_angle_d0.53739441
X-RAY DIFFRACTIONf_dihedral_angle_d16.52916799
X-RAY DIFFRACTIONf_chiral_restr0.0544371
X-RAY DIFFRACTIONf_plane_restr0.0034418
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5023-4.64750.38821420.40332670X-RAY DIFFRACTION97
4.6475-4.81350.37541440.37842746X-RAY DIFFRACTION99
4.8135-5.0060.41321460.37162771X-RAY DIFFRACTION99
5.006-5.23360.4031430.39392708X-RAY DIFFRACTION97
5.2336-5.50920.37381450.36962748X-RAY DIFFRACTION99
5.5092-5.85390.40891460.37382773X-RAY DIFFRACTION100
5.8539-6.3050.39961450.37642757X-RAY DIFFRACTION100
6.305-6.9380.38491460.35042795X-RAY DIFFRACTION100
6.938-7.93840.32211430.32612719X-RAY DIFFRACTION97
7.9384-9.98810.26751470.22282793X-RAY DIFFRACTION100
9.9881-49.58610.26581480.20162765X-RAY DIFFRACTION97
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)
15.27936.5802-0.88984.519-5.64015.85730.9818-0.28260.03930.3314-0.8967-2.3309-2.2612.95470.00123.20620.3639-0.1893.5599-0.10153.276739.699449.6231-43.8662
21.0392.5310.68178.9693-0.3681-2.50581.77451.37261.9645-2.9589-0.91-1.5595-1.505-0.90790.00094.88430.4844-0.58144.37670.54964.363326.995339.0211-55.864
35.82560.9494-2.48017.42350.2998-0.27420.7026-0.74230.1955-2.5411.4565-0.81070.9695-1.0947-0.00034.4775-0.52620.26595.10150.30353.342840.69789.8024-68.752
40.3341-0.28870.91441.5336-1.85621.47881.53599.77253.3119-1.77281.0241.5254.5413-1.70310.00044.5483-0.03320.07267.0130.14865.193532.795516.3702-71.7693
50.26150.4626-0.34961.4354-0.8670.5619-4.72441.5986-1.4348-1.23831.6947-4.25572.61123.73430.01365.48980.56011.18564.2266-0.52833.766542.825835.2481-67.5748
60.7409-0.68450.08350.6075-0.14460.2557-2.71722.4706-6.5446-1.0962-2.77731.2634-0.14872.13940.01433.7627-0.0752-0.4294.68980.03224.574438.244437.4527-47.8784
70.3399-0.39470.36640.78620.26740.69671.578-3.31112.0276-0.4087-2.23764.9123-3.5531-1.0592-0.00043.941.3140.3765.7830.82494.541425.029846.3157-39.7952
80.5105-0.06320.1611.53681.47631.12071.5273.05798.1885-2.61010.5743-2.2694-3.83443.5871-0.00143.51640.5461-0.22793.70570.5953.59719.859235.7957-38.4152
90.5827-0.77280.282.0045-8.81085.57396.4932-6.0578-7.13014.2647.53841.9555-3.1432-2.07532.34537.3306-1.20140.2355.8285-1.41564.2008-7.473441.6672-36.3858
100.6445-0.5562-0.03492.35351.58671.08251.13032.17541.1256-2.42290.72435.4865-0.88232.26460.00773.93670.6101-1.29325.15750.18326.8286-29.119240.3846-36.8977
110.2116-0.3029-0.47330.50791.01270.8899-4.2912-1.18686.96112.38014.97858.53790.43124.66680.00466.1469-0.6124-0.01056.4488-0.19746.8478-24.900342.4624-18.1754
122.1315-0.2721-1.5311.6077-3.61665.29582.87430.05984.4071-2.0521-1.431-1.9889-0.0792-0.9845-0.00235.09030.6653-0.06755.6826-1.01856.0479-18.76339.2937-30.4927
130.05970.27610.24330.62360.54220.59031.8999-1.7332-0.5051-0.25132.2686-6.10250.3069-0.82420.00043.608-0.6018-0.49685.36620.94166.22479.598841.7951-33.0209
140.32040.80611.00091.31482.04652.70373.25215.2607-0.4826-7.34190.9562-2.72960.33162.84140.03493.4355-0.25170.46556.31430.94354.119624.13140.259-44.2877
151.5243-2.09742.24275.0722-0.41011.40610.3635-0.20580.26061.54951.25292.22634.15630.8793-0.00015.7598-0.0792-0.20924.7171-0.63814.353936.593225.7837-65.6094
165.58545.13612.70195.08195.41516.5701-0.79410.4725-0.86051.18091.5295-6.2856-0.33450.76480.02193.5920.887-1.22354.4540.58174.698944.6907-103.794-23.467
178.8539-0.9706-3.42225.0009-5.58328.58590.81241.7030.7270.9174-0.8185-0.3481.4810.8034-0.00042.82420.21530.00742.8092-0.12223.175426.2053-106.3954-59.2456
18-0.11041.03271.20520.49093.28133.19191.62642.2961-1.6718-2.35013.6425-0.7023-2.8394-3.18820.0724.59920.41530.64574.4126-0.11437.95516.7494-110.2083-53.5524
19-0.10330.50251.27161.38120.98113.98044.0203-0.66712.9441-4.0599-7.2936-4.99837.4323-2.3261-0.00575.78030.30380.20765.2651-0.42385.35518.7007-103.214-62.4245
202.1067-1.88251.28690.28850.42883.242-0.18790.00520.89470.90652.0423-0.17780.1702-3.5592-0.00314.69620.4953-0.1815.9701-1.0276.938735.2063-109.6942-43.3261
210.22110.42960.70263.5942.03530.5867-0.25730.53181.96530.17872.5487-12.4647-0.19070.35810.03835.88150.8172-0.09934.12490.09136.885228.7207-89.9397-21.7547
222.02871.36993.6641.18470.68433.6694-1.9838-1.1433-0.66131.3992-0.10190.1688-0.0036-0.437-0.00095.6727-0.08490.52045.0577-0.36795.612617.5522-52.0543-11.4088
233.63281.59695.23390.15862.38294.0213-3.32636.89180.1362-3.87454.9787-0.1829-1.07511.1326-0.06335.8656-0.89370.75434.9249-0.57253.2313.5924-47.9028-5.9736
249.65310.92658.55310.7198-1.246810.2688-1.2261-2.2112-4.37670.67555.3866-1.6163-2.20111.46480.20687.32030.51340.63694.5089-0.40597.223825.8079-81.1704-23.1427
258.3-3.3461-2.07662.89633.88412.65980.0525-1.69441.02220.9149-0.7509-2.15320.42663.09530.00073.5215-0.6285-0.08943.85630.32474.332526.5919-106.5712-53.5533
264.282-3.8042-8.3507-5.04842.04042.72292.20740.18325.37780.46990.8877-0.5972-2.0833-1.41090.24013.87750.1176-0.27154.16020.12044.699127.367714.5978-40.999
2710.7516-7.3456-5.41986.7558-1.93678.0755-1.34460.0751-0.5374-0.52971.5838-1.34491.0521.22310.01644.15860.3649-0.79533.7276-0.32372.645812.65652.5272-16.8285
282.79990.4507-1.2344.8841-0.67856.4709-0.22720.2611-0.7023-0.528-0.2756-0.59550.11430.0806-0.00032.68620.40850.12323.1342-0.18242.8792-8.52344.2786-45.4645
294.94890.068-0.81122.2438-1.13455.6459-0.12170.3989-0.90670.56750.43120.9839-0.6-0.9522-03.12690.2062-0.06173.19670.37343.7151-34.5153-1.0329-37.3916
303.36750.29742.4177.67960.2461-1.9673-0.9711-1.00510.0753-0.07560.79531.9706-0.6275-1.2138-0.00034.43991.00320.53334.6710.40683.6883-35.963815.8671-20.2815
312.4725-5.0825-4.28111.87146.29463.6241-0.378-1.1621-0.77941.72571.223-1.55842.50032.066-0.00025.58950.69940.01773.5020.50734.28328.1129-103.6146-32.9949
323.65628.41363.65384.20148.99238.78471.30962.39430.03141.1699-0.248-1.36461.4135-0.77010.00024.8406-0.0705-0.50423.2840.41363.8199-9.3729-99.3814-13.1322
33-2.7223-2.0161-0.77951.28981.80653.05631.04691.32980.80731.4827-0.7660.3216-1.0101-0.8294-0.00023.8738-0.2409-0.09954.73570.97174.8327-29.8651-70.7685-26.0017
343.32521.788-2.67446.1974-4.24438.64460.54490.0159-1.3880.5550.26711.1990.79720.1245-0.00143.3166-0.293-0.27692.3252-0.33643.2324-9.6942-76.4043-35.757
350.2518-2.6536-6.37073.10772.13225.59842.3149-0.41141.67910.85110.78170.3045-1.07841.020.00023.5794-0.15520.12624.06460.07164.3464-5.0116-65.4056-36.1345
36-1.47683.958-1.598.2603-3.99225.197-0.4927-0.0790.78250.24410.55921.8741-1.3628-0.7594-0.00023.74180.139-0.06493.50950.53784.7922-25.7639-46.0907-32.9895
373.75835.5772-1.05615.8198-6.207410.32830.5908-1.05711.85520.8607-0.11420.17012.00534.06650.00755.62590.42551.25013.8675-0.08194.3726-10.3055-32.5398-16.4275
383.49573.51450.3672.98960.35021.58260.8846-1.37250.6642.0288-0.89981.3437-0.423-1.0343-0.00014.95190.04880.28393.6596-0.12093.5175-14.998-52.3077-6.8342
393.8891.8091-1.30041.1237-0.5239-0.01720.1133-0.25925.36321.50971.47740.1122-3.5679-1.05720.00084.65890.53751.03284.3884-0.49786.3623-39.115965.0903-45.2293
402.6025-1.44370.07336.21142.061110.5433-0.52350.5639-0.1369-0.0757-0.1043-1.08390.0203-0.59220.00023.250.11030.06743.82460.39584.8202-32.355251.185-52.902
417.1691-6.0827-4.24583.30453.97015.7581-0.79020.68763.44640.0540.0526-0.76410.91480.6488-0.00063.9827-0.06770.4173.67910.81125.0704-15.938545.7704-59.5617
422.94963.8953-0.4272.6921-0.21615.8343-0.33821.9879-0.8412-2.08231.6131-1.13912.83941.0862-0.00073.6177-0.06620.1894.2730.80652.7583-12.992337.1536-66.2085
435.633-9.37367.98612.03861.83221.7431.3529-0.72317.47533.7247-3.8465-5.21.22436.6786-4.0935.6646-1.7426-0.33855.7811-2.8838.06840.4281-28.4246-19.8308
444.07720.39220.61593.8389-4.72675.78940.3124-8.12228.07693.2837-3.8502-1.154-3.20196.1565-1.87674.2503-1.28151.02563.6527-1.87085.4131.7454-21.8493-17.477
451.0094-0.5101-0.71731.064-0.14830.57683.00731.216-5.83250.13623.75270.56680.5119-1.97310.00575.0947-0.5641-0.18553.6566-0.20334.564316.777-31.244-25.6008
460.9576-0.03370.64970.17380.11410.4258-2.6556-2.04452.57611.8260.97135.2049-2.7865-1.4039-05.4893-0.46631.0693.397-1.22574.504429.3026-25.2552-37.1508
473.5745-1.73732.64232.4167-0.95186.455-2.9855-0.9356-0.3225-0.6810.65712.93345.0306-8.5479-0.09934.0753-0.91820.32533.6613-1.32214.052628.3517-40.9178-27.3752
481.2148-1.6906-2.26281.78022.50043.40361.7107-2.8184-0.538-2.5125-0.4980.30621.7229-0.0005-0.00013.8082-1.0217-0.46014.0294-0.71294.910633.5011-40.2208-30.534
491.36721.6562-2.86144.2531-5.1096.5989-0.1554-9.90942.33441.6623-0.9824-9.55333.8855-0.1138-1.61964.2978-0.5695-0.57875.5499-1.85716.24237.2271-49.6381-32.2411
504.4453-1.3517-0.2716.5888-2.693.91783.8538-0.8405-0.9861-2.97532.3693-6.9391.98530.16224.84864.1072-1.41210.16174.5857-1.62886.159333.2467-41.906-38.3612
513.667-1.04293.88963.6006-3.41634.7807-0.13113.3653-2.4307-1.52220.3459-4.9061.24620.71720.0244.4119-1.46580.35283.69-1.32363.302722.6583-59.4159-44.0177
527.23-0.4734-4.10970.02921.27355.1616-1.58623.7541-1.416-3.54262.0469-1.7687-0.12181.60390.00014.6207-0.86520.31223.8291-0.54733.821224.4692-56.1535-47.8701
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 43 through 92 )
2X-RAY DIFFRACTION2chain 'C' and (resid 93 through 169 )
3X-RAY DIFFRACTION3chain 'C' and (resid 170 through 234 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'D' and (resid 11 through 15 )
6X-RAY DIFFRACTION6chain 'D' and (resid 16 through 20 )
7X-RAY DIFFRACTION7chain 'D' and (resid 21 through 25 )
8X-RAY DIFFRACTION8chain 'D' and (resid 26 through 30 )
9X-RAY DIFFRACTION9chain 'D' and (resid 31 through 35 )
10X-RAY DIFFRACTION10chain 'D' and (resid 36 through 44 )
11X-RAY DIFFRACTION11chain 'D' and (resid 45 through 50 )
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 20 )
13X-RAY DIFFRACTION13chain 'E' and (resid 21 through 25 )
14X-RAY DIFFRACTION14chain 'E' and (resid 26 through 30 )
15X-RAY DIFFRACTION15chain 'E' and (resid 31 through 50 )
16X-RAY DIFFRACTION16chain 'G' and (resid 43 through 122 )
17X-RAY DIFFRACTION17chain 'G' and (resid 123 through 197 )
18X-RAY DIFFRACTION18chain 'G' and (resid 198 through 234 )
19X-RAY DIFFRACTION19chain 'H' and (resid 1 through 10 )
20X-RAY DIFFRACTION20chain 'H' and (resid 11 through 20 )
21X-RAY DIFFRACTION21chain 'H' and (resid 21 through 30 )
22X-RAY DIFFRACTION22chain 'H' and (resid 31 through 50 )
23X-RAY DIFFRACTION23chain 'I' and (resid 1 through 15 )
24X-RAY DIFFRACTION24chain 'I' and (resid 16 through 30 )
25X-RAY DIFFRACTION25chain 'I' and (resid 31 through 50 )
26X-RAY DIFFRACTION26chain 'A' and (resid 122 through 251 )
27X-RAY DIFFRACTION27chain 'A' and (resid 252 through 378 )
28X-RAY DIFFRACTION28chain 'A' and (resid 379 through 645 )
29X-RAY DIFFRACTION29chain 'A' and (resid 646 through 934 )
30X-RAY DIFFRACTION30chain 'A' and (resid 935 through 1230 )
31X-RAY DIFFRACTION31chain 'B' and (resid 122 through 251 )
32X-RAY DIFFRACTION32chain 'B' and (resid 252 through 354 )
33X-RAY DIFFRACTION33chain 'B' and (resid 355 through 423 )
34X-RAY DIFFRACTION34chain 'B' and (resid 424 through 586 )
35X-RAY DIFFRACTION35chain 'B' and (resid 587 through 688 )
36X-RAY DIFFRACTION36chain 'B' and (resid 689 through 934 )
37X-RAY DIFFRACTION37chain 'B' and (resid 935 through 1024 )
38X-RAY DIFFRACTION38chain 'B' and (resid 1025 through 1230 )
39X-RAY DIFFRACTION39chain 'F' and (resid 72 through 153 )
40X-RAY DIFFRACTION40chain 'F' and (resid 154 through 238 )
41X-RAY DIFFRACTION41chain 'F' and (resid 239 through 353 )
42X-RAY DIFFRACTION42chain 'F' and (resid 354 through 392 )
43X-RAY DIFFRACTION43chain 'J' and (resid 72 through 126 )
44X-RAY DIFFRACTION44chain 'J' and (resid 127 through 153 )
45X-RAY DIFFRACTION45chain 'J' and (resid 154 through 168 )
46X-RAY DIFFRACTION46chain 'J' and (resid 169 through 189 )
47X-RAY DIFFRACTION47chain 'J' and (resid 190 through 213 )
48X-RAY DIFFRACTION48chain 'J' and (resid 214 through 238 )
49X-RAY DIFFRACTION49chain 'J' and (resid 239 through 266 )
50X-RAY DIFFRACTION50chain 'J' and (resid 267 through 316 )
51X-RAY DIFFRACTION51chain 'J' and (resid 317 through 353 )
52X-RAY DIFFRACTION52chain 'J' and (resid 354 through 392 )

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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