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- PDB-6upz: RNA polymerase II elongation complex with 5-guanidinohydantoin le... -

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基本情報

登録情報
データベース: PDB / ID: 6upz
タイトルRNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3
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/DNA / RNA polymerase II / 5-guanidinohydantoin / elongation complex / DNA lesion / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA 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 / Dual incision in TC-NER / transcription by RNA polymerase III / translesion synthesis / transcription by RNA polymerase I / 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 / : / : / : / : / : / : / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / DNA-directed RNA polymerase activity / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / 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
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit ...Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; 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 / Homeodomain-like / 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. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / 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
類似検索 - ドメイン・相同性
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 ...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: 3.1 Å
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: Proc.Natl.Acad.Sci.USA / 年: 2020
タイトル: RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
著者: Oh, J. / Fleming, A.M. / Xu, J. / Chong, J. / Burrows, C.J. / Wang, D.
履歴
登録2019年10月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年6月10日Provider: repository / タイプ: Initial release
改定 1.12023年10月11日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
改定 1.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
R: RNA
T: 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)488,02523
ポリマ－487,29913
非ポリマー72610
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)167.664, 222.901, 193.486
Angle α, β, γ (deg.)90.000, 100.850, 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: 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

#2: DNA鎖 Template strand DNA


分子量: 8745.599 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: 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 , 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-PPV / PYROPHOSPHATE / ピロりん酸


分子量: 177.975 Da / 分子数: 1 / 由来タイプ: 合成 / 式: H4O7P2 / 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: 3.64 Å3/Da / 溶媒含有率: 66.24 % / Mosaicity: 0.13 °
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: 5.0.3 / 波長: 0.9765 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2018年10月20日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9765 Å / 相対比: 1
反射解像度: 3.02→49.04 Å / Num. obs: 136357 / % possible obs: 100 % / 冗長度: 7.7 % / Biso Wilson estimate: 64.32 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.356 / Rpim(I) all: 0.137 / Rrim(I) all: 0.381 / Net I/σ(I): 7.7 / Num. measured all: 1050776 / Scaling rejects: 2
反射 シェル解像度: 3.02→3.07 Å / 冗長度: 7.7 % / Rmerge(I) obs: 3.318 / Num. measured all: 51823 / Num. unique obs: 6691 / CC1/2: 0.318 / Rpim(I) all: 1.272 / Rrim(I) all: 3.555 / Net I/σ(I) obs: 0.8 / % 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_2998精密化
Aimless0.7.3データスケーリング
PDB_EXTRACT3.25データ抽出
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
開始モデル: 6BLO

6blo


解像度: 3.1→49.039 Å / SU ML: 0.43 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 30.33 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2692 1849 1.47 %
Rwork0.2242 124145 -
obs0.2249 125994 99.95 %
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: 275.04 Å2 / Biso mean: 85.9092 Å2 / Biso min: 21.28 Å2
精密化ステップサイクル: final / 解像度: 3.1→49.039 Å
タンパク質核酸リガンド溶媒全体
原子数27999 1058 18 0 29075
Biso mean--132.24 --
残基数----3594
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.1-3.18380.38651410.35519448
3.1838-3.27750.3891420.33599533
3.2775-3.38320.36971410.30799495
3.3832-3.50410.32791430.28289549
3.5041-3.64440.31891420.26049568
3.6444-3.81020.28781410.23789499
3.8102-4.0110.26841420.21979545
4.011-4.26210.29491430.19519543
4.2621-4.5910.19571420.17429558
4.591-5.05260.19741420.17349541
5.0526-5.78270.26451430.20569599
5.7827-7.28180.28821420.22649585
7.2818-49.0390.21111450.19129682
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.94240.08510.40122.90850.28752.0756-0.21270.0821-0.22560.3608-0.2283-0.4591-0.03140.36040.0051.0132-0.0641-0.21151.04830.01361.224312.642511.585140.673
20.57370.41860.77020.31720.56831.05520.2783-0.03620.4442-0.04040.3149-0.5706-0.26460.53760.01162.3759-0.1963-0.26741.88290.03742.311345.986912.153773.5744
31.07030.77730.25891.20990.69050.4965-0.25690.11380.02780.347-0.3708-0.2128-0.20540.1692-0.0941.1681-0.2632-0.041.1212-0.10810.923614.820710.842138.873
40.98830.15061.1280.02560.09731.283-0.4432-0.4716-0.01420.74570.0708-0.7832-0.04890.4370.05751.7203-0.2866-0.44022.3310.03352.184945.361910.383874.7572
50.8076-0.05760.14690.5371-0.1561.05910.01230.17390.32070.0587-0.1221-0.4956-0.19220.6179-0.13710.5985-0.1121-0.19710.66790.16020.979641.68165.437336.056
60.3566-0.15190.0320.3921-0.13760.64170.1556-0.1383-0.18910.28670.0648-0.0660.4205-0.066-0.12980.8467-0.0875-0.22480.37160.0780.49771.2599-18.957458.5743
70.20520.14650.20460.93330.0390.31740.0328-0.07970.02860.5250.0633-0.01640.28440.0521-0.08391.33960.0553-0.40610.5213-0.00520.733520.4303-16.11681.2084
80.3628-0.06590.12881.15370.11011.086-0.031-0.14290.1510.56570.1603-0.30080.13830.2443-0.16320.98170.0912-0.46230.4849-0.0740.758627.9358-10.100269.1829
91.26350.2762-0.17971.3391-0.09171.0641-0.2534-0.21910.5258-0.20780.0518-0.1762-0.64160.2186-0.14310.776-0.1771-0.06130.35520.09520.59830.253343.576246.3132
100.2542-0.0179-0.09821.3491-0.34280.90950.1310.11290.29770.434-0.0424-0.1185-0.07110.2140.05310.689-0.1314-0.01030.36160.06880.53536.132837.022345.8842
110.38790.10630.4580.08540.46491.13760.02160.03640.13710.4277-0.0019-0.3214-0.26760.4043-0.05640.6997-0.1023-0.04070.5121-0.00660.648220.528536.420365.7018
121.15040.07780.08531.46020.1651.54620.039-0.08770.18060.51760.0427-0.1122-0.2547-0.1366-0.04960.558-0.00720.06710.40940.04440.3232-7.870734.155669.5555
130.14920.08790.11750.7694-0.00041.53780.08260.0154-0.04210.0094-0.0354-0.0653-0.01030.1145-0.09030.2992-0.0361-0.00630.37140.06740.3449-7.99449.78633.2854
140.9865-0.25090.38050.6445-0.26540.71540.04640.36410.10650.0555-0.1549-0.37560.06880.2908-0.12670.4781-0.0499-0.06430.42750.11360.573723.9513-4.766831.6544
151.70251.0089-0.6941.5673-1.00111.9838-0.0898-0.0976-0.361-0.3017-0.01330.1290.229-0.5061-0.13790.5623-0.2394-0.13740.59990.07570.4537-35.7549-12.718625.8826
160.54-0.42510.02440.49830.51671.43010.0745-0.0442-0.1529-0.05140.08570.00110.2654-0.316-0.09470.5333-0.0741-0.05460.54190.05770.3055-23.97644.117810.7749
170.692-0.04650.00691.39220.07391.2372-0.05010.34370.1041-0.51630.01730.4685-0.1406-0.4021-0.07830.52820.0457-0.12440.5840.03670.3789-29.139710.269615.8126
180.34360.3669-0.41670.90590.1541.52050.448-0.3372-0.53290.44390.186-0.06440.2755-0.5747-0.11330.8772-0.3376-0.19510.76260.1730.5697-35.9387-14.85449.7763
190.7297-0.74790.44882.5986-1.6192.63910.1774-0.2078-0.43350.18710.28630.34950.6317-0.3922-0.16390.7059-0.3141-0.12460.82760.11760.5892-39.2845-19.938240.675
201.4472-0.11630.41631.8189-0.3271.00920.23570.5052-0.1711-0.51820.10990.07480.7919-0.2139-0.09730.9593-0.1677-0.33520.6446-0.07570.5312-28.7495-23.102615.4926
211.02190.05260.90131.0176-0.51611.6666-0.1195-0.30180.02020.61980.1213-0.22-0.04110.04410.14561.67710.3184-0.8190.9238-0.14121.045739.5603-19.21695.3102
220.8832-0.03880.32250.9268-0.94911.0651-0.4928-0.61020.17230.51940.2117-0.14420.02510.0945-0.14632.0580.5425-0.70210.99370.04251.097541.6833-28.409298.4034
230.0056-0.00060.02780.0002-0.00970.15890.1184-0.09910.02150.549-0.1117-0.4190.18680.2642-0.11792.28090.3389-0.88721.6923-0.15141.202147.4849-15.4286106.7535
240.74970.01080.96850.78590.62573.89-0.096-0.1303-0.09490.2223-0.0511-0.37250.45710.429-0.75471.47140.5681-0.77790.8982-0.1611.100551.9816-32.882285.527
250.6520.010.67520.0152-0.11911.7814-0.1428-0.01230.27860.63490.3169-0.6154-0.15520.3247-0.12351.62810.4589-0.93351.2646-0.54851.492153.5169-18.558789.5279
260.0636-0.2027-0.04240.76590.06890.0652-0.0121-0.3730.20410.76110.016-0.13960.04610.4647-0.06441.3295-0.0392-0.89481.7835-0.6812.465962.3774-13.032290.3423
273.1502-0.7796-1.73550.9124-0.20093.00460.05250.08020.61680.49430.7212-1.0183-0.33560.98950.57141.15050.2283-0.83991.1053-0.41871.57151.6847-12.758386.0822
280.67120.5350.18790.49320.22211.6719-0.235-0.14970.01410.53590.0771-0.9810.33880.3238-0.34971.10080.229-0.60570.6104-0.03790.990840.8259-24.49968.8627
290.34410.1851-0.12680.2256-0.0910.05040.16010.2227-0.2972-0.19630.1691-0.97930.35910.73-0.23521.66280.3067-0.36171.5205-0.17971.518450.6607-30.491740.4514
301.6554-0.55210.69641.9345-1.01232.34740.10760.3514-0.12740.2820.1161-0.14120.78150.4206-0.20860.98610.2261-0.16630.4367-0.00430.526629.4063-33.313536.4498
313.2382-0.1990.03272.89140.13041.77580.24040.141-0.573-0.0967-0.0188-0.11750.68870.2286-0.15781.03230.3804-0.20430.8052-0.07520.667719.6413-36.01919.4893
320.5527-1.17291.80424.0524-4.08336.00350.07280.1045-0.5722-0.0553-0.1950.4370.7534-0.251-0.20541.24170.0865-0.18350.5265-0.03660.619618.571-35.095227.3809
337.16954.9618-1.70963.6209-1.29150.5972-0.06770.4917-0.9653-0.16070.0951-0.52460.77940.325-0.22981.4110.1809-0.19780.5495-0.15820.59627.0756-40.01828.5616
340.24910.2558-0.08350.3905-0.03690.08810.24520.1653-0.05890.1625-0.0103-0.6390.35330.807-0.23350.8670.05080.05640.6504-0.05270.781539.2465-29.874141.6539
356.75231.87090.24742.298-0.37761.71840.26110.1277-0.3715-0.19450.0578-0.35240.49070.7212-0.21270.85710.2131-0.26630.589-0.09160.871932.0048-38.387338.8733
361.1958-0.13540.08922.07870.0771.2267-0.077-0.4373-0.42190.36790.51570.17130.1853-0.0701-0.08951.0869-0.3963-0.11930.63070.31991.0033-27.0714-43.166164.959
370.41321.1781-1.36614.9409-4.19374.6311-0.0217-0.0038-0.4891-0.1809-0.21460.06340.7804-0.0409-0.13391.2715-0.1216-0.2110.64030.12520.9323-21.0966-48.275541.3051
380.93050.5842-0.67842.1802-0.11810.7693-0.0514-0.0754-0.48820.15850.0083-0.04570.6957-0.1545-0.29431.4139-0.712-0.30560.5050.51270.9224-19.8287-47.831258.5881
392.0004-0.6655-0.1862.3402-0.55723.63820.0359-0.4102-0.7471-0.0098-0.33160.14690.74910.2151-0.15011.402-0.2152-0.32170.74460.37151.1313-19.7605-53.15659.1325
400.0459-0.0846-0.12991.0397-0.20850.64730.33270.0168-0.06390.2543-0.0674-0.35960.10740.3857-0.02591.4995-0.0789-0.27420.6675-0.18130.911228.396636.3603104.1176
411.0991-0.2767-0.12891.39990.5222.77260.1568-0.5529-0.13650.2605-0.26720.1523-0.1021-0.2836-0.04360.8716-0.0061-0.04960.61330.00580.4681-7.948827.615293.0443
423.3963-1.6475-0.37774.06430.01081.95730.0375-0.3802-0.32670.59560.0259-0.16440.31990.1676-0.11160.87470.0427-0.12890.64960.04450.56840.119720.979795.4315
431.06580.2717-0.23040.5427-0.01272.110.25890.31090.0721-0.0760.04290.3877-0.3758-0.5498-0.0813-0.0575-0.0440.02210.61060.25030.3828-30.82411.734430.9649
441.4316-0.1604-0.540.54140.18810.3788-0.15520.0351-0.05770.1244-0.16240.1987-0.0258-0.1324-0.7601-0.048-0.38340.27340.72820.29670.4329-38.869312.320238.7067
451.0338-0.11210.08840.53790.01571.06010.21530.31590.1975-0.01440.00840.17150.0675-0.29840.0756-0.0417-0.17310.15890.4861-0.03390.3414-27.56189.239937.3299
463.4381-0.54461.35221.42590.4050.8177-0.01350.24420.2271-0.13740.1203-0.1079-0.1287-0.0585-0.21850.0954-0.02880.41690.3571-0.00540.3192-19.137926.864627.3557
470.0164-0.0199-0.0050.02450.01780.03210.18910.2678-0.505-0.0457-0.2755-0.36260.1782-0.392-0.16860.34260.11610.01760.50780.03480.3777-9.7269-8.447120.1149
482.2632-1.26910.80548.7547-1.81922.69060.68420.3328-0.595-0.05410.1321-0.42251.07820.30950.01840.5684-0.0636-0.18740.4706-0.14320.4254-13.8866-29.250420.1854
490.9532-0.21170.08870.7456-0.24080.5030.45060.3508-0.6810.1451-0.01630.27060.7894-0.35210.02620.7747-0.402-0.40780.4983-0.01090.6555-28.2329-28.223625.6099
500.91360.1170.52271.0587-1.05061.49680.1009-0.40540.60070.35780.0189-0.0009-0.529-0.1479-0.19191.51610.2196-0.28520.9530.05551.0377-7.469932.780512.492
510.92760.84621.21872.27150.32152.58910.0940.57190.055-0.50370.1286-0.4444-0.37330.3524-0.07221.6724-0.11520.08231.30730.36561.4723-1.999436.70877.9992
520.72560.7455-0.26412.0224-1.46761.5774-0.06910.18410.2516-0.29750.078-0.0788-0.44090.3714-0.12690.7761-0.1114-0.28690.73770.29810.161-8.348219.514412.3046
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 2 through 16 )N2 - 16
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 429 )A3 - 429
6X-RAY DIFFRACTION6chain 'A' and (resid 430 through 946 )A430 - 946
7X-RAY DIFFRACTION7chain 'A' and (resid 947 through 1257 )A947 - 1257
8X-RAY DIFFRACTION8chain 'A' and (resid 1258 through 1446 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 113 )B20 - 113
10X-RAY DIFFRACTION10chain 'B' and (resid 114 through 251 )B114 - 251
11X-RAY DIFFRACTION11chain 'B' and (resid 252 through 515 )B252 - 515
12X-RAY DIFFRACTION12chain 'B' and (resid 516 through 748 )B516 - 748
13X-RAY DIFFRACTION13chain 'B' and (resid 749 through 1071 )B749 - 1071
14X-RAY DIFFRACTION14chain 'B' and (resid 1072 through 1221 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 51 )C2 - 51
16X-RAY DIFFRACTION16chain 'C' and (resid 52 through 104 )C52 - 104
17X-RAY DIFFRACTION17chain 'C' and (resid 105 through 175 )C105 - 175
18X-RAY DIFFRACTION18chain 'C' and (resid 176 through 209 )C176 - 209
19X-RAY DIFFRACTION19chain 'C' and (resid 210 through 239 )C210 - 239
20X-RAY DIFFRACTION20chain 'C' and (resid 240 through 268 )C240 - 268
21X-RAY DIFFRACTION21chain 'E' and (resid 4 through 26 )E4 - 26
22X-RAY DIFFRACTION22chain 'E' and (resid 27 through 45 )E27 - 45
23X-RAY DIFFRACTION23chain 'E' and (resid 46 through 58 )E46 - 58
24X-RAY DIFFRACTION24chain 'E' and (resid 59 through 71 )E59 - 71
25X-RAY DIFFRACTION25chain 'E' and (resid 72 through 89 )E72 - 89
26X-RAY DIFFRACTION26chain 'E' and (resid 90 through 103 )E90 - 103
27X-RAY DIFFRACTION27chain 'E' and (resid 104 through 143 )E104 - 143
28X-RAY DIFFRACTION28chain 'E' and (resid 144 through 215 )E144 - 215
29X-RAY DIFFRACTION29chain 'F' and (resid 69 through 73 )F69 - 73
30X-RAY DIFFRACTION30chain 'F' and (resid 74 through 102 )F74 - 102
31X-RAY DIFFRACTION31chain 'F' and (resid 103 through 116 )F103 - 116
32X-RAY DIFFRACTION32chain 'F' and (resid 117 through 126 )F117 - 126
33X-RAY DIFFRACTION33chain 'F' and (resid 127 through 132 )F127 - 132
34X-RAY DIFFRACTION34chain 'F' and (resid 133 through 142 )F133 - 142
35X-RAY DIFFRACTION35chain 'F' and (resid 143 through 154 )F143 - 154
36X-RAY DIFFRACTION36chain 'H' and (resid 2 through 60 )H2 - 60
37X-RAY DIFFRACTION37chain 'H' and (resid 61 through 82 )H61 - 82
38X-RAY DIFFRACTION38chain 'H' and (resid 83 through 127 )H83 - 127
39X-RAY DIFFRACTION39chain 'H' and (resid 128 through 146 )H128 - 146
40X-RAY DIFFRACTION40chain 'I' and (resid 2 through 52 )I2 - 52
41X-RAY DIFFRACTION41chain 'I' and (resid 53 through 86 )I53 - 86
42X-RAY DIFFRACTION42chain 'I' and (resid 87 through 119 )I87 - 119
43X-RAY DIFFRACTION43chain 'J' and (resid 1 through 26 )J1 - 26
44X-RAY DIFFRACTION44chain 'J' and (resid 27 through 43 )J27 - 43
45X-RAY DIFFRACTION45chain 'J' and (resid 44 through 55 )J44 - 55
46X-RAY DIFFRACTION46chain 'J' and (resid 56 through 65 )J56 - 65
47X-RAY DIFFRACTION47chain 'K' and (resid 1 through 9 )K1 - 9
48X-RAY DIFFRACTION48chain 'K' and (resid 10 through 39 )K10 - 39
49X-RAY DIFFRACTION49chain 'K' and (resid 40 through 114 )K40 - 114
50X-RAY DIFFRACTION50chain 'L' and (resid 28 through 36 )L28 - 36
51X-RAY DIFFRACTION51chain 'L' and (resid 37 through 51 )L37 - 51
52X-RAY DIFFRACTION52chain 'L' and (resid 52 through 70 )L52 - 70

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万見について

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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