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- PDB-7kef: RNA polymerase II elongation complex with unnatural base dTPT3, r... -

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基本情報

登録情報
データベース: PDB / ID: 7kef
タイトルRNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state
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/DNA/RNA / RNA polymerase II / elongation complex / unnatural base / TPT3 / NAM / swing state / TRANSCRIPTION / 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
Gyrase A; domain 2 - #140 / RNA polymerase Rpb1, domain 3 / Enzyme I; Chain A, domain 2 / 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 ...Gyrase A; domain 2 - #140 / RNA polymerase Rpb1, domain 3 / Enzyme I; Chain A, domain 2 / 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 / Gyrase A; domain 2 / 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
類似検索 - ドメイン・相同性
Chem-WC4 / 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-WC4 / 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 (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: 3.89 Å
Model detailsRNA polymerase II, 5-guanidinohydantoin, elongation complex, DNA lesion
データ登録者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: Nat.Chem.Biol. / 年: 2021
タイトル: Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.
著者: Oh, J. / Shin, J. / Unarta, I.C. / Wang, W. / Feldman, A.W. / Karadeema, R.J. / Xu, L. / Xu, J. / Chong, J. / Krishnamurthy, R. / Huang, X. / Romesberg, F.E. / Wang, D.
履歴
登録2020年10月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年6月23日Provider: repository / タイプ: Initial release
改定 1.12021年7月14日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22021年8月11日Group: Database references / カテゴリ: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
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
R: RNA
T: Template strand DNA
N: Non-template strand DNA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)487,62423
ポリマ－486,70613
非ポリマー91810
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)167.713, 221.711, 193.255
Angle α, β, γ (deg.)90.000, 101.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11N-17-

DG

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要素

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

#1: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P04050, DNA-directed RNA polymerase
#2: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P08518, DNA-directed RNA polymerase
#3: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P16370
#7: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P27999
#9: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P38902

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

#4: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20434
#5: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20435
#6: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20436
#8: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P22139
#10: 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P40422

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RNA鎖 , 1種, 1分子 R

#11: RNA鎖 RNA


分子量: 3264.036 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

#12: DNA鎖 Template strand DNA


分子量: 8895.848 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#13: DNA鎖 Non-template strand DNA


分子量: 4920.188 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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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-WC4 / (1S)-1,4-anhydro-1-(3-methoxynaphthalen-2-yl)-5-O-phosphono-D-ribitol


分子量: 370.291 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C16H19O8P / 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

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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: 3.61 Å3/Da / 溶媒含有率: 65.95 % / Mosaicity: 0.31 °
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
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: 8.2.1 / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2019年4月28日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.89→48.701 Å / Num. obs: 63384 / % possible obs: 99.9 % / 冗長度: 7.4 % / Biso Wilson estimate: 107.58 Å2 / CC1/2: 0.904 / Rmerge(I) obs: 1.008 / Rpim(I) all: 0.4 / Rrim(I) all: 1.085 / Net I/σ(I): 2.5
反射 シェル解像度: 3.89→3.99 Å / 冗長度: 7.5 % / Rmerge(I) obs: 5.216 / Num. measured all: 33419 / Num. unique obs: 4484 / CC1/2: 0.296 / Rpim(I) all: 2.049 / Rrim(I) all: 5.607 / Net I/σ(I) obs: 0.4 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13精密化
MOSFLMデータ削減
Aimless0.7.3データスケーリング
PDB_EXTRACT3.25データ抽出
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2e2j

2e2j


解像度: 3.89→48.7 Å / SU ML: 0.65 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 35.14 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3255 1979 3.17 %
Rwork0.2683 60536 -
obs0.2701 62515 98.61 %
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
原子変位パラメータBiso max: 277.75 Å2 / Biso mean: 115.2594 Å2 / Biso min: 48.05 Å2
精密化ステップサイクル: final / 解像度: 3.89→48.7 Å
タンパク質核酸リガンド溶媒全体
原子数28079 1090 33 0 29202
Biso mean--116.93 --
残基数----3590
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.89-3.98720.43281280.3649370484
3.9872-4.0950.37351400.3348433899
4.095-4.21540.35131420.3181431299
4.2154-4.35140.36661420.29514358100
4.3514-4.50680.33351430.29134382100
4.5068-4.68710.37011410.27954335100
4.6871-4.90030.29971440.27384399100
4.9003-5.15840.33981410.2764357100
5.1584-5.48110.33051430.28744362100
5.4811-5.90370.37751410.28864359100
5.9037-6.49650.32351440.29114399100
6.4965-7.43380.33421440.27344410100
7.4338-9.35490.27211420.21414400100
9.3549-48.70.26821440.2073442199
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)
10.61490.1206-0.58070.52260.21050.51170.29410.24940.06320.0542-0.0922-0.25520.32590.4690.00030.8255-0.002-0.17851.07470.12851.2136219.25868.553941.3198
20.0470.19010.30620.7751-0.12730.02790.33320.02450.01750.3244-0.0904-0.22350.35630.09540.00290.2393-0.0620.06310.46510.03520.3898181.2537-8.605333.4032
30.1809-0.1105-0.07630.02380.00210.22280.0599-0.0479-0.05630.17170.0303-0.14070.16570.013400.6254-0.0547-0.01910.37440.04320.4921180.3074-15.184472.0054
40.1081-0.2105-0.37720.60240.41030.45690.38420.0336-0.12460.3434-0.1699-0.20450.03320.09050.0380.624-0.13260.07560.50790.13630.5246165.843940.695340.5386
50.46740.2933-0.16250.1080.08480.24440.42080.23850.0590.2236-0.1902-0.13520.99490.7971-0.00150.8649-0.0915-0.0850.6234-0.02850.7963190.634332.824273.8274
60.2821-0.1221-0.3080.05860.09880.1707-0.3233-0.02820.80930.37110.16250.6851-1.0487-0.0903-0.00350.8355-0.1106-0.08290.58270.09930.9504194.631442.604280.3936
70.1523-0.0175-0.05070.26540.1870.08990.01930.69760.1532-0.25720.07270.38160.20420.44070.02090.5492-0.1779-0.01110.8459-0.05590.6159182.972936.829662.3582
8-0.07680.24940.11490.22850.02360.1017-0.03480.5285-0.367-0.321-0.07050.205-0.6936-0.0423-0.04220.71010.0071-0.01590.4706-0.02270.6178174.335129.867950.2371
90.1072-0.0983-0.00210.1904-0.0785-0.0017-0.01480.2349-0.5776-0.04710.11990.5292-0.41360.04050.00240.49260.02510.14090.4545-0.01530.506166.490442.151575.8403
100.2212-0.28070.11710.2668-0.1769-0.01150.1126-0.07110.1305-0.0813-0.2406-0.1263-0.1633-0.55940.00010.68120.1298-0.00270.7229-0.02280.5438150.070224.997564.0348
110.51960.48530.29740.4278-0.3480.4031-0.17770.1590.0931-0.2078-0.24140.0177-0.7854-0.0599-0.2136-0.9908-0.08390.8310.38130.02690.2325161.777313.156829.0297
120.0312-0.1514-0.02530.50690.21960.0586-0.01980.39260.40480.3267-0.1567-0.1989-0.6386-0.2471-0.00360.0523-0.39340.36920.74650.34730.3973171.031316.481116.5825
130.4076-0.6436-0.01930.5283-0.390.0827-0.2462-0.02960.4355-0.3185-0.01990.51190.02750.002-0.054-0.252-0.21590.47160.47370.28930.2793156.087-1.257642.2724
140.1645-0.0085-0.1810.0462-0.13160.1468-0.4091-0.0088-0.53940.41550.0461-0.747-0.76290.3301-0.00960.48310.14730.09490.81110.04790.9032210.3842-6.532929.0417
150.0817-0.0440.08840.0833-0.00360.046-0.21070.2755-0.1427-0.2657-0.3681-0.00490.02-0.41180.00040.8047-0.2327-0.04810.9050.00090.6487127.6069-15.516829.0374
160.12540.12710.18330.06470.18090.2771-0.332-0.3211-0.33440.0962-0.08360.072-0.30670.496-0.83060.0355-0.37280.54290.21440.8658-0.397143.45683.787514.0913
170.32020.0943-0.0740.0267-0.01870.04450.0347-0.18520.6127-0.15160.05510.06280.28910.25030.01440.5254-0.1165-0.03610.87640.03350.4701144.19343.54223.6529
18-0.00780.07830.08110.0468-0.031500.3920.56070.0351-0.31-0.0404-0.0940.18580.51240.00060.58290.0375-0.13270.59180.11210.6413135.670315.185614.8684
190.4708-0.02490.1335-0.0385-0.1052-0.0151-0.0221-0.1008-0.27130.2738-0.2355-0.38390.43560.3085-0.00070.9969-0.0808-0.08470.4809-0.10520.472134.3269-9.386938.0518
200.25420.0644-0.13260.02940.00811.76010.21640.29280.25610.04540.14440.27610.8099-0.07010.3192-0.1780.09110.2360.7829-0.02370.6408134.0996-20.807825.5821
210.23590.263-0.08370.2757-0.05710.04930.10240.01790.44030.0544-0.06490.36730.04870.15950.02571.19750.1622-0.22130.6795-0.22860.7616208.6157-22.369798.9354
220.05430.0543-0.11110.23670.0240.09680.0154-0.41950.07330.04120.2972-0.3282-0.36740.07930.37120.81390.0361-0.31850.7077-0.17380.8561221.2527-16.416387.7149
230.0605-0.0116-0.0651-0.0029-0.15330.1623-0.18470.2806-0.1898-0.32260.20160.21220.6416-0.2786-0.0180.8590.1207-0.33350.6404-0.08640.6559207.085-23.882570.3697
241.4602-0.61620.84070.8996-1.00441.16570.53510.0587-0.0950.39990.506-0.0147-0.0822-0.04270.31270.5236-0.01250.2030.5494-0.25110.5865203.6098-37.917243.7804
250.06020.0214-0.02060.0188-0.02050.0496-0.65460.1093-0.10310.12930.0799-0.0469-0.1850.35390.00230.52810.1172-0.15870.9909-0.11380.8087191.9844-28.640129.8729
260.35510.07160.18030.020.04160.0870.68270.006-0.2389-0.15340.6503-0.47630.16590.25120.03061.0220.11940.26250.83180.1040.7042186.0275-36.494319.6797
270.0338-0.0080.00180.0215-0.00290.00520.21930.07910.0539-0.06850.0944-0.2705-0.0881-0.24870.00080.56920.02160.07850.7480.07230.8847185.6349-35.771427.5448
280.0980.02010.04290.0384-0.01350.02670.1187-0.55750.44820.1777-0.1218-0.3928-0.34260.6125-0.0020.8234-0.20.02590.93550.13150.9763199.9778-34.768434.0762
290.013-0.0337-0.00140.0827-0.00270.0515-0.1833-0.31980.32320.2110.11760.3515-0.35250.16330.00051.39380.1438-0.11190.7298-0.09590.7726200.569-35.724540.7726
300.2273-0.11210.24550.0777-0.12320.1606-0.55180.0390.0744-0.2512-0.6149-0.5025-0.46670.1238-0.06240.7627-0.11540.21630.6762-0.03320.8486139.1834-42.569164.5386
310.01650.0020.02240.0029-0.00650.01620.00360.15910.2591-0.1726-0.1525-0.004-0.085-0.16530.00051.5448-0.1962-0.1871.32080.12651.014144.6756-47.767541.024
320.4188-0.2375-0.15070.12770.07260.0466-0.77210.1475-0.2364-0.60420.35210.32840.7347-0.1902-0.05631.1703-0.36580.05680.58820.21070.7702146.5916-47.08558.3756
330.00140.0118-0.00210.0162-0.00110.01930.0639-0.2801-0.30920.1361-0.48820.40040.0923-0.3594-0.00011.49460.124-0.08261.2498-0.19711.044151.3185-55.350161.2943
340.01320.00140.0150.0033-0.00260.0229-0.23950.06010.12050.0205-0.6760.08460.25510.0413-0.00380.60630.00610.29111.11770.47961.1021136.4168-46.948956.6194
350.0165-0.04290.05730.075-0.06140.04980.08660.38980.1615-0.0175-0.0269-0.18160.23820.17440.00021.0331-0.0384-0.0490.885-0.20860.8933194.944636.2924103.8399
360.20710.10640.10540.28890.08040.1684-0.2412-0.6640.003-0.4412-0.07090.0277-0.09940.295-0.03650.7359-0.38960.27770.71120.13190.3808160.771928.676989.8179
370.02680.0303-0.01940.081-0.09170.0951-0.219-0.3-0.0843-0.049-0.58860.31670.3686-0.2992-0.00060.70.07360.1271.2224-0.09150.7881162.943524.015194.3176
380.01840.0060.0260.04670.01410.02770.1652-0.0348-0.1949-0.07660.36050.255-0.1467-0.0738-0.00031.19410.1622-0.47241.18020.11571.748167.188218.3333102.8753
390.8713-0.17790.29180.09860.09290.44280.6215-0.29390.47390.00530.2706-0.0222-0.1704-0.09270.76210.0678-0.03790.74461.09960.40180.2488142.19227.748629.1972
400.1290.0136-0.0550.0006-0.00140.144-0.13480.0075-0.1285-0.093-0.1344-0.09020.2648-0.0927-0.152-0.11660.14750.48880.6446-0.04111.1148134.33987.97227.9092
410.0277-0.01260.03380.0135-0.00250.04130.04730.01220.1109-0.09290.07380.3304-0.18450.2390.00120.4985-0.21270.63430.49020.05661.3454129.521220.468835.5739
420.1230.0760.00060.05690.01260.0117-0.0243-0.1291-0.06850.0421-0.03270.015-0.0565-0.0342-0.02570.32870.39050.42361.2985-0.22890.7518128.286312.502539.2893
430.0656-0.0157-0.07190.04750.03830.08780.12320.2250.0757-0.00630.00210.0996-0.0307-0.22420.02720.151-0.19210.17391.03330.56060.9679133.27893.7436.5284
440.09120.15580.10560.29350.18470.1537-0.01620.0972-0.09040.0769-0.22450.10970.3139-0.00450.13910.2250.2420.33590.8341-0.06670.2575140.329812.007136.1913
450.0221-0.0531-0.03610.09920.06550.03730.04850.14-0.1197-0.07080.0590.0069-0.0874-0.01850.05830.2376-0.16050.45320.7352-0.01340.9418148.360227.476227.0517
460.22060.08010.01820.1260.09690.0588-0.02890.0441-0.0240.0176-0.12210.03260.1640.10.01140.2505-0.09080.8310.5755-0.05670.7138157.6122-8.062519.5817
470.0222-0.047-0.01440.08270.0126-0.00920.2722-0.07030.213-0.1272-0.1796-0.33070.0094-0.33220.00140.625-0.0946-0.00680.7779-0.07880.5347154.5598-30.459319.5052
480.1340.0187-0.02140.2350.17750.22220.1107-0.2362-0.6999-0.1203-0.05040.21660.090.120.26161.2229-0.2785-0.47880.54990.40241.1895143.8694-29.199227.5664
490.3020.01780.57820.06330.06091.32730.34430.5603-0.26430.05490.2770.02291.31130.04320.20680.6939-0.319-0.11920.5230.10850.892137.1162-26.134822.9538
500.02130.0204-0.0070.0172-0.00450.0017-0.0417-0.1039-0.01020.0197-0.0545-0.1920.0685-0.00220.00051.3040.0509-0.69810.9705-0.25551.4713161.084827.92074.5434
510.01360.00960.01670.01440.01540.01520.07510.04370.17810.17850.12950.2886-0.11570.4853-0.00112.24410.06570.44361.92580.5061.2697163.314234.0628.9494
520.0682-0.0077-0.01860.08530.02740.01170.1456-0.1171-0.01640.00660.1464-0.0457-0.2530.05320.11680.42550.03430.87671.1240.22961.7063164.820340.046613.2468
530.00950.0114-0.00740.0286-0.03010.02570.0991-0.00730.09720.0519-0.0426-0.0385-0.16170.12470.00061.535-0.1613-0.34110.81840.26950.8595164.03128.934513.2613
540.27840.0071-0.29030.3405-0.22970.6454-0.2827-0.00890.2597-0.2784-0.0095-0.4122-0.14010.0373-0.57860.63910.28990.10330.880.22580.7467155.776710.511110.0531
550.1030.0863-0.0420.0860.02760.0308-0.01180.097-0.4737-0.2409-0.3518-0.4345-0.143-0.0068-0.00421.38430.4520.34720.92150.02781.0896181.323713.242138.8131
560.02580.01610.08840.0110.04130.05450.59480.1110.0918-0.34680.5382-0.5914-0.280.24180.01741.9605-0.25830.94151.91540.2821.9569213.790512.376676.4069
570.0181-0.0610.00920.0580.009-0.0190.43230.1208-0.2496-0.18360.07380.05950.5937-0.40270.00080.89210.0410.09480.9916-0.07751.0104182.959511.770839.5743
580.0156-0.0540.03730.08290.106-0.0085-0.1091-0.52180.40570.7040.0107-0.5220.16340.66610.00231.8896-0.05330.27782.0771-0.07691.4407213.39699.920377.0585
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 260 )A3 - 260
2X-RAY DIFFRACTION2chain 'A' and (resid 261 through 573 )A261 - 573
3X-RAY DIFFRACTION3chain 'A' and (resid 574 through 1445 )A574 - 1445
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 212 )B20 - 212
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 297 )B213 - 297
6X-RAY DIFFRACTION6chain 'B' and (resid 298 through 372 )B298 - 372
7X-RAY DIFFRACTION7chain 'B' and (resid 373 through 433 )B373 - 433
8X-RAY DIFFRACTION8chain 'B' and (resid 434 through 560 )B434 - 560
9X-RAY DIFFRACTION9chain 'B' and (resid 561 through 643 )B561 - 643
10X-RAY DIFFRACTION10chain 'B' and (resid 644 through 776 )B644 - 776
11X-RAY DIFFRACTION11chain 'B' and (resid 777 through 887 )B777 - 887
12X-RAY DIFFRACTION12chain 'B' and (resid 888 through 982 )B888 - 982
13X-RAY DIFFRACTION13chain 'B' and (resid 983 through 1140 )B983 - 1140
14X-RAY DIFFRACTION14chain 'B' and (resid 1141 through 1224 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 39 )C3 - 39
16X-RAY DIFFRACTION16chain 'C' and (resid 40 through 84 )C40 - 84
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 104 )C85 - 104
18X-RAY DIFFRACTION18chain 'C' and (resid 105 through 151 )C105 - 151
19X-RAY DIFFRACTION19chain 'C' and (resid 152 through 214 )C152 - 214
20X-RAY DIFFRACTION20chain 'C' and (resid 215 through 268 )C215 - 268
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 65 )E2 - 65
22X-RAY DIFFRACTION22chain 'E' and (resid 66 through 137 )E66 - 137
23X-RAY DIFFRACTION23chain 'E' and (resid 138 through 215 )E138 - 215
24X-RAY DIFFRACTION24chain 'F' and (resid 72 through 86 )F72 - 86
25X-RAY DIFFRACTION25chain 'F' and (resid 87 through 103 )F87 - 103
26X-RAY DIFFRACTION26chain 'F' and (resid 104 through 116 )F104 - 116
27X-RAY DIFFRACTION27chain 'F' and (resid 117 through 127 )F117 - 127
28X-RAY DIFFRACTION28chain 'F' and (resid 128 through 137 )F128 - 137
29X-RAY DIFFRACTION29chain 'F' and (resid 138 through 155 )F138 - 155
30X-RAY DIFFRACTION30chain 'H' and (resid 2 through 60 )H2 - 60
31X-RAY DIFFRACTION31chain 'H' and (resid 61 through 82 )H61 - 82
32X-RAY DIFFRACTION32chain 'H' and (resid 83 through 126 )H83 - 126
33X-RAY DIFFRACTION33chain 'H' and (resid 127 through 140 )H127 - 140
34X-RAY DIFFRACTION34chain 'H' and (resid 141 through 146 )H141 - 146
35X-RAY DIFFRACTION35chain 'I' and (resid 2 through 52 )I2 - 52
36X-RAY DIFFRACTION36chain 'I' and (resid 53 through 74 )I53 - 74
37X-RAY DIFFRACTION37chain 'I' and (resid 75 through 111 )I75 - 111
38X-RAY DIFFRACTION38chain 'I' and (resid 112 through 120 )I112 - 120
39X-RAY DIFFRACTION39chain 'J' and (resid 1 through 10 )J1 - 10
40X-RAY DIFFRACTION40chain 'J' and (resid 11 through 17 )J11 - 17
41X-RAY DIFFRACTION41chain 'J' and (resid 18 through 31 )J18 - 31
42X-RAY DIFFRACTION42chain 'J' and (resid 32 through 38 )J32 - 38
43X-RAY DIFFRACTION43chain 'J' and (resid 39 through 46 )J39 - 46
44X-RAY DIFFRACTION44chain 'J' and (resid 47 through 55 )J47 - 55
45X-RAY DIFFRACTION45chain 'J' and (resid 56 through 65 )J56 - 65
46X-RAY DIFFRACTION46chain 'K' and (resid 1 through 9 )K1 - 9
47X-RAY DIFFRACTION47chain 'K' and (resid 10 through 34 )K10 - 34
48X-RAY DIFFRACTION48chain 'K' and (resid 35 through 63 )K35 - 63
49X-RAY DIFFRACTION49chain 'K' and (resid 64 through 114 )K64 - 114
50X-RAY DIFFRACTION50chain 'L' and (resid 25 through 29 )L25 - 29
51X-RAY DIFFRACTION51chain 'L' and (resid 30 through 44 )L30 - 44
52X-RAY DIFFRACTION52chain 'L' and (resid 45 through 54 )L45 - 54
53X-RAY DIFFRACTION53chain 'L' and (resid 55 through 59 )L55 - 59
54X-RAY DIFFRACTION54chain 'L' and (resid 60 through 70 )L60 - 70
55X-RAY DIFFRACTION55chain 'R' and (resid 1 through 10 )R1 - 10
56X-RAY DIFFRACTION56chain 'T' and (resid 1 through 15 )T1 - 15
57X-RAY DIFFRACTION57chain 'T' and (resid 16 through 28 )T16 - 28
58X-RAY DIFFRACTION58chain 'N' and (resid 3 through 17 )N3 - 17

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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