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- PDB-8ukr: RNA polymerase II elongation complex with Fapy-dG lesion soaking ... -

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基本情報

登録情報
データベース: PDB / ID: 8ukr
タイトルRNA polymerase II elongation complex with Fapy-dG lesion soaking with ATP before chemistry
要素
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • RNA
  • ntsDNA
  • tsDNA with Fapy-dG lesion
キーワードTRANSCRIPTION/DNA/RNA / RNA polymerase II / elongation complex / Fapy-dG / DNA lesion / TRANSCRIPTION / ATP / TRANSCRIPTION-DNA-RNA complex
機能・相同性
機能・相同性情報


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / transcription by RNA polymerase III / transcription by RNA polymerase I / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
類似検索 - 分子機能
RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 ...RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
類似検索 - 構成要素
生物種synthetic construct (人工物)
Saccharomyces cerevisiae S288C (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.78 Å
データ登録者Hou, P. / Oh, J. / Wang, D.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102362 米国
引用ジャーナル: J.Am.Chem.Soc. / 年: 2024
タイトル: Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG.
著者: Gao, S. / Hou, P. / Oh, J. / Wang, D. / Greenberg, M.M.
履歴
登録2023年10月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年4月24日Provider: repository / タイプ: Initial release
改定 1.12024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
R: RNA
T: tsDNA with Fapy-dG lesion
N: ntsDNA
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)488,03523
ポリマ－486,98013
非ポリマー1,05510
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
単位格子
Length a, b, c (Å)159.617, 222.632, 190.697
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number5
Space group name H-MC121

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要素

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RNA鎖 , 1種, 1分子 R

#1: RNA鎖 RNA


分子量: 2934.831 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: synthetic construct (人工物)

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DNA鎖 , 2種, 2分子 TN

#2: DNA鎖 tsDNA with Fapy-dG lesion


分子量: 8755.594 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: synthetic construct (人工物)
#3: DNA鎖 ntsDNA


分子量: 5663.694 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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DNA-directed RNA polymerase II subunit ... , 5種, 5分子 ABCIK

#4: タンパク質 DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


分子量: 191821.578 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P04050, DNA-directed RNA polymerase
#5: タンパク質 DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


分子量: 138937.297 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPB2, RPB150, RPO22, YOR151C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P08518, DNA-directed RNA polymerase
#6: タンパク質 DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


分子量: 35330.457 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPB3, YIL021W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P16370
#10: タンパク質 DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


分子量: 14308.161 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPB9, YGL070C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P27999
#12: タンパク質 DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


分子量: 13633.493 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPB11, YOL005C / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5種, 5分子 EFHJL

#7: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


分子量: 25117.094 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPB5, RPA7, RPC9, YBR154C, YBR1204 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P20434
#8: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


分子量: 17931.834 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPO26, RPB6, YPR187W, P9677.8 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P20435
#9: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


分子量: 16525.363 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPB8, YOR224C, YOR50-14 / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P20436
#11: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


分子量: 8290.732 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPB10, YOR210W / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P22139
#13: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


分子量: 7729.969 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母)
遺伝子: RPC10, RPB12, YHR143W-A, YHR143BW / 発現宿主: Saccharomyces cerevisiae S288C (パン酵母) / 参照: UniProt: P40422

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非ポリマー , 3種, 10分子

#14: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn
#15: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg
#16: 化合物 ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: ATP, エネルギー貯蔵分子*YM

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 3.45 Å3/Da / 溶媒含有率: 64.32 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 390 mM ammonium phosphate (pH 6.0), 5 mM DTT, 5 mM dioxane, and 9-13% (w/v) PEG 6,000

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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: ALS / ビームライン: 5.0.3 / 波長: 0.9765 Å
検出器タイプ: DECTRIS PILATUS3 2M / 検出器: PIXEL / 日付: 2023年4月27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: 0.9765 Å / 相対比: 1
反射解像度: 3.59→47.96 Å / Num. obs: 76483 / % possible obs: 99.4 % / 冗長度: 7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.574 / Rpim(I) all: 0.232 / Rrim(I) all: 0.62 / Χ2: 1.04 / Net I/σ(I): 4.5
反射 シェル解像度: 3.59→3.66 Å / Rmerge(I) obs: 4.892 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4424 / CC1/2: 0.464 / Rpim(I) all: 2.161 / Rrim(I) all: 2.161 / Χ2: 1.05

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487: ???)精密化
Aimlessデータスケーリング
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.78→47.96 Å / SU ML: 0.66 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 36.79 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3098 1996 3.1 %
Rwork0.2608 --
obs0.2623 64331 97.6 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.78→47.96 Å
タンパク質核酸リガンド溶媒全体
原子数27995 950 40 0 28985
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00529602
X-RAY DIFFRACTIONf_angle_d0.89840200
X-RAY DIFFRACTIONf_dihedral_angle_d13.4394304
X-RAY DIFFRACTIONf_chiral_restr0.0554535
X-RAY DIFFRACTIONf_plane_restr0.0075039
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.78-3.870.40181300.38384079X-RAY DIFFRACTION90
3.87-3.980.49511250.37933880X-RAY DIFFRACTION85
3.98-4.10.35631450.32314505X-RAY DIFFRACTION100
4.1-4.230.37161440.30074535X-RAY DIFFRACTION100
4.23-4.380.31541450.27884533X-RAY DIFFRACTION100
4.38-4.550.31381460.26854558X-RAY DIFFRACTION100
4.55-4.760.30971440.25874482X-RAY DIFFRACTION99
4.76-5.010.3341440.25944512X-RAY DIFFRACTION99
5.01-5.330.34881430.27644488X-RAY DIFFRACTION99
5.33-5.740.32611460.27934511X-RAY DIFFRACTION99
5.74-6.310.35931450.2824539X-RAY DIFFRACTION100
6.31-7.220.32111470.2674587X-RAY DIFFRACTION100
7.22-9.090.22921460.21324577X-RAY DIFFRACTION100
9.09-47.960.23591460.20284549X-RAY DIFFRACTION98
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)
13.69213.69850.86723.80310.90245.4080.14361.3195-0.7915-0.1988-0.4842-1.59860.5752-0.33610.36481.51920.077-0.16841.0131-0.00451.213414.652813.396938.1731
21.7274-0.10910.00191.26530.05821.354-0.4794-0.23430.58540.2949-0.41880.16520.754-0.31550.83833.49010.3383-0.3363.2842-1.01834.521657.139.439776.2302
30.16910.3366-0.08920.9724-1.52816.0771-0.14640.82320.1795-0.7587-0.58580.260.74590.63630.75752.24160.26630.30752.6462-0.1132.511142.672814.732268.51
45.5706-4.43625.22043.5512-4.16744.88480.1248-1.09321.50490.6365-1.3473-1.3778-0.22050.47591.39442.1194-0.2521-0.48271.46210.16891.32221.50797.162543.7392
50.02470.0999-0.15790.3963-0.62780.99080.1468-0.5685-0.73670.01520.1247-0.12410.2181-0.4469-0.27564.37570.077-1.14051.67910.41171.982315.479423.035330.6799
60.80791.21281.21513.9569-1.02975.6209-0.57040.2331.34480.8204-0.62240.8864-0.2456-0.991.04472.3573-0.43060.33042.7318-0.36052.642845.89511.52169.5551
71.8351-0.3052-0.02394.3177-0.92532.91540.0470.98480.2116-0.8068-0.0276-0.39430.14481.65890.0061.6385-0.2922-0.16041.35210.45441.525350.67437.639928.3771
81.50530.55410.70870.2438-0.05495.58810.3971-0.55410.73780.7224-0.5989-1.3751.0432.1696-0.06061.6613-0.3104-0.61941.78020.21082.065863.44238.152252.2285
93.31490.51650.63473.37551.64781.5628-0.35190.5691.1794-0.71940.18450.5651-0.01570.65890.11341.8136-0.1349-0.5381.23590.37511.620946.107422.17433.3962
101.283-0.26950.60331.5966-0.32631.47030.50620.1124-0.17890.48810.0202-0.28480.31870.67760.63072.3233-0.074-0.88160.07490.5690.3495.9676-19.926536.0123
110.1962-0.15680.03170.2753-0.2640.55710.266-0.7310.37030.9393-0.1957-0.06730.2486-0.00620.07182.6676-0.243-0.89670.59820.72410.19186.2422-14.643667.3078
120.8106-0.64090.18092.0382-1.28112.342-0.4535-0.1262-0.0914-0.0129-0.01080.4560.39540.1627-0.59782.37030.155-0.8990.82920.49370.686919.1445-44.104962.368
130.46740.34120.29520.30660.35861.1431-0.1304-0.38390.02290.36920.10920.512-0.057-0.11260.05042.807-0.1586-0.64450.62070.01041.000823.2562-12.067472.4803
142.37661.19451.2414.45143.44892.5745-0.229-1.02030.10680.9655-0.3969-0.1719-1.2004-0.33720.29282.9844-0.2172-0.66811.094-0.02331.077629.61496.4371100.6498
150.9874-0.114-0.02840.44-0.15961.2346-0.3321-0.19760.08110.98460.0788-0.3303-1.01860.77920.26391.9311-0.5114-0.51740.91020.28550.891434.2067-11.27356.5728
161.3387-0.29580.17540.40050.24721.06250.38140.04610.7840.2079-0.0220.07540.07750.00010.13352.8748-0.3333-0.38880.5269-0.08930.9415.089439.769643.91
172.47210.2177-1.02063.894-0.7483.408-0.1718-0.369-0.09490.5678-0.3754-0.04370.25530.23870.31982.0367-0.262-0.41750.5007-0.19671.099131.422238.175178.761
182.0204-0.19110.94080.3988-0.09651.1476-0.41480.23740.41260.2910.6409-0.83280.1708-0.1905-0.11352.6243-0.793-0.53060.8623-0.22571.067122.922638.803571.0786
193.43612.73291.00866.14781.02991.7024-0.06380.1508-0.26140.2502-0.2487-1.522-0.13050.83210.09422.283-0.3285-0.56820.87780.0330.917319.195639.259537.9003
201.9630.63690.45541.75330.21311.70680.28-0.68830.22830.2729-0.2089-0.1928-0.3529-0.4795-0.06582.5045-0.024-0.37020.6865-0.01010.7221-3.812632.264766.3103
211.1932-0.2873-0.31581.4726-0.02041.20330.1554-0.0740.180.3864-0.1887-0.3579-0.60970.34680.0480.5793-0.2784-0.06160.52950.06030.47894.5124.698531.2672
222.05471.5642-1.34251.6831-1.39361.52690.3018-0.2057-0.42560.31450.0520.880.1458-0.4910.3791-0.1277-0.28820.1321.04270.36160.9057-34.5559-12.762227.3923
232.14690.061-0.12062.75961.10762.5138-0.5350.3938-0.1485-0.15920.29210.564-0.01240.27220.17210.57310.03310.0360.86060.08110.3225-27.30556.745512.81
241.6358-0.05730.95560.89631.29112.56790.6381-0.3285-0.62651.21030.162-0.0821.5482-0.4636-0.4871.56730.1773-0.28730.8056-0.22080.5249-27.231-2.988733.8734
251.30441.00981.75790.83861.40282.3984-0.6732-1.02750.34880.18090.7901-0.7547-0.0855-0.6341-0.09892.05980.0731-0.23871.6732-0.00361.5319-38.4363-21.817549.8701
263.32432.10631.18623.7555-2.21414.02210.5182-0.2849-0.0857-0.52420.0946-0.02471.0404-0.0939-0.6231.0133-0.1844-0.09280.80090.2340.4199-30.7153-19.04420.9415
273.77061.0055-0.00283.39212.08358.5422-0.4240.0760.417-0.56420.28871.17720.77060.8780.12211.8754-0.3119-0.86171.25490.44971.460146.0765-21.648292.2074
280.19190.65310.72432.20872.45012.7144-0.45251.5540.4073-1.06080.3040.6142-1.09330.83050.08413.4167-0.2124-1.39992.86190.44491.883749.3317-16.6898105.0472
294.1270.71.83345.1158-1.26826.1811-1.4474-0.5610.36051.06260.1951-0.6789-0.1150.88590.91081.52110.3718-0.13133.326-0.74831.39657.3953-27.194483.8314
300.07970.04360.00630.04110.00670.0023-0.20990.46420.68860.5796-0.8295-0.1578-0.0047-0.78020.92073.2021-0.2974-0.74462.83140.15432.318361.1554-10.537386.323
310.7191-0.15180.58631.48480.28073.5493-0.04970.09290.2932-0.04560.0289-0.187-0.26580.73180.47722.59620.075-1.11311.14420.28961.125946.1547-21.851569.4969
322.88982.8115-3.22732.8326-3.16423.6342-0.32640.05650.8348-0.9447-0.2294-0.8951-0.68941.05990.55492.56930.3114-0.74162.55620.0251.879252.3986-30.398737.9906
335.639-0.61-0.29652.64862.34553.9264-1.29490.4549-0.26781.03480.45560.2455-0.11340.25490.60851.27410.0517-0.07110.81810.2610.502530.8397-33.093535.2593
345.86453.6308-2.2488.21743.09624.3226-0.18281.2955-0.1959-1.04680.7884-0.7314-0.2233-0.0114-0.68451.41950.2042-0.17421.0314-0.35310.610620.4817-35.842918.9031
353.70091.7433-3.94184.77240.65335.79370.6567-0.3684-1.661-0.4959-0.9847-0.1990.33180.420.22880.84370.11590.14060.82280.38351.131222.971-37.067527.2232
362.40772.2319-3.68052.5937-3.9896.26190.27521.06960.4479-0.6625-0.2129-0.8197-0.69681.3366-0.20250.6335-0.06670.5191.10820.06730.709638.1492-31.675536.7831
371.857-0.5112-0.91849.18955.3693.3458-0.33330.3769-0.3411-0.54540.7347-0.3501-0.98621.3669-0.36732.37980.0503-0.2241.085-0.0930.65741.7713-32.410240.768
383.2059-0.56322.18473.7424-3.6474.4095-0.01290.1439-1.9841-0.2429-0.0599-0.00881.390.67470.1931.49510.4362-0.10540.57590.08661.025428.6383-40.39837.0485
391.07811.0605-1.06781.4464-0.5472.26180.0624-0.4471-0.77040.9474-0.45290.36630.92320.05290.36441.4702-0.4670.2311.51980.931.6967-22.5372-42.398265.2877
400.83481.7084-1.18585.5137-2.89634.01190.1821-1.1262-0.07320.3785-0.27050.44640.0575-0.4904-0.14750.7253-0.52870.31830.83220.00081.2334-24.1844-41.623568.1041
410.64770.79860.09922.5715-0.69864.4442-0.180.51210.3048-0.51750.2517-0.4505-0.0429-0.0293-0.0821.2463-0.9705-0.04591.21950.16361.5988-21.5999-48.487950.1737
424.78282.5268-1.40024.7772-2.75582.524-0.71181.02150.2899-1.24830.55210.37930.204-0.0810.19042.2937-1.10270.23911.37950.50732.5096-29.5063-49.789347.4323
435.03592.2919-0.59813.29520.70830.79270.648-0.7789-0.46370.5663-0.2526-0.8404-0.54180.34180.17411.6768-0.5802-0.09731.16940.83271.5295-12.6361-45.667760.5055
440.0682-0.1881-0.11340.6232-0.04220.8539-0.0414-0.67-0.9630.4938-0.4575-0.50610.51210.15020.56271.1256-0.8137-0.03211.2270.39930.8548-12.1789-46.448467.088
450.01360.011-0.00310.0076-0.00240.00070.72-0.5687-1.19520.710.88921.0529-0.8664-0.6871-1.52242.5126-0.24240.11352.2970.30953.0611-11.8117-55.238563.0725
464.3116-2.3325-3.94694.08893.03143.8974-0.11751.4544-0.11240.7171-0.21171.40590.5275-1.86160.07150.9165-0.30990.22161.44750.54321.0858-25.6983-47.987857.9987
473.70131.09820.97564.9735-0.0123.74320.4116-0.1058-0.6843-0.49820.2398-0.43510.4218-0.4858-0.46512.0926-0.2275-0.44080.9218-0.48841.320934.905841.4045102.9022
481.5688-0.19931.43610.0248-0.18161.2936-0.7243-0.44380.34020.35160.2458-0.1814-1.1457-0.47020.58723.03530.2691-0.44171.0852-0.05971.07997.662827.262991.7613
492.37471.6627-2.35883.39280.12136.34950.1866-1.143-0.41561.44750.1572-0.3586-0.8288-0.9912-0.37463.68860.567-0.47331.63310.15061.25782.665623.37794.6241
500.02250.05260.00260.412-0.09790.0338-0.01830.26450.0015-0.091-0.0734-0.0323-0.0313-0.1816-0.17060.10820.12930.3120.46360.1113-0.0004-25.366.222730.1189
518.12913.65892.51296.25230.82361.16760.29450.07520.9154-0.4283-0.05870.946-0.2729-0.443-0.24781.6005-0.62150.18040.8944-0.29391.1298-35.372117.659234.4326
522.71981.3092-1.37151.9761-0.89942.07170.2443-0.34690.07490.44290.34960.4674-0.2621-0.3232-0.0150.2555-0.35440.43770.55210.07710.3625-27.520914.788335.745
531.9216-3.1892-2.20088.18380.35756.3555-0.44391.07391.36160.0482-0.5733-0.1473-0.2472-0.75191.01980.91330.4674-0.15611.46430.03241.1926-9.6616-9.488820.0246
545.85425.9891-2.67278.513-3.96342.4695-0.82550.5214-0.0752-1.18020.7768-1.3733-0.78610.23750.10511.5421-0.0754-0.63990.4843-0.23311.154-12.0288-21.407513.7991
551.99550.5712-0.20353.6492-2.06913.67660.4724-0.0282-0.94011.05230.2046-0.29120.6497-0.235-0.48831.0843-0.5748-0.65690.6575-0.1060.666-17.6795-31.298526.3082
565.8644.4937-0.31983.443-0.2680.00980.0133-0.2110.17560.2781-0.25870.74160.6766-0.92450.1292.3433-0.6442-0.37180.8561-0.05381.0032-17.0856-32.709728.9109
570.7639-0.9683-0.0261.17660.0065-0.0063-0.06130.0101-0.36010.09340.26860.74050.0689-0.2267-0.09330.42-0.67090.43521.083-0.06210.8019-38.3766-23.941823.8148
585.00880.9715.18670.26050.86755.63270.5837-0.72921.98010.0635-0.40020.1938-2.6402-1.6874-0.1463.36580.3727-0.17372.20260.03354.7097-5.918632.14168.9806
592.08323.51172.18529.61546.67066.06260.2766-0.06230.7238-0.0469-0.74070.74850.0686-1.01280.36413.2301-1.08310.17763.91390.5624.36762.020435.09565.884
600.8-0.48241.96080.2906-1.18254.80710.32940.571-0.2122-1.18620.43332.17440.7702-2.2838-0.79353.05750.1975-0.65553.0314-0.36243.3443-4.180440.627311.9337
610.05630.1433-0.29810.5475-1.27842.9343-0.1685-0.00910.8502-0.0186-0.35-0.25-1.1152-0.75560.50041.55460.5204-0.46051.0417-0.05551.1806-8.584216.7611.1806
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'R' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'T' and (resid 5 through 9 )
3X-RAY DIFFRACTION3chain 'T' and (resid 10 through 14 )
4X-RAY DIFFRACTION4chain 'T' and (resid 15 through 25 )
5X-RAY DIFFRACTION5chain 'T' and (resid 26 through 28 )
6X-RAY DIFFRACTION6chain 'N' and (resid 2 through 14 )
7X-RAY DIFFRACTION7chain 'A' and (resid 3 through 119 )
8X-RAY DIFFRACTION8chain 'A' and (resid 120 through 237 )
9X-RAY DIFFRACTION9chain 'A' and (resid 238 through 324 )
10X-RAY DIFFRACTION10chain 'A' and (resid 325 through 628 )
11X-RAY DIFFRACTION11chain 'A' and (resid 629 through 946 )
12X-RAY DIFFRACTION12chain 'A' and (resid 947 through 1038 )
13X-RAY DIFFRACTION13chain 'A' and (resid 1039 through 1154 )
14X-RAY DIFFRACTION14chain 'A' and (resid 1155 through 1317 )
15X-RAY DIFFRACTION15chain 'A' and (resid 1318 through 1446 )
16X-RAY DIFFRACTION16chain 'B' and (resid 20 through 242 )
17X-RAY DIFFRACTION17chain 'B' and (resid 243 through 345 )
18X-RAY DIFFRACTION18chain 'B' and (resid 346 through 408 )
19X-RAY DIFFRACTION19chain 'B' and (resid 409 through 487 )
20X-RAY DIFFRACTION20chain 'B' and (resid 488 through 763 )
21X-RAY DIFFRACTION21chain 'B' and (resid 764 through 1221 )
22X-RAY DIFFRACTION22chain 'C' and (resid 2 through 51 )
23X-RAY DIFFRACTION23chain 'C' and (resid 52 through 139 )
24X-RAY DIFFRACTION24chain 'C' and (resid 140 through 200 )
25X-RAY DIFFRACTION25chain 'C' and (resid 201 through 227 )
26X-RAY DIFFRACTION26chain 'C' and (resid 228 through 268 )
27X-RAY DIFFRACTION27chain 'E' and (resid 4 through 38 )
28X-RAY DIFFRACTION28chain 'E' and (resid 39 through 54 )
29X-RAY DIFFRACTION29chain 'E' and (resid 55 through 78 )
30X-RAY DIFFRACTION30chain 'E' and (resid 79 through 124 )
31X-RAY DIFFRACTION31chain 'E' and (resid 125 through 215 )
32X-RAY DIFFRACTION32chain 'F' and (resid 69 through 73 )
33X-RAY DIFFRACTION33chain 'F' and (resid 74 through 102 )
34X-RAY DIFFRACTION34chain 'F' and (resid 103 through 116 )
35X-RAY DIFFRACTION35chain 'F' and (resid 117 through 132 )
36X-RAY DIFFRACTION36chain 'F' and (resid 133 through 137 )
37X-RAY DIFFRACTION37chain 'F' and (resid 138 through 147 )
38X-RAY DIFFRACTION38chain 'F' and (resid 148 through 154 )
39X-RAY DIFFRACTION39chain 'H' and (resid 2 through 22 )
40X-RAY DIFFRACTION40chain 'H' and (resid 23 through 53 )
41X-RAY DIFFRACTION41chain 'H' and (resid 54 through 82 )
42X-RAY DIFFRACTION42chain 'H' and (resid 83 through 94 )
43X-RAY DIFFRACTION43chain 'H' and (resid 95 through 106 )
44X-RAY DIFFRACTION44chain 'H' and (resid 107 through 126 )
45X-RAY DIFFRACTION45chain 'H' and (resid 127 through 139 )
46X-RAY DIFFRACTION46chain 'H' and (resid 140 through 146 )
47X-RAY DIFFRACTION47chain 'I' and (resid 2 through 42 )
48X-RAY DIFFRACTION48chain 'I' and (resid 43 through 74 )
49X-RAY DIFFRACTION49chain 'I' and (resid 75 through 119 )
50X-RAY DIFFRACTION50chain 'J' and (resid 1 through 14 )
51X-RAY DIFFRACTION51chain 'J' and (resid 15 through 28 )
52X-RAY DIFFRACTION52chain 'J' and (resid 29 through 65 )
53X-RAY DIFFRACTION53chain 'K' and (resid 1 through 10 )
54X-RAY DIFFRACTION54chain 'K' and (resid 11 through 18 )
55X-RAY DIFFRACTION55chain 'K' and (resid 19 through 52 )
56X-RAY DIFFRACTION56chain 'K' and (resid 53 through 82 )
57X-RAY DIFFRACTION57chain 'K' and (resid 83 through 114 )
58X-RAY DIFFRACTION58chain 'L' and (resid 28 through 38 )
59X-RAY DIFFRACTION59chain 'L' and (resid 39 through 48 )
60X-RAY DIFFRACTION60chain 'L' and (resid 49 through 53 )
61X-RAY DIFFRACTION61chain 'L' and (resid 54 through 70 )

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万見について

-
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