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- PDB-9n5b: RNA polymerase II elongation complex containing 8-oxoG at +1 site... -

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基本情報

登録情報
データベース: PDB / ID: 9n5b
タイトルRNA polymerase II elongation complex containing 8-oxoG at +1 site, apo form
要素
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • Non-template strand DNA
  • RNA
  • Template strand DNA
キーワードTRANSCRIPTION / RNA polymerase II / oxidative damage / in vitro transcription / 8-oxoguanine
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 / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...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 / 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 II transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / 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 / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translesion synthesis / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / 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. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / 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. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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 Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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, 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 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / 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
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 / 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Saccharomyces cerevisiae S288C (パン酵母)
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: 3.1 Å
データ登録者Oh, J. / Wang, D.
資金援助 米国, 韓国, 3件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102362 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM147652 米国
National Research Foundation (NRF, Korea)RS-2024-00344054 韓国
引用ジャーナル: J.Am.Chem.Soc. / 年: 2025
タイトル: Transcription-Coupled Template Reconfiguration of 8-Oxoguanine for Error-Prone Transcription Revealed by Time-Resolved X-ray Crystallography and Molecular Dynamics.
著者: Oh, J. / Konovalov, K.A. / Hou, P. / Chong, J. / Huang, X. / Wang, D.
履歴
登録2025年2月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年8月13日Provider: repository / タイプ: Initial release

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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: Template strand DNA
N: Non-template strand DNA
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)487,52822
ポリマ－486,98013
非ポリマー5489
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)157.839, 221.722, 190.842
Angle α, β, γ (deg.)90.00, 97.41, 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: 合成 / 由来: (合成) synthetic construct (人工物)

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DNA鎖 , 2種, 2分子 TN

#2: DNA鎖 Template strand DNA


分子量: 8755.594 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: DNA鎖 Non-template strand DNA


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 , 2種, 9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


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg

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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 modificationN

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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: 3.4 Å3/Da / 溶媒含有率: 63.82 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000

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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: 8.2.2 / 波長: 0.984 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2018年11月11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: 0.984 Å / 相対比: 1
反射解像度: 3→47.83 Å / Num. obs: 129746 / % possible obs: 100 % / 冗長度: 7.7 % / CC1/2: 0.983 / Rmerge(I) obs: 0.41 / Rpim(I) all: 0.158 / Rrim(I) all: 0.439 / Χ2: 1.02 / Net I/σ(I): 6.3 / Num. measured all: 998460
反射 シェル解像度: 3→3.05 Å / % possible obs: 100 % / 冗長度: 7.7 % / Rmerge(I) obs: 3.831 / Num. measured all: 49801 / Num. unique obs: 6439 / CC1/2: 0.228 / Rpim(I) all: 1.471 / Rrim(I) all: 4.105 / Χ2: 1 / Net I/σ(I) obs: 0.6

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.19.2_4158: ???)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: 3.1→46.28 Å / SU ML: 0.35 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.256 1813 1.54 %
Rwork0.2131 --
obs0.2138 117474 99.89 %
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
精密化ステップサイクル: LAST / 解像度: 3.1→46.28 Å
タンパク質核酸リガンド溶媒全体
原子数28005 1033 9 0 29047
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00429673
X-RAY DIFFRACTIONf_angle_d0.69440309
X-RAY DIFFRACTIONf_dihedral_angle_d19.4284343
X-RAY DIFFRACTIONf_chiral_restr0.0474548
X-RAY DIFFRACTIONf_plane_restr0.0055043
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.38391390.3368852X-RAY DIFFRACTION100
3.18-3.280.31591390.31538852X-RAY DIFFRACTION100
3.28-3.380.37311390.2988853X-RAY DIFFRACTION100
3.38-3.50.32521390.28048908X-RAY DIFFRACTION100
3.5-3.640.2871390.24718866X-RAY DIFFRACTION100
3.64-3.810.29861390.22858871X-RAY DIFFRACTION100
3.81-4.010.28691400.21158907X-RAY DIFFRACTION100
4.01-4.260.23841400.19028927X-RAY DIFFRACTION100
4.26-4.590.22851390.16788852X-RAY DIFFRACTION100
4.59-5.050.22761390.178930X-RAY DIFFRACTION100
5.05-5.780.22671400.19188910X-RAY DIFFRACTION100
5.78-7.280.2061390.2128953X-RAY DIFFRACTION100
7.28-46.280.20651420.17698980X-RAY DIFFRACTION100
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)
11.16140.51540.25912.2805-0.14480.8253-0.01370.1557-0.106-0.673-0.5098-0.18190.12590.76370.12660.98970.03090.11640.96980.04730.705515.076912.98338.2595
20.04580.09650.29650.18980.58761.7731-0.27670.15180.21750.26540.0348-0.31330.08170.37310.06961.6506-0.30520.15782.10450.04522.159255.678312.402376.9395
31.80691.32711.26181.02450.93960.89280.0383-0.054-0.03720.02270.3643-0.173-0.26140.3467-0.12392.1438-0.4327-0.6331.45080.51372.240338.344213.826157.015
41.117-0.2188-0.37062.6848-0.55191.1357-0.5830.22910.4604-0.01220.0577-0.6876-0.3450.72650.31610.9965-0.1489-0.07540.90850.10920.739516.365910.702437.1157
50.66630.47720.61530.33210.42990.5516-0.3357-0.2448-0.39050.66080.0838-0.0862-0.33130.02470.10691.8136-0.2546-0.18082.28870.13672.334249.062910.975371.6727
61.5097-0.2589-0.25231.1080.11240.8117-0.00360.15150.5338-0.0076-0.0381-0.4805-0.38210.78040.0760.5862-0.29470.01531.13280.17691.089555.279510.752937.3505
71.05950.05070.10880.3503-0.12420.65420.13290.0331-0.06540.0265-0.0525-0.02260.32760.0715-0.07570.4166-0.0501-0.02640.22930.02860.31956.6801-18.142337.558
80.87990.96021.06941.99241.36311.95530.3437-0.2637-0.08860.3870.003-0.05940.5065-0.1405-0.24760.6579-0.08660.08830.46010.01020.395-2.94471.661182.9576
90.2439-0.3894-0.02610.2269-0.05070.44630.1164-0.1693-0.12010.11010.01070.05040.22220.0019-0.1070.5971-0.0371-0.11150.41550.0890.470311.7782-21.6365.8298
100.31420.61240.17471.7855-0.74731.3658-0.11-0.01-0.1252-0.26130.3102-0.03170.68180.1919-0.13150.91080.0918-0.14290.4508-0.01390.501523.5253-39.75658.3512
110.2677-0.0663-0.06760.69610.82891.123-0.0161-0.27070.09780.2318-0.19060.006-0.1861-0.2790.16650.82650.03-0.170.5815-0.07250.499125.0307-0.884283.9075
121.23930.13130.45652.48130.29471.572-0.0919-0.32580.11391.09620.035-0.03980.21650.06250.12141.2723-0.0288-0.2650.5828-0.11750.659132.721414.666109.5424
130.22530.13050.15190.82080.4681.44890.0015-0.09280.1610.11810.1101-0.0764-0.02230.2959-0.05710.35950.0405-0.09820.4479-0.02690.479232.1065-9.052467.1101
141.16880.07980.43870.4039-0.04740.6269-0.12840.06560.33330.0165-0.0324-0.0405-0.47030.3110.10210.8564-0.15430.03380.35450.06810.56962.697843.54840.2902
151.64740.07852.17080.77220.16433.51160.0750.11990.18450.1299-0.0071-0.15020.16420.33750.08510.5272-0.14690.10320.3797-0.01140.403617.572529.990659.5341
161.2844-0.11930.82530.28040.07011.204-0.04550.03160.25920.0750.0962-0.148-0.04330.0656-0.09330.6818-0.24250.04560.4549-0.07780.545327.619640.648770.7771
170.45230.09540.05730.7465-0.14591.36010.053-0.08790.04220.0860.0288-0.0908-0.2864-0.0119-0.06920.4433-0.01590.03820.24240.00610.3273-0.523731.034159.5685
180.6571-0.0415-0.28020.55230.16741.1866-0.04450.1980.0043-0.16830.0754-0.127-0.25250.1360.02470.3728-0.12570.01540.38680.01960.3605-3.56019.542427.8982
190.3197-0.1790.12190.4445-0.05340.5775-0.07750.14940.05110.0198-0.0413-0.11990.08060.20720.09410.3751-0.05760.0090.42360.08190.429216.7911-3.303234.3331
202.5159-0.5181-0.30234.3499-1.13342.4156-0.0426-0.0563-0.0369-0.0589-0.16880.45-0.1522-0.34130.10450.391-0.1449-0.04840.73640.0170.4707-42.5332-16.359732.124
210.52680.4468-0.52861.9108-0.28390.8606-0.17510.1731-0.21-0.20750.1614-0.1173-0.1396-0.10990.05270.3225-0.0586-0.0530.41840.04890.3463-22.48730.491821.1942
220.9321-0.6559-0.92350.4660.6560.91730.2050.4443-0.2703-0.183-0.42740.21820.044-0.13470.06640.7935-0.0312-0.06010.59110.10770.4183-27.6438-5.82910.6205
231.13320.3041-0.21622.2250.81191.5503-0.08870.12080.1289-0.37630.14250.0055-0.2403-0.30810.07140.36690.0195-0.02660.43270.08390.3476-26.735813.135211.7202
240.7184-0.0598-0.09980.7806-0.08161.0169-0.01470.13110.0356-0.29050.18020.31040.0848-0.3233-0.15550.4492-0.0293-0.0890.3984-0.00330.3013-28.23686.951416.4343
250.41870.01020.25371.1207-0.04371.33280.1295-0.0604-0.10840.02690.02510.03050.2824-0.3546-0.05820.4036-0.1861-0.09930.51880.08160.5024-32.9056-18.730838.933
261.74540.3561-0.40870.5428-0.45631.73910.3081-0.8761-0.416-0.082-0.13040.27240.80080.7275-0.04170.78030.0233-0.15441.1222-0.00570.691146.0773-21.29392.542
270.02320.1880.19781.60351.78712.03880.33-0.17070.05840.07860.0265-0.3633-0.04390.611-0.17071.05640.3964-0.27821.8293-0.39170.849449.5961-17.3279105.0153
280.7428-0.2134-0.36181.67730.99491.48230.4076-0.3861-0.16060.30080.2204-0.9945-0.07760.7549-0.24490.6980.3027-0.19481.571-0.19350.82357.8204-22.426186.174
290.31690.1309-0.01890.0536-0.01250.02450.2951-0.340.57850.0605-0.3399-0.622-0.38080.6624-0.01750.891-0.0542-0.16661.6583-0.37721.190162.6309-10.652384.4646
300.4986-0.46120.10770.97310.35071.6934-0.213-0.36710.23920.12040.1525-0.26610.28650.58420.07480.43690.1099-0.10810.813-0.04420.557346.7654-21.842169.2494
310.0048-0.02240.00260.1019-0.01180.0013-0.02990.5241-0.8932-0.66880.1012-1.03290.2350.36150.05541.12360.31510.07531.2003-0.15071.465653.0771-31.111437.4158
320.01190.0370.03750.35280.35770.365-0.0096-0.001-0.3966-0.02980.0228-0.17930.4668-0.0305-0.01471.24280.4841-0.37061.1334-0.27661.034145.2307-41.065740.7623
331.59960.26670.48312.5249-1.62271.31870.2290.0143-0.37440.1467-0.4075-0.40140.54830.4194-0.17981.21780.304-0.26070.80830.07680.482533.184-37.109342.7431
340.11230.09260.42430.07770.49955.19260.29690.4683-0.0413-0.0754-0.0979-0.0954-0.0806-0.2014-0.05760.64780.05420.01230.55620.01690.376826.601-29.001428.58
354.6039-0.54710.04092.70760.2281.1425-0.28790.3651-0.3865-0.00440.09220.26090.5085-0.25110.05020.95730.1447-0.08670.8115-0.13040.672619.944-37.197719.1059
360.4948-0.05771.03163.9396-2.54293.6401-0.23-0.0296-0.5649-0.0140.17070.39950.0945-0.2172-0.00430.99560.0153-0.14970.7304-0.09380.649520.1459-36.021226.8271
371.2478-0.72560.06720.4924-0.41672.32470.32690.0668-0.1715-0.29520.2527-0.02090.04410.2438-0.22650.8090.21170.02320.6362-0.0630.377834.705-34.989232.3198
380.4163-0.4102-0.48820.40990.47780.5732-0.23940.1875-0.4881-0.38110.0724-0.21250.12850.2942-0.07930.59280.0230.07390.8076-0.23370.764242.1878-32.372140.2711
394.44070.8312.70234.8699-1.98852.9749-0.04780.3306-0.4549-0.1249-0.2728-0.10310.44310.24090.12340.70890.0973-0.0910.42550.02050.703229.0989-40.385336.9265
401.16640.2539-0.1361.3171-0.45590.50060.1809-0.4688-0.03810.22550.20820.44010.07620.0583-0.04871.2206-0.15970.18790.86650.26051.0153-22.7237-48.213266.7752
412.81770.4513-2.12971.1671-0.45921.6506-0.0626-0.25820.19810.30520.0645-0.0726-0.18280.0750.07180.4806-0.2235-0.0391.11490.05590.9567-20.7818-27.341263.206
420.40250.467-0.41391.0801-0.29571.1767-0.1259-0.5641-0.27430.37060.30810.49030.2152-0.096-0.05640.8874-0.27330.09440.70630.26940.8207-23.7474-41.899268.4675
430.7607-0.24130.81982.0767-0.75831.00980.0547-0.0205-0.2831-0.3181-0.12750.03470.16880.44460.05150.9383-0.19140.020.64270.16710.7832-20.5436-48.84150.9685
442.2190.4886-0.26932.0439-0.12590.1622-0.0430.44280.234-0.32390.2571-0.0514-0.0302-0.03390.05791.267-0.70540.31160.83060.01451.0825-28.4784-50.254742.6618
451.5691-2.2164-1.23894.86940.45784.99870.02010.2189-0.41160.07190.17360.4858-0.0651-0.54180.00710.9667-0.1702-0.08380.45120.26410.8837-24.2722-45.728755.5687
461.3432-1.14881.76091.1287-2.04444.28270.0676-0.2959-0.56720.1290.166-0.08940.6676-0.0524-0.12531.4104-0.136-0.07190.67150.53380.8684-5.8739-47.04764.8155
470.7477-0.10520.03210.86570.22571.7081-0.2635-0.7258-0.72520.4713-0.13980.01150.25460.0058-0.01311.0102-0.34660.02390.78850.44560.7365-11.5125-46.376467.2734
481.4189-0.85280.25651.68840.43970.3450.02610.3181-0.6827-0.1723-0.1488-0.11660.32640.130.09311.4875-0.3058-0.12751.01150.36210.9863-11.0741-55.018161.6742
490.1901-0.64520.45544.30881.33265.0205-0.07820.1933-0.48160.1456-0.13450.69890.2167-0.71710.11570.678-0.0825-0.11420.67820.18381.0349-26.0458-48.116958.2948
500.10630.3334-0.06291.8133-0.02170.2773-0.17440.0653-0.13660.29290.4486-0.4565-0.15250.2429-0.18131.0539-0.1591-0.15590.6147-0.17350.667133.210937.846101.861
510.1551-0.1044-0.02830.99410.37061.9527-0.069-0.4289-0.35110.06830.05-0.1592-0.2858-0.01520.00630.5067-0.04550.06140.6375-0.02860.4136-2.021328.263591.9797
521.6265-0.4923-0.09123.1763-0.54441.9433-0.136-0.4797-0.11550.05070.3428-0.1780.3198-0.0315-0.15520.57070.0887-0.06140.6298-0.03040.44435.902821.99194.3924
530.096-0.15980.27010.9561-0.24820.98220.00780.1274-0.02650.0241-0.2411-0.0118-0.06820.215-0.28290.0085-0.09510.0660.6420.06150.4505-25.07226.405930.32
541.01340.66410.04741.9938-0.15312.5593-0.1512-0.01310.3930.2534-0.22150.5898-0.4084-0.62980.18190.3060.02020.11130.5897-0.02010.7132-35.343114.518337.5453
551.1238-0.181-0.21680.2142-0.29641.4840.41180.3924-0.0709-0.1795-0.24120.06220.2519-0.2521-0.11150.2208-0.0579-0.01340.52530.12040.4491-25.56739.28238.2133
561.9748-1.04890.67791.21130.99673.04450.28450.25410.62-0.4786-0.1524-0.0717-0.41210.2635-0.03360.3664-0.02170.12010.4712-0.01820.6254-17.957326.792727.3568
570.59680.6284-0.01923.38220.12060.31390.01860.2321-0.2166-0.315-0.1032-0.43630.16950.12510.06390.6514-0.0638-0.06520.4726-0.05610.4357-11.7248-24.26920.9911
580.9361-0.5697-0.06750.4373-0.32130.78930.34650.2299-0.40660.1315-0.11570.25260.6086-0.2016-0.0690.5011-0.5457-0.21790.4148-0.06190.581-26.7766-28.358427.3078
592.91131.27920.06612.7573-3.48537.82690.1179-0.28420.44410.08280.1979-0.1533-0.5498-0.0299-0.30342.01120.2049-0.35030.7049-0.26861.3729-5.070729.98889.5963
600.0011-0.0019-0.00280.00270.00460.00730.0639-0.39920.21380.2290.01730.0651-0.22910.2746-0.0011.84050.6131-0.29172.1433-0.48031.5304-10.234434.484712.3671
614.71940.74490.04621.2224-1.08831.08610.0510.4455-0.0916-0.61450.1781-0.3180.11990.26050.06191.5224-0.44410.01971.4201-0.08861.142.06334.93915.4952
623.7339-0.71983.35090.1534-0.59253.2008-0.0552-1.2801-0.00910.87660.16810.3889-0.1566-0.6229-0.03731.50560.11950.11281.52340.58911.7925-5.606240.505610.4321
634.08562.6056-0.38462.4661-1.45431.8223-0.49490.33970.2279-0.0361-0.1571-0.062-0.9322-0.21630.44560.8831-0.0389-0.10720.92470.13150.5265-6.499721.430110.5182
640.45890.6868-0.55282.3541-1.04880.7032-0.11840.31710.2195-0.2249-0.4232-0.5583-0.15140.84740.08860.54020.2565-0.07090.89480.22350.428-14.85282.418717.3505
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 3 through 12 )
3X-RAY DIFFRACTION3chain 'T' and (resid 13 through 17 )
4X-RAY DIFFRACTION4chain 'T' and (resid 18 through 28 )
5X-RAY DIFFRACTION5chain 'N' and (resid 2 through 16 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3 through 302 )
7X-RAY DIFFRACTION7chain 'A' and (resid 303 through 672 )
8X-RAY DIFFRACTION8chain 'A' and (resid 673 through 736 )
9X-RAY DIFFRACTION9chain 'A' and (resid 737 through 982 )
10X-RAY DIFFRACTION10chain 'A' and (resid 983 through 1077 )
11X-RAY DIFFRACTION11chain 'A' and (resid 1078 through 1154 )
12X-RAY DIFFRACTION12chain 'A' and (resid 1155 through 1257 )
13X-RAY DIFFRACTION13chain 'A' and (resid 1258 through 1446 )
14X-RAY DIFFRACTION14chain 'B' and (resid 20 through 191 )
15X-RAY DIFFRACTION15chain 'B' and (resid 192 through 268 )
16X-RAY DIFFRACTION16chain 'B' and (resid 269 through 433 )
17X-RAY DIFFRACTION17chain 'B' and (resid 434 through 796 )
18X-RAY DIFFRACTION18chain 'B' and (resid 797 through 1038 )
19X-RAY DIFFRACTION19chain 'B' and (resid 1039 through 1221 )
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 26 )
21X-RAY DIFFRACTION21chain 'C' and (resid 27 through 68 )
22X-RAY DIFFRACTION22chain 'C' and (resid 69 through 88 )
23X-RAY DIFFRACTION23chain 'C' and (resid 89 through 118 )
24X-RAY DIFFRACTION24chain 'C' and (resid 119 through 175 )
25X-RAY DIFFRACTION25chain 'C' and (resid 176 through 268 )
26X-RAY DIFFRACTION26chain 'E' and (resid 3 through 38 )
27X-RAY DIFFRACTION27chain 'E' and (resid 39 through 54 )
28X-RAY DIFFRACTION28chain 'E' and (resid 55 through 89 )
29X-RAY DIFFRACTION29chain 'E' and (resid 90 through 123 )
30X-RAY DIFFRACTION30chain 'E' and (resid 124 through 215 )
31X-RAY DIFFRACTION31chain 'F' and (resid 69 through 73 )
32X-RAY DIFFRACTION32chain 'F' and (resid 74 through 78 )
33X-RAY DIFFRACTION33chain 'F' and (resid 79 through 86 )
34X-RAY DIFFRACTION34chain 'F' and (resid 87 through 103 )
35X-RAY DIFFRACTION35chain 'F' and (resid 104 through 116 )
36X-RAY DIFFRACTION36chain 'F' and (resid 117 through 127 )
37X-RAY DIFFRACTION37chain 'F' and (resid 128 through 137 )
38X-RAY DIFFRACTION38chain 'F' and (resid 138 through 147 )
39X-RAY DIFFRACTION39chain 'F' and (resid 148 through 154 )
40X-RAY DIFFRACTION40chain 'H' and (resid 2 through 16 )
41X-RAY DIFFRACTION41chain 'H' and (resid 17 through 23 )
42X-RAY DIFFRACTION42chain 'H' and (resid 24 through 53 )
43X-RAY DIFFRACTION43chain 'H' and (resid 54 through 81 )
44X-RAY DIFFRACTION44chain 'H' and (resid 82 through 91 )
45X-RAY DIFFRACTION45chain 'H' and (resid 92 through 99 )
46X-RAY DIFFRACTION46chain 'H' and (resid 100 through 106 )
47X-RAY DIFFRACTION47chain 'H' and (resid 107 through 127 )
48X-RAY DIFFRACTION48chain 'H' and (resid 128 through 140 )
49X-RAY DIFFRACTION49chain 'H' and (resid 141 through 146 )
50X-RAY DIFFRACTION50chain 'I' and (resid 2 through 52 )
51X-RAY DIFFRACTION51chain 'I' and (resid 53 through 87 )
52X-RAY DIFFRACTION52chain 'I' and (resid 88 through 119 )
53X-RAY DIFFRACTION53chain 'J' and (resid 1 through 14 )
54X-RAY DIFFRACTION54chain 'J' and (resid 15 through 43 )
55X-RAY DIFFRACTION55chain 'J' and (resid 44 through 55 )
56X-RAY DIFFRACTION56chain 'J' and (resid 56 through 65 )
57X-RAY DIFFRACTION57chain 'K' and (resid 1 through 39 )
58X-RAY DIFFRACTION58chain 'K' and (resid 40 through 114 )
59X-RAY DIFFRACTION59chain 'L' and (resid 28 through 32 )
60X-RAY DIFFRACTION60chain 'L' and (resid 33 through 37 )
61X-RAY DIFFRACTION61chain 'L' and (resid 38 through 47 )
62X-RAY DIFFRACTION62chain 'L' and (resid 48 through 52 )
63X-RAY DIFFRACTION63chain 'L' and (resid 53 through 67 )
64X-RAY DIFFRACTION64chain 'L' and (resid 68 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