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- PDB-9n5c: RNA polymerase II elongation complex with 8-oxoG at +1 site, CMPC... -

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基本情報

登録情報
データベース: PDB / ID: 9n5c
タイトルRNA polymerase II elongation complex with 8-oxoG at +1 site, CMPCPP-bound
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 / 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 / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / 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 / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / 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. / 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, 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, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / 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, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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
Chem-2TM / 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 ...Chem-2TM / 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: 3.6 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)488,00923
ポリマ－486,98013
非ポリマー1,02910
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)162.638, 222.985, 192.256
Angle α, β, γ (deg.)90.00, 98.55, 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 , 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-2TM / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine / CMPcPP / 5′-シチジルオキシホスホニルメチルホスホニルオキシホスホン酸


分子量: 481.184 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H18N3O13P3 / タイプ: SUBJECT OF INVESTIGATION

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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: 3.54 Å3/Da / 溶媒含有率: 65.25 %
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: 3.53→48.77 Å / Num. obs: 82990 / % possible obs: 99.9 % / 冗長度: 7.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.514 / Rpim(I) all: 0.199 / Rrim(I) all: 0.551 / Χ2: 1.03 / Net I/σ(I): 5.2 / Num. measured all: 636204
反射 シェル解像度: 3.53→3.6 Å / % possible obs: 99.9 % / 冗長度: 7.7 % / Rmerge(I) obs: 5.842 / Num. measured all: 34852 / Num. unique obs: 4521 / CC1/2: 0.234 / Rpim(I) all: 2.249 / Rrim(I) all: 6.262 / Χ2: 1.04 / Net I/σ(I) obs: 0.5

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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: 3.6→48.77 Å / SU ML: 0.55 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 35.54 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2973 1877 2.41 %
Rwork0.2522 --
obs0.2533 77929 99.5 %
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: 3.6→48.77 Å
タンパク質核酸リガンド溶媒全体
原子数27971 1037 38 0 29046
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00329675
X-RAY DIFFRACTIONf_angle_d0.69940329
X-RAY DIFFRACTIONf_dihedral_angle_d19.5944342
X-RAY DIFFRACTIONf_chiral_restr0.0454553
X-RAY DIFFRACTIONf_plane_restr0.015040
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.70.43131440.38115761X-RAY DIFFRACTION98
3.7-3.810.38591440.35565776X-RAY DIFFRACTION99
3.81-3.930.40611430.34575826X-RAY DIFFRACTION99
3.93-4.070.33211450.30725835X-RAY DIFFRACTION100
4.07-4.230.31361420.27225798X-RAY DIFFRACTION100
4.23-4.420.31571450.25475873X-RAY DIFFRACTION100
4.42-4.660.26041430.24295876X-RAY DIFFRACTION100
4.66-4.950.29751450.23455857X-RAY DIFFRACTION100
4.95-5.330.32071450.24695866X-RAY DIFFRACTION100
5.33-5.870.31421450.26125873X-RAY DIFFRACTION100
5.87-6.710.32321440.26685883X-RAY DIFFRACTION100
6.71-8.450.31871460.22315904X-RAY DIFFRACTION100
8.45-48.770.19831460.18865924X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.75442.15062.59322.3512-0.47053.4534-0.24061.113-0.0034-0.91560.0699-1.46780.34460.71230.2221.0708-0.0110.530.853-0.13440.905214.736612.987538.7221
2-0.0001-0.0096-0.02550.48221.5875.1556-0.04140.14780.04850.12510.457-0.7184-0.46611.0491-0.41651.9638-0.21420.1652.4566-0.2412.837754.598612.792278.2122
30.7043-0.5372-0.80220.51160.71880.9908-0.5203-0.1660.68470.3919-0.0544-1.2073-0.86660.48050.65331.9593-0.3354-0.58890.94820.0041.232222.623112.004244.226
42.14141.71982.93781.512.01944.683-0.5207-1.2887-0.08490.3409-0.4430.38530.20060.42920.93720.8896-0.13530.5031.7748-0.08611.88847.792611.433572.5402
51.17020.2587-0.08210.7079-0.16021.45890.0670.22720.3719-0.1564-0.0368-0.33540.03710.90140.0410.9483-0.126-0.15671.11990.13291.133451.845311.083838.5801
60.99440.08440.26550.58980.17410.52630.3001-0.0976-0.13220.1215-0.00740.23660.76270.0185-0.10681.9996-0.1659-0.60320.43030.25960.60331.2876-18.105545.5004
70.3778-0.16760.390.4785-0.08770.52990.4591-0.3907-0.04840.2586-0.06620.10070.42490.11870.18112.64260.1138-0.8030.44230.41470.41911.0665-18.051666.9077
80.3818-0.09140.63141.04460.49241.3726-0.0677-0.19520.12180.55090.06720.10870.08730.1531-0.02011.98810.0217-0.53410.71950.01860.878526.6958-12.722475.5483
91.25470.58810.45020.74160.08810.5691-0.11330.28820.6394-0.1030.09560.0867-0.04270.17780.01771.3798-0.07960.01760.47070.13250.933.505144.194741.7252
100.8579-0.38141.88960.3684-0.70684.557-0.5731-0.20170.77180.7260.1668-0.3052-0.940.56110.50371.7093-0.1391-0.27610.6905-0.13840.90258.247132.268751.1821
112.32110.33771.00640.37450.25441.77730.1349-0.1870.18830.60690.1006-0.29190.50450.1589-0.22431.6007-0.136-0.4020.6551-0.18661.049827.519238.251377.7526
120.26120.1934-0.12830.5864-0.1760.9893-0.02350.09520.01630.1679-0.135-0.2618-0.21030.44580.14341.46040.0383-0.3350.4474-0.00870.895911.659833.394147.8853
131.16870.2950.68971.59170.52251.3221-0.0056-0.13660.18371.4950.3761-0.50420.0994-0.2239-0.0678-0.0974-0.19930.24110.35140.10990.4298-5.88220.200646.791
141.4384-0.36580.11721.05490.06811.1958-0.0570.32130.21370.02650.0428-0.30490.33690.2662-0.0180.7261-0.0159-0.21010.42670.0520.564818.8436-4.257833.3358
151.5248-0.7328-0.88553.1932-0.36921.0673-0.0114-0.07060.07790.01850.12420.34790.0532-0.060.00630.3711-0.56640.2510.90030.23140.8105-42.98-16.553231.5438
162.19241.8073-0.0743.99710.14420.86970.3280.3655-0.32390.0905-0.07490.06530.44310.2414-0.10731.52170.3442-0.32860.70680.0430.3932-22.66070.562821.0246
170.2546-0.0809-0.17270.15390.22090.3219-0.1080.330.04850.4333-0.45930.02140.2346-0.06790.14592.2258-0.0179-0.09041.32910.19660.3881-27.2049-6.06489.0744
182.10790.11440.36350.9976-0.01421.97890.35110.74120.0019-0.3137-0.10080.53670.255-0.522-0.26671.27570.1122-0.26830.79790.0980.6449-28.11289.4714.7452
192.45960.86710.03713.4224-0.19120.0148-0.0187-0.6256-0.10510.0102-0.42890.1753-0.6550.47280.34712.4677-0.2982-0.43141.06920.21451.0329-31.7961-16.888749.4602
200.9160.32820.0861.3103-0.4261.27110.0925-0.0566-0.2150.17220.02130.39510.163-0.3844-0.12181.6047-0.2583-0.34290.99820.15120.8361-34.1321-19.478835.015
213.65990.3888-0.00721.6384-1.17783.4628-0.0573-0.72-0.2537-0.36490.28490.37351.25130.4522-0.25741.2971-0.1622-0.48211.30410.15311.035745.0429-21.421993.3843
220.9788-0.2992-1.13710.12570.39921.57060.2125-0.3767-0.05790.1217-0.1551-0.2132-0.47490.325-0.04852.21320.2038-0.60342.1369-0.31461.179554.2364-20.721193.2167
23-0.0013-0.0017-0.00380.0021-0.00290.00130.6788-0.57540.35740.32020.3184-0.50710.04311.1191-0.82711.53430.0124-0.47372.0391-0.38331.609861.5497-10.529385.685
241.8475-0.4850.21542.00911.26443.5622-0.2093-0.4325-0.1196-0.2570.09340.0211-0.13350.57610.07061.45050.0822-0.4960.8016-0.03120.782545.9287-21.817770.0894
250.64171.3032-0.55783.2488-0.74491.2058-0.4547-0.238-0.9195-0.03350.0212-1.00290.28480.28920.30931.13340.3759-0.25920.85130.00290.822240.4349-36.705941.9495
261.52410.75132.08571.71620.43227.3835-0.43240.14980.1122-0.31530.1413-0.13830.35990.30390.18610.37270.08190.14090.94860.05270.379226.1359-28.969929.8594
273.1051-0.29490.6692.8944-0.12741.2807-0.37710.792-0.1522-0.43670.23190.32530.0066-0.20120.13241.6278-0.0031-0.47621.2154-0.29870.654920.3682-35.942219.1906
284.3875-1.53653.00580.5429-1.12493.52970.11190.0676-0.462-0.17120.35020.06420.0115-0.2284-0.46751.8920.1587-0.31860.7786-0.17540.934727.1644-35.418830.142
290.0085-0.0650.06240.4459-0.42160.395-0.25150.2468-0.3610.2490.1668-0.16310.02020.2248-0.04380.7570.37430.29990.9498-0.24310.839841.7591-32.410341.1555
303.76220.3420.82975.1911-5.90957.1248-0.09960.8554-1.5112-0.6799-0.22150.14841.07910.13520.34091.33010.2433-0.19620.3949-0.18640.82428.5992-40.474737.5946
311.72440.9271-0.85240.8587-1.18382.13220.2057-0.21870.41220.3484-0.06070.13790.135-0.1642-0.16611.2379-0.45080.46141.1350.70571.6991-24.0487-48.777666.1714
323.91232.06320.55854.22232.24931.2986-0.85120.07180.22840.6631-0.65510.1696-0.04290.02721.19231.4885-0.8196-0.15931.31520.23341.1671-22.1413-33.671666.2273
331.04850.3177-0.21172.1422-2.0823.4388-0.206-0.5316-0.49090.02720.29730.1984-0.2885-0.2932-0.0321.2291-0.1447-0.5270.6250.1721.6176-25.6502-42.799267.5902
341.0687-0.67530.15081.6904-2.65375.22890.13410.06010.0291-0.5014-0.4682-0.37220.38680.41560.33811.8049-0.7644-0.28331.00890.44471.4377-21.5913-49.110951.3189
352.47040.0982-0.50722.2114-1.17780.7111-0.32810.7528-0.0824-0.96050.52340.11260.3504-0.3387-0.21061.5812-0.82370.14730.91050.37641.6054-28.7956-50.286943.0457
361.05250.337-0.82982.6591-1.17491.8399-0.0921-0.4103-0.65630.0165-0.06530.02840.06180.22660.20941.4716-0.7115-0.29420.90640.67581.2424-14.5025-46.696363.6527
377.4343-0.7719-0.25995.07912.68871.4271-0.2281-0.3773-0.9797-0.00270.09480.38810.86090.10450.15611.9774-0.7762-0.44761.24760.49911.8686-12.1365-55.363862.195
383.55443.606-3.10056.8925-2.58852.80210.1370.54050.0540.0535-0.34530.4684-0.057-0.49150.22391.4574-0.0782-0.14871.58130.57521.4155-26.9349-47.741757.7276
391.68271.361-0.67173.6729-0.2271.5364-0.01030.1788-0.61060.22040.2315-0.51920.45160.157-0.33972.4157-0.2558-0.64741.1264-0.42751.040433.966541.161104.1941
401.65630.23951.79730.0820.30892.02750.1033-0.8257-0.3970.19970.2058-0.18230.4384-0.1986-0.26591.89840.1161-0.29630.91430.03110.9344.547327.298794.0909
414.60770.789-0.76656.4022-0.39626.74380.3156-1.0063-0.02260.256-0.3918-0.9129-0.2892-0.92520.08752.13510.5094-0.38871.4722-0.29110.98132.138422.574894.5265
420.78940.49-0.38460.43380.00080.68320.01160.25760.0837-0.2628-0.0786-0.15940.03020.0726-0.14290.18730.08550.21310.5186-0.08490.3288-25.48496.632130.293
432.61421.08491.84843.93750.58811.31380.22660.0830.19020.0716-0.12460.2974-0.2736-0.73050.20630.3280.09630.37140.3715-0.01550.6636-35.343217.858834.428
447.7281.3759-1.37986.59882.18358.9075-0.0044-0.30170.3139-0.401-0.35830.2933-0.633-0.75670.1480.9616-0.10760.45170.7312-0.13040.5086-38.015113.931941.4945
451.1879-0.4259-0.35390.56050.10740.5311-0.1226-0.1561-0.0790.1357-0.02340.22510.0448-0.0698-0.1644-0.2069-0.08830.15270.57940.01690.2393-24.17815.330433.8667
460.06840.14970.30330.38710.75111.4662-0.09480.2497-0.0127-0.00790.0542-0.1420.3876-0.12750.05371.2478-0.1151-0.42770.68160.09880.8762-8.7232-8.671520.2829
472.55531.2182.78562.1708-0.75685.77110.11180.0796-0.0867-0.58410.0424-0.88370.13940.6476-0.10251.32930.2432-0.47430.9281-0.24071.1898-12.7357-20.006214.15
484.45621.2592-0.43341.5527-0.00222.2820.1187-0.5589-0.55370.2691-0.3685-0.02850.30.06910.15510.1772-0.4117-0.00280.58670.10660.7506-10.8976-38.807824.8523
492.82662.7157-1.71932.6076-1.63231.34550.2064-0.29850.08840.15810.19050.1316-0.0792-0.0830.19940.0817-0.14950.01640.76850.0045-0.0435-15.1292-27.295722.9012
502.27343.33391.12864.89681.63940.56750.4281-0.5971-0.73010.7526-0.36150.1098-0.3464-0.0818-0.03421.2484-0.1465-0.4020.82430.12521.0043-24.9527-28.314330.1677
510.54170.9113-0.72144.3634-1.37091.00130.03630.0396-0.2323-0.24660.10760.6440.1477-0.49760.01781.5641-0.7125-0.61510.7859-0.04050.9856-16.4359-28.944230.4568
524.17522.4740.48296.54321.2932.44790.16040.0617-0.74010.2078-0.17780.31820.2841-0.21420.11391.5555-0.7479-0.42510.9219-0.16341.1673-17.9019-37.513726.8772
530.30960.5971-0.07011.1634-0.17540.15180.12160.08780.017-0.03880.22980.59720.049-0.17870.37590.1134-0.6966-0.0941.0072-0.15710.7406-38.3867-24.03923.6059
540.98240.62331.51431.69810.80522.3514-0.1159-0.41160.67930.06590.29890.2696-0.7770.2972-0.24222.614-0.3289-0.19832.02020.1722.9545-3.774535.29939.2417
552.00013.69485.90014.9453-2.22358.7294-0.6391-1.02791.36190.69730.03961.2363-2.6155-1.43660.59892.54170.4294-0.72392.22430.28911.1831-2.21133.302615.7052
565.68067.1353-2.94388.9696-3.70161.53-0.51540.51830.085-1.16330.1886-0.58910.2038-0.04720.34191.7341-0.2484-0.37210.94790.16430.8814-10.547712.419810.2053
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 28 )
4X-RAY DIFFRACTION4chain 'N' and (resid 2 through 16 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 347 )
6X-RAY DIFFRACTION6chain 'A' and (resid 348 through 736 )
7X-RAY DIFFRACTION7chain 'A' and (resid 737 through 946 )
8X-RAY DIFFRACTION8chain 'A' and (resid 947 through 1446 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 179 )
10X-RAY DIFFRACTION10chain 'B' and (resid 180 through 251 )
11X-RAY DIFFRACTION11chain 'B' and (resid 252 through 408 )
12X-RAY DIFFRACTION12chain 'B' and (resid 409 through 560 )
13X-RAY DIFFRACTION13chain 'B' and (resid 561 through 1051 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1052 through 1221 )
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 26 )
16X-RAY DIFFRACTION16chain 'C' and (resid 27 through 69 )
17X-RAY DIFFRACTION17chain 'C' and (resid 70 through 89 )
18X-RAY DIFFRACTION18chain 'C' and (resid 90 through 175 )
19X-RAY DIFFRACTION19chain 'C' and (resid 176 through 194 )
20X-RAY DIFFRACTION20chain 'C' and (resid 195 through 268 )
21X-RAY DIFFRACTION21chain 'E' and (resid 3 through 38 )
22X-RAY DIFFRACTION22chain 'E' and (resid 39 through 89 )
23X-RAY DIFFRACTION23chain 'E' and (resid 90 through 123 )
24X-RAY DIFFRACTION24chain 'E' and (resid 124 through 215 )
25X-RAY DIFFRACTION25chain 'F' and (resid 69 through 86 )
26X-RAY DIFFRACTION26chain 'F' and (resid 87 through 102 )
27X-RAY DIFFRACTION27chain 'F' and (resid 103 through 116 )
28X-RAY DIFFRACTION28chain 'F' and (resid 117 through 137 )
29X-RAY DIFFRACTION29chain 'F' and (resid 138 through 147 )
30X-RAY DIFFRACTION30chain 'F' and (resid 148 through 154 )
31X-RAY DIFFRACTION31chain 'H' and (resid 2 through 16 )
32X-RAY DIFFRACTION32chain 'H' and (resid 17 through 30 )
33X-RAY DIFFRACTION33chain 'H' and (resid 31 through 53 )
34X-RAY DIFFRACTION34chain 'H' and (resid 54 through 81 )
35X-RAY DIFFRACTION35chain 'H' and (resid 82 through 91 )
36X-RAY DIFFRACTION36chain 'H' and (resid 92 through 127 )
37X-RAY DIFFRACTION37chain 'H' and (resid 128 through 140 )
38X-RAY DIFFRACTION38chain 'H' and (resid 141 through 146 )
39X-RAY DIFFRACTION39chain 'I' and (resid 2 through 42 )
40X-RAY DIFFRACTION40chain 'I' and (resid 43 through 79 )
41X-RAY DIFFRACTION41chain 'I' and (resid 80 through 119 )
42X-RAY DIFFRACTION42chain 'J' and (resid 1 through 14 )
43X-RAY DIFFRACTION43chain 'J' and (resid 15 through 28 )
44X-RAY DIFFRACTION44chain 'J' and (resid 29 through 39 )
45X-RAY DIFFRACTION45chain 'J' and (resid 40 through 65 )
46X-RAY DIFFRACTION46chain 'K' and (resid 1 through 9 )
47X-RAY DIFFRACTION47chain 'K' and (resid 10 through 18 )
48X-RAY DIFFRACTION48chain 'K' and (resid 19 through 29 )
49X-RAY DIFFRACTION49chain 'K' and (resid 30 through 39 )
50X-RAY DIFFRACTION50chain 'K' and (resid 40 through 52 )
51X-RAY DIFFRACTION51chain 'K' and (resid 53 through 69 )
52X-RAY DIFFRACTION52chain 'K' and (resid 70 through 82 )
53X-RAY DIFFRACTION53chain 'K' and (resid 83 through 114 )
54X-RAY DIFFRACTION54chain 'L' and (resid 28 through 52 )
55X-RAY DIFFRACTION55chain 'L' and (resid 53 through 57 )
56X-RAY DIFFRACTION56chain 'L' and (resid 58 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