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- PDB-7rip: RNA polymerase II elongation complex with hairpin polyamide Py-Im... -

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基本情報

登録情報
データベース: PDB / ID: 7rip
タイトルRNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 soaked with CTP
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DNA BINDING PROTEIN/DNA/RNA / RNA polymerase II / elongation complex / polyamide / small molecule / TRANSCRIPTION / DNA BINDING PROTEIN-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 / 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
Gyrase A; domain 2 - #140 / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / 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 / Gyrase A; domain 2 ...Gyrase A; domain 2 - #140 / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / 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 / Gyrase A; domain 2 / 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 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 Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3
類似検索 - ドメイン・相同性
Chem-5N0 / PYROPHOSPHATE / 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 ...Chem-5N0 / PYROPHOSPHATE / 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: 3.3 Å
Model detailsRNA polymerase II, 5-guanidinohydantoin, elongation complex, DNA lesion
データ登録者Oh, J. / Dervan, P.B. / 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: Proc.Natl.Acad.Sci.USA / 年: 2022
タイトル: RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
著者: Oh, J. / Jia, T. / Xu, J. / Chong, J. / Dervan, P.B. / Wang, D.
履歴
登録2021年7月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年1月12日Provider: repository / タイプ: Initial release
改定 1.12022年7月27日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023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
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)490,30024
ポリマ－488,21613
非ポリマー2,08411
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)168.158, 223.041, 193.464
Angle α, β, γ (deg.)90.000, 100.670, 90.000
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: 3240.012 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: 9092.825 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: 6257.069 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: 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
#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: 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
#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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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: 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

#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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 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: 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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非ポリマー , 4種, 11分子

#14: 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
#15: 化合物 ChemComp-5N0 / 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid


分子量: 1358.427 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C64H75N23O12 / タイプ: SUBJECT OF INVESTIGATION
#16: 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
#17: 化合物 ChemComp-PPV / PYROPHOSPHATE


分子量: 177.975 Da / 分子数: 1 / 由来タイプ: 合成 / 式: H4O7P2

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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: 3.65 Å3/Da / 溶媒含有率: 66.31 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法
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: 1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2019年8月23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: 3.27→49.23 Å / Num. obs: 107923 / % possible obs: 100 % / 冗長度: 7.7 % / Biso Wilson estimate: 90.98 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.38 / Rpim(I) all: 0.147 / Rrim(I) all: 0.408 / Net I/σ(I): 6.7 / Num. measured all: 829562 / Scaling rejects: 27
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.27-3.337.74.0134147553630.2391.5464.3020.6100
17.91-49.237.30.03147996580.9990.0120.03451.995.3

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解析

ソフトウェア
名称バージョン分類
Aimless0.7.3データスケーリング
PHENIX1.13精密化
PDB_EXTRACT3.27データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7RIM

7rim


解像度: 3.3→49.225 Å / SU ML: 0.56 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 31.38 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2607 1942 1.85 %
Rwork0.219 102965 -
obs0.2198 104907 99.87 %
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: 312.41 Å2 / Biso mean: 111.4559 Å2 / Biso min: 36.59 Å2
精密化ステップサイクル: final / 解像度: 3.3→49.225 Å
タンパク質核酸リガンド溶媒全体
原子数28043 1033 117 0 29193
Biso mean--214.74 --
残基数----3601
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 (%)
3.3-3.38250.42681360.3889728599
3.3825-3.47390.38161390.35987328100
3.4739-3.57610.34441380.3287347100
3.5761-3.69150.41481360.29817305100
3.6915-3.82340.31081390.27727353100
3.8234-3.97640.32311390.25797322100
3.9764-4.15730.25921390.21667348100
4.1573-4.37640.2341390.19737372100
4.3764-4.65040.22661390.18187363100
4.6504-5.00910.25361400.17447363100
5.0091-5.51260.23291380.19137354100
5.5126-6.30890.24541390.20617380100
6.3089-7.94310.24321400.19547386100
7.9431-49.2250.18761410.17167459100
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1871-0.33090.7747.2623-1.84523.92970.79380.46560.1208-0.1602-0.6999-0.90.27180.6888-0.05330.99510.06340.0221.08790.07981.19112.595411.551640.7216
22.6245-2.13271.94341.8196-1.30011.97470.0339-0.4120.4264-1.0155-0.25530.0143-0.2025-0.06220.22642.1652-0.2651-0.25162.1714-0.05222.539843.919412.205470.3156
31.52641.4110.36715.289-0.43851.9277-0.2749-0.24660.7337-0.2683-0.0296-0.5442-0.20240.29740.41781.3295-0.0252-0.1741.11820.0310.97614.42910.897838.6181
44.6481.85046.50890.72132.58479.1479-0.95070.13770.8890.52130.2726-0.15311.12310.32230.04852.3197-0.2142-0.10192.04450.22242.085244.0611.717673.8718
50.97750.644-0.09481.71160.91542.18780.18340.29680.60910.1525-0.11-0.90080.29691.2892-0.09990.9099-0.191-0.45191.35340.07691.795953.28319.75840.767
61.57330.1152-0.04080.8314-0.20541.24150.17980.14240.06510.0844-0.0441-0.1070.40690.0675-0.10430.86530.0231-0.27550.45040.01770.610410.8503-13.041534.1462
70.2294-0.2385-0.13560.5713-0.17670.4220.1442-0.1438-0.17730.390.076-0.08910.4419-0.0542-0.20471.219-0.1081-0.29730.58620.0760.68460.8124-14.686866.2039
80.29730.04550.1040.73760.01210.60690.0427-0.1013-0.0730.38390.09870.01850.28580.0345-0.11541.60450.0671-0.49330.64340.02050.91719.3515-28.311171.1167
93.50490.40171.60575.40032.51795.61460.1996-0.2135-0.18010.8666-0.06-0.14440.76190.2727-0.22732.0285-0.0021-0.38690.6272-0.07870.834327.819413.0863108.659
100.3681-0.4613-0.34391.2011-0.24232.26670.0056-0.13540.28550.70590.1056-0.4156-0.15310.2115-0.15271.32710.1063-0.63330.6521-0.12191.049628.336-12.012666.7397
111.78960.4251-0.08171.415-0.13571.1765-0.03940.17150.6022-0.31110.0555-0.0386-0.54870.1674-0.00310.8471-0.09640.00450.41220.14670.68040.585241.929941.0864
124.18112.8792.83952.42523.0775.0440.11340.25890.00870.05560.18350.0080.86141.0299-0.36151.1819-0.1754-0.06230.571-0.13620.708723.927732.277873.4206
130.1749-0.1610.62590.2621-0.15962.0634-0.01450.02780.08810.4421-0.0294-0.3014-0.40250.33080.0350.7603-0.12-0.03420.514-0.00910.689717.877435.256562.6879
140.8945-0.03930.17011.78680.55391.84630.1508-0.19750.10250.38250.0117-0.0072-0.2116-0.4334-0.15080.5203-0.00070.12730.51510.08430.401-7.981731.123765.2099
150.83760.1890.29190.99740.05461.83880.06240.168-0.0989-0.0005-0.1057-0.2287-0.1230.11120.03960.2576-0.00240.07610.47690.08680.4181-7.9718.825431.5988
161.3041-0.72290.2940.8066-0.07520.95440.09930.30410.35190.1562-0.2227-0.59580.10240.45570.0660.7537-0.0098-0.19980.59620.17170.914324.5427-4.659431.2502
176.5595-0.0516-0.78999.8345-3.11796.674-0.0392-0.3794-0.28940.20440.25010.36690.1574-0.0652-0.28410.6592-0.3332-0.01941.16810.21210.6304-44.1124-16.537630.0101
182.90660.97350.48731.80340.9840.5548-0.09820.0088-0.5330.0399-0.1818-0.09650.35590.24290.2780.6058-0.1085-0.1610.8476-0.00960.6475-26.8366-9.070521.843
191.42010.69120.31553.56311.41173.3997-0.13350.40790.0922-0.48290.03650.34780.0177-0.22340.07490.46440.0253-0.03960.77730.1220.4027-26.80957.534313.7348
201.5733-0.25980.02211.4321-0.91471.50460.2069-0.0076-0.49220.04240.01840.27390.457-0.4631-0.17791.0662-0.3174-0.3350.86380.12890.7848-34.654-18.985537.1344
213.2315-1.0405-0.14271.6873-0.80694.065-0.6633-0.91330.18940.72290.5256-0.1910.38230.5966-0.23062.67090.4361-1.15721.182-0.20321.533742.0224-22.64794.2389
220.90240.40190.00470.26320.04780.0263-0.0481-0.66710.01280.4455-0.4377-0.2368-0.30360.7839-0.15492.34740.7169-1.23332.2222-0.15681.34347.0066-17.7203105.0306
238.6339-0.7228-0.86066.41833.38732.2179-0.4145-0.3205-0.52821.39190.2931-0.50420.77481.32740.07821.70110.4012-0.64381.18-0.14471.500753.4209-33.100483.7598
241.3630.1529-0.66710.2541-0.18680.4240.0392-0.35360.231.13950.5222-1.2778-0.67681.0507-0.50782.21830.1221-0.96751.9145-0.19911.688754.6642-17.942488.7639
250.0081-0.0022-0.01780.05160.02750.0370.6230.1723-0.536-0.2392-0.05450.08150.79781.0251-0.61211.87160.3152-1.14813.286-0.77323.087763.3224-12.022288.7543
266.8185-2.8389-4.49264.29080.38043.66470.648-0.10660.1009-0.04330.7558-0.6928-0.13751.8364-0.81241.5269-0.0201-0.80331.8088-0.42851.882653.5746-12.202887.8064
273.3816-2.72860.66622.5043-0.03521.50990.94140.23790.2127-0.48460.0987-0.68680.92131.2571-0.89192.30840.2235-0.87262.1983-0.75792.45660.0592-9.118879.8022
280.6584-0.12990.24412.25651.14443.5747-0.0257-0.1111-0.02210.14950.0627-0.926-0.1670.8-0.08521.41130.3705-1.04740.8614-0.03671.334944.4152-21.811272.0356
293.51293.4640.38943.63360.34091.8996-0.321-0.05090.45321.14950.1924-0.551-0.11150.26360.03721.66090.4053-0.59440.73-0.11271.046735.4998-26.004567.498
300.0148-0.0469-0.01980.26270.0480.02810.07170.1615-0.6167-0.46720.2002-0.10790.33520.1357-0.20462.28510.6963-0.51681.72810.152.44551.1423-31.534639.5269
314.23864.8079-1.75375.5946-1.17246.003-0.34640.0973-1.64430.0910.0623-0.57941.22280.57140.19171.60340.3573-0.34990.7805-0.11510.946135.304-38.678643.727
323.05210.609-2.13513.06572.7439.8385-0.23880.409-0.3385-0.3341-0.53620.1797-0.10010.54540.51971.02330.2385-0.13480.71880.06010.75325.284-29.049930.5311
339.32513.0770.5249.18930.26486.88730.26261.3298-0.6759-0.1918-0.2685-0.32030.68810.37420.07761.50280.3677-0.38141.12630.04540.802719.7449-35.980519.44
346.224-5.6045.95755.1187-5.38245.70430.14710.2892-0.4228-0.2271-0.16430.93840.5883-0.85940.07051.38440.1065-0.28780.7849-0.03850.778318.7464-35.170427.2762
351.15740.29350.03771.16290.26883.57740.32710.2667-0.4667-0.61360.4422-0.87120.1770.7914-0.71271.38640.1915-0.09670.9336-0.18741.253835.8199-34.305237.258
366.01234.09871.05216.1846-2.20322.6999-0.24711.1582-1.0947-0.4317-0.2174-0.02361.23410.51970.13571.19980.2999-0.13080.8245-0.12220.970427.3705-40.469938.0143
372.9422-1.8236-2.51643.59840.70656.35440.2629-0.1189-0.55090.83270.38330.27210.9629-0.1477-0.2471.657-0.4298-0.33991.00950.54981.8665-26.3999-49.273164.6391
382.952-1.12390.45298.7505-2.37463.9033-0.4153-0.1581-0.14310.5388-0.18220.1247-0.3252-0.2320.55571.4595-0.5418-0.0461.1610.18781.1342-24.3201-34.26865.076
394.31670.51490.7366.8301-0.36072.68940.2659-0.802-1.13311.532-0.20170.01230.3415-0.1272-0.09911.4749-0.5789-0.2110.75310.28391.448-24.7597-47.314768.9062
404.0193-0.2448-1.48193.0464-0.83764.2042-0.7485-0.1099-0.4909-0.01540.37990.775-0.2007-0.35490.52861.386-0.2226-0.42350.8140.28831.2839-31.3397-42.697161.881
412.29033.8622-4.41119.6528-7.72888.6358-0.12320.2752-0.2564-1.03660.20990.43790.6417-0.0301-0.04021.7556-0.1885-0.22330.9764-0.03911.3176-20.7824-48.584341.2734
424.07662.90350.15814.267-0.4240.7017-0.61920.9717-0.0904-1.16280.56710.47770.2984-0.36250.17171.6889-1.0441-0.21141.09960.09871.6385-31.2914-51.509242.1532
434.8833-0.20490.17053.36640.62624.686-0.3997-0.2806-0.8889-0.49970.0750.00130.30030.12490.14661.5674-0.4269-0.34410.85640.45611.6995-18.0174-46.828658.606
443.68770.6405-2.12065.481-2.68622.2177-0.655-0.5893-0.60430.67390.17680.31420.79810.20290.33191.8887-0.3981-0.24021.14480.54471.0309-13.4019-49.761866.8628
455.00592.0873-4.57028.0612-2.11054.18040.3258-1.0846-1.35991.2438-0.4834-1.03640.32060.55920.54221.5812-0.6978-0.32941.09950.3361.0372-17.5381-44.285264.3919
463.2725-2.66984.05716.2486-3.24086.9971-0.4068-0.5637-2.01430.00550.00950.95811.7293-0.04170.26722.2211-0.0081-0.2141.18380.50771.3624-14.6358-55.791260.1265
475.8546-3.8513-1.53089.31482.0353.2274-0.5843-0.4857-1.7768-0.0135-0.38060.06480.5967-0.96250.50381.5682-0.4312-0.26920.98650.36361.2742-29.4596-48.672256.3812
480.22070.0328-0.48764.0594-1.19591.55060.22490.0668-0.20640.4362-0.0269-0.5637-0.03230.7604-0.04911.8569-0.0457-0.37650.8344-0.18511.00728.612436.6431104.1586
492.6607-1.415-1.85453.282.12558.78090.3195-0.4089-0.4413-0.0084-0.18840.119-0.83311.0497-0.12871.0306-0.1581-0.07780.7977-0.02360.6884-7.229627.107192.9094
502.7436-4.3202-1.55117.79190.8787.10470.5548-0.2667-0.53420.3507-0.0789-0.91591.09170.4992-0.55141.2411-0.0347-0.25090.87980.05080.90.536620.950395.5674
514.10873.60440.33225.6099-1.48161.55780.0760.45870.3733-0.1246-0.34940.4464-0.458-0.1253-0.0720.51790.18460.15850.66940.0140.3499-26.54776.40929.6159
526.22270.6223-2.51036.11882.0334.71820.15930.62430.87560.0364-0.42430.7146-1.0915-0.8165-0.03030.48290.01830.15320.65880.12290.8509-36.946418.020935.0728
532.10211.2287-0.26590.7972-0.00550.33810.17580.04570.58570.1712-0.16520.41820.0298-0.1888-0.0372-0.26680.0620.27471.09950.13440.4377-32.07048.737438.0076
545.3919-1.85644.28024.407-3.50844.4974-0.1263-0.23860.9254-0.54510.2275-0.3941-0.21730.0478-0.04690.49680.01880.11350.5905-0.02140.8543-19.120726.76627.4572
550.32960.22990.21760.64670.47770.36490.39750.2303-0.41980.71630.281-0.68650.131-0.9056-0.50421.06140.0555-0.22910.94880.13060.7672-9.5082-8.28920.0642
565.16312.8429-0.73184.4118-5.20188.19530.29480.7272-0.7948-0.6243-0.0425-1.53510.297-0.0071-0.01840.8724-0.0374-0.0150.879-0.07060.8511-12.8929-25.058215.5023
573.37314.582-0.86257.828-4.13935.72880.0876-0.4182-0.79640.7161-0.6203-0.38710.69220.65990.42391.89780.044-0.13851.31550.03191.2549-11.2001-43.401928.1031
581.97471.9643-1.56476.5976-1.13344.24960.52340.01980.11530.09980.26880.5781.1836-0.4283-0.53541.1107-0.1373-0.46730.7113-0.02920.7489-21.5399-27.807925.9952
594.0063.8758-1.15769.1944-1.06723.79020.51590.0307-0.6803-0.2365-0.19710.29520.1138-1.0523-0.33481.1074-0.11-0.40030.84220.05980.7389-17.5255-29.163529.6076
602.80461.0201-0.85043.19971.54221.47110.53750.4016-1.20150.1712-0.0689-0.35331.1705-0.6257-0.28091.5065-0.2248-0.50180.8828-0.10410.9972-18.4811-37.388925.7732
611.1366-0.27510.53681.2277-0.08451.28830.45190.3716-0.6160.2583-0.06020.49070.6144-0.2210.83790.4941-0.5036-0.14411.0126-0.00591.2346-39.0526-23.912522.0091
627.29242.70270.17284.8157-3.4363.23810.6368-0.80760.9380.51020.24930.1595-1.1307-0.1324-0.68562.65880.1412-0.39881.0781-0.1111.5113-7.680132.902812.7037
630.5916-0.8682-0.61271.37080.34844.1514-0.30960.22140.1242-1.0798-0.2857-1.1941-0.99052.41450.45732.2645-0.42440.21332.44680.95422.0095-0.436834.14716.0496
645.331-0.15921.05490.1064-0.34731.1917-0.85620.52271.2697-0.96160.17571.1449-2.21850.03420.44081.8306-0.1582-0.60761.4290.46441.2283-3.664336.846914.2081
652.64722.2712-2.71932.1455-2.41522.87830.03880.5671-0.006-0.4984-0.2048-0.3234-0.25180.2410.33420.99110.0707-0.21591.14540.28670.7506-11.710911.411910.3129
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'R' and (resid 1 through 10 )R1 - 10
2X-RAY DIFFRACTION2chain 'T' and (resid 3 through 17 )T3 - 17
3X-RAY DIFFRACTION3chain 'T' and (resid 18 through 28 )T18 - 28
4X-RAY DIFFRACTION4chain 'N' and (resid 4 through 17 )N4 - 17
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 281 )A3 - 281
6X-RAY DIFFRACTION6chain 'A' and (resid 282 through 590 )A282 - 590
7X-RAY DIFFRACTION7chain 'A' and (resid 591 through 922 )A591 - 922
8X-RAY DIFFRACTION8chain 'A' and (resid 923 through 1164 )A923 - 1164
9X-RAY DIFFRACTION9chain 'A' and (resid 1165 through 1269 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 1270 through 1446 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 212 )B20 - 212
12X-RAY DIFFRACTION12chain 'B' and (resid 213 through 293 )B213 - 293
13X-RAY DIFFRACTION13chain 'B' and (resid 294 through 528 )B294 - 528
14X-RAY DIFFRACTION14chain 'B' and (resid 529 through 796 )B529 - 796
15X-RAY DIFFRACTION15chain 'B' and (resid 797 through 1072 )B797 - 1072
16X-RAY DIFFRACTION16chain 'B' and (resid 1073 through 1221 )B0
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 26 )C2 - 26
18X-RAY DIFFRACTION18chain 'C' and (resid 27 through 51 )C27 - 51
19X-RAY DIFFRACTION19chain 'C' and (resid 52 through 175 )C52 - 175
20X-RAY DIFFRACTION20chain 'C' and (resid 176 through 268 )C176 - 268
21X-RAY DIFFRACTION21chain 'E' and (resid 4 through 38 )E4 - 38
22X-RAY DIFFRACTION22chain 'E' and (resid 39 through 59 )E39 - 59
23X-RAY DIFFRACTION23chain 'E' and (resid 60 through 71 )E60 - 71
24X-RAY DIFFRACTION24chain 'E' and (resid 72 through 89 )E72 - 89
25X-RAY DIFFRACTION25chain 'E' and (resid 90 through 103 )E90 - 103
26X-RAY DIFFRACTION26chain 'E' and (resid 104 through 117 )E104 - 117
27X-RAY DIFFRACTION27chain 'E' and (resid 118 through 130 )E118 - 130
28X-RAY DIFFRACTION28chain 'E' and (resid 131 through 194 )E131 - 194
29X-RAY DIFFRACTION29chain 'E' and (resid 195 through 215 )E195 - 215
30X-RAY DIFFRACTION30chain 'F' and (resid 69 through 73 )F69 - 73
31X-RAY DIFFRACTION31chain 'F' and (resid 74 through 86 )F74 - 86
32X-RAY DIFFRACTION32chain 'F' and (resid 87 through 102 )F87 - 102
33X-RAY DIFFRACTION33chain 'F' and (resid 103 through 116 )F103 - 116
34X-RAY DIFFRACTION34chain 'F' and (resid 117 through 126 )F117 - 126
35X-RAY DIFFRACTION35chain 'F' and (resid 127 through 147 )F127 - 147
36X-RAY DIFFRACTION36chain 'F' and (resid 148 through 154 )F148 - 154
37X-RAY DIFFRACTION37chain 'H' and (resid 2 through 16 )H2 - 16
38X-RAY DIFFRACTION38chain 'H' and (resid 17 through 30 )H17 - 30
39X-RAY DIFFRACTION39chain 'H' and (resid 31 through 43 )H31 - 43
40X-RAY DIFFRACTION40chain 'H' and (resid 44 through 60 )H44 - 60
41X-RAY DIFFRACTION41chain 'H' and (resid 61 through 82 )H61 - 82
42X-RAY DIFFRACTION42chain 'H' and (resid 83 through 92 )H83 - 92
43X-RAY DIFFRACTION43chain 'H' and (resid 93 through 106 )H93 - 106
44X-RAY DIFFRACTION44chain 'H' and (resid 107 through 118 )H107 - 118
45X-RAY DIFFRACTION45chain 'H' and (resid 119 through 127 )H119 - 127
46X-RAY DIFFRACTION46chain 'H' and (resid 128 through 140 )H128 - 140
47X-RAY DIFFRACTION47chain 'H' and (resid 141 through 146 )H141 - 146
48X-RAY DIFFRACTION48chain 'I' and (resid 2 through 52 )I2 - 52
49X-RAY DIFFRACTION49chain 'I' and (resid 53 through 87 )I53 - 87
50X-RAY DIFFRACTION50chain 'I' and (resid 88 through 119 )I88 - 119
51X-RAY DIFFRACTION51chain 'J' and (resid 1 through 14 )J1 - 14
52X-RAY DIFFRACTION52chain 'J' and (resid 15 through 31 )J15 - 31
53X-RAY DIFFRACTION53chain 'J' and (resid 32 through 55 )J32 - 55
54X-RAY DIFFRACTION54chain 'J' and (resid 56 through 65 )J56 - 65
55X-RAY DIFFRACTION55chain 'K' and (resid 1 through 9 )K1 - 9
56X-RAY DIFFRACTION56chain 'K' and (resid 10 through 23 )K10 - 23
57X-RAY DIFFRACTION57chain 'K' and (resid 24 through 29 )K24 - 29
58X-RAY DIFFRACTION58chain 'K' and (resid 30 through 52 )K30 - 52
59X-RAY DIFFRACTION59chain 'K' and (resid 53 through 69 )K53 - 69
60X-RAY DIFFRACTION60chain 'K' and (resid 70 through 82 )K70 - 82
61X-RAY DIFFRACTION61chain 'K' and (resid 83 through 114 )K83 - 114
62X-RAY DIFFRACTION62chain 'L' and (resid 28 through 36 )L28 - 36
63X-RAY DIFFRACTION63chain 'L' and (resid 37 through 46 )L37 - 46
64X-RAY DIFFRACTION64chain 'L' and (resid 47 through 58 )L47 - 58
65X-RAY DIFFRACTION65chain 'L' and (resid 59 through 70 )L59 - 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

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