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- PDB-6uq3: 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: 6uq3
タイトルRNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 5
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 / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / 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 / nucleus / metal ion binding / 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 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 ...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 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Gyrase A; domain 2 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / Homeodomain-like / 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, 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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 / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus
類似検索 - ドメイン・相同性
PYROPHOSPHATE / DNA / DNA (> 10) / RNA / RNA (> 10) / 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 ...PYROPHOSPHATE / DNA / DNA (> 10) / RNA / RNA (> 10) / 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: 3.47 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

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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)488,33123
ポリマ－487,60513
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)169.189, 222.584, 194.612
Angle α, β, γ (deg.)90.000, 101.340, 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: 3570.202 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-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
#15: 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
#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

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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: 3.68 Å3/Da / 溶媒含有率: 66.61 % / Mosaicity: 0.27 °
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: 5.0.2 / 波長: 0.97665 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2019年3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: 0.97665 Å / 相対比: 1
反射解像度: 3.47→49.27 Å / Num. obs: 91067 / % possible obs: 100 % / 冗長度: 7 % / Biso Wilson estimate: 75.41 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.58 / Rpim(I) all: 0.235 / Rrim(I) all: 0.626 / Net I/σ(I): 4.9 / Num. measured all: 636868 / Scaling rejects: 1
反射 シェル解像度: 3.47→3.53 Å / 冗長度: 7.2 % / Rmerge(I) obs: 2.776 / Num. measured all: 32397 / Num. unique obs: 4503 / CC1/2: 0.333 / Rpim(I) all: 1.105 / Rrim(I) all: 2.99 / Net I/σ(I) obs: 0.9 / % possible all: 100

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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
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: 3.47→49.268 Å / SU ML: 0.51 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 31.42 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2857 2000 2.2 %
Rwork0.2338 88995 -
obs0.235 90995 99.9 %
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: 288.67 Å2 / Biso mean: 98.3183 Å2 / Biso min: 11.95 Å2
精密化ステップサイクル: final / 解像度: 3.47→49.268 Å
タンパク質核酸リガンド溶媒全体
原子数28025 1077 18 0 29120
Biso mean--139.16 --
残基数----3599
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
3.47-3.55680.40581420.34756310
3.5568-3.65290.38931420.32746325
3.6529-3.76030.38081440.3086357
3.7603-3.88170.34541420.29996338
3.8817-4.02030.32411420.27186333
4.0203-4.18120.28241420.24086329
4.1812-4.37140.28141440.21666365
4.3714-4.60170.25831420.21246342
4.6017-4.88980.23341420.19816341
4.8898-5.26690.29971440.21396388
5.2669-5.79620.29381430.22586371
5.7962-6.63320.28631430.22996374
6.6332-8.35060.2531430.19816379
8.3506-49.2680.20651450.18326443
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)
10.78960.71370.39381.6217-0.19990.5055-0.15960.4525-0.7816-0.2040.0436-0.5553-0.3880.58350.18211.0118-0.13630.19931.15550.10981.083912.68711.897941.0037
20.37360.18920.60360.09820.31951.0320.16760.01910.3606-0.17390.4433-0.42940.09450.0942-0.27581.7639-0.15750.06932.13340.1152.136445.649412.263474.0966
31.11370.66050.19610.53230.27070.2036-0.5421-0.5297-0.0602-0.106-0.0855-0.2743-0.2693-0.02480.38981.31350.1694-0.161.1132-0.14951.108715.152611.211339.5391
41.5040.0745-0.35791.345-0.31821.20340.3195-0.18830.36790.35060.5869-0.3313-0.32180.1053-0.55341.3567-0.2146-0.16882.0723-0.13231.950836.69611.123967.2441
53.22762.2482-0.37152.01330.93093.20490.27170.60980.102-0.23920.07790.34-0.1093-0.4974-0.14932.52580.3889-0.18482.24850.1792.884454.42919.852486.4138
60.93050.2859-0.24440.66120.14270.99380.1130.19530.46050.0554-0.2216-0.36170.04860.77820.12660.4136-0.1216-0.14960.66570.06320.905853.27368.2842.9555
70.74340.00220.17910.5491-0.19060.70060.19410.1625-0.03960.1406-0.0443-0.15950.39790.1299-0.01290.64270.0007-0.27080.27950.0480.473912.8895-10.3734.3605
80.38520.12750.23990.80930.0890.77540.1093-0.0987-0.00160.50890.0847-0.35710.1836-0.1327-0.05440.8251-0.0944-0.15380.34640.1240.3096-5.925-6.644766.7099
90.5426-0.0077-0.06811.2054-0.61170.5566-0.06250.0145-0.0927-0.0270.09870.15130.0448-0.0373-0.0691.27130.0536-0.52780.40250.0130.699517.9296-38.907363.5492
100.54330.04330.24821.67360.42150.86320.0604-0.17460.10490.3552-0.19320.370.1477-0.166401.15490.0013-0.25210.43150.03320.587922.19786.5602103.5522
110.330.71530.59312.8941.86561.314-0.15570.03320.11450.35510.18630.0513-0.13420.10740.04731.43620.1199-0.34040.4518-0.08050.686723.47170.207898.2755
120.4986-0.16740.4990.1867-0.11821.0775-0.0685-0.0030.12180.40230.0329-0.4347-0.18860.14520.08810.8893-0.0082-0.43670.4095-0.07960.74431.0042-11.862259.2063
130.73990.1817-0.03460.57240.00440.61440.04880.010.3244-0.07950.08420.014-0.1940.2553-0.09260.6865-0.1377-0.050.37120.14020.52880.17842.190541.4688
141.87890.61580.98250.66990.85261.1149-0.3130.08030.15050.1230.241-0.96290.06880.1530.26351.3919-0.1008-0.32350.419-0.12830.849320.115529.173471.9586
150.3304-0.10940.60840.38190.13621.33670.0010.01320.18020.49630.0288-0.2242-0.30810.2077-0.05250.5945-0.0993-0.15430.32730.01220.639420.81638.398165.634
160.91020.35370.28121.4773-0.11130.9499-0.0599-0.25590.16810.56890.0386-0.2859-0.3198-0.2342-0.05760.24810.08480.26870.41790.04880.1989-7.382333.261269.0971
170.1748-0.07940.20250.33380.00360.2145-0.03020.02120.1517-0.2825-0.1978-0.0657-0.17580.0784-0.0126-1.0433-0.48371.02150.13480.4801-0.2974-6.467510.80731.9621
180.4908-0.18760.32940.4035-0.00250.3473-0.10040.36390.34970.15090.0338-0.2390.0470.11580.00120.4972-0.1093-0.08460.35560.11960.503217.3839-4.133634.5888
191.60870.8631-0.78291.592-0.83571.3943-0.1218-0.1377-0.3139-0.0672-0.150.13930.3781-0.11960.00580.47-0.3419-0.26980.50640.08030.3501-35.8922-12.517125.7297
200.3886-0.71410.00361.3928-0.11391.77270.0050.2120.0091-0.3224-0.05110.29350.5574-0.1925-0.03790.3312-0.07430.14460.51470.03480.0997-23.54632.689911.0034
210.58380.1325-0.01721.00320.27770.71630.25160.23480.0630.0618-0.09950.00880.0013-0.32580.03470.73230.174-0.19250.55920.08150.3423-28.863711.073515.0585
220.88750.07910.58020.9261-0.22850.8650.1310.0151-0.16680.02740.07460.15740.2467-0.1501-0.12490.6561-0.2396-0.1570.46980.09840.4336-35.1003-18.671936.9094
232.50550.2835-0.78840.4892-0.19023.08330.0674-0.60450.14120.3545-0.1672-0.0322-0.0391-0.02690.21341.59890.2257-0.58310.9288-0.12480.968639.8899-22.679695.5227
240.33130.1970.02940.87240.42270.6278-0.2783-0.49840.16180.39470.479-0.2588-0.4425-0.0423-0.1831.57790.4455-0.84291.29-0.31441.290249.4306-21.78495.7988
252.91640.0033-1.4041-0.002-0.00330.67240.0038-0.26670.99440.12940.6851-0.78440.12910.63320.86211.04610.0301-0.71741.3666-0.26771.84956.73-12.301287.2188
260.31590.26330.13470.29680.38511.3012-0.084-0.06920.13980.30510.0074-0.4269-0.1290.2057-0.08211.08820.0938-0.62370.53050.03630.992640.576-23.706570.7334
270.7010.5370.44260.42720.48181.54340.0109-0.0135-0.2976-0.04530.0987-0.08050.0180.0999-0.02771.44030.1222-0.16091.5116-0.15581.769150.5509-30.076440.5243
280.11030.2792-0.01271.1077-0.22611.4892-0.08170.2268-0.26660.08360.2329-0.37090.4389-0.0542-0.00881.12960.1472-0.21240.4886-0.01570.719634.8414-38.511644.1897
291.95930.2401-0.44252.05680.55377.26310.09510.2109-0.319-0.5349-0.1671-0.18160.1575-0.1622-0.05350.52380.1752-0.19810.47270.06860.532225.0414-28.902530.7566
303.8013-1.26290.42331.36441.22962.0364-0.15690.2255-0.23180.0866-0.01190.28450.14430.2662-0.04290.85190.3549-0.20410.965-0.01910.695919.516-35.757519.6612
310.81740.33130.77211.7016-1.00541.8437-0.19670.0792-0.3426-0.00280.02730.1268-0.1576-0.0850.05281.21890.242-0.24730.6588-0.01890.61221.7536-36.778927.9555
320.2246-0.066-0.28190.47710.48440.70310.26220.12720.15270.0465-0.1159-0.2239-0.16750.2221-0.07440.5219-0.11240.37110.842-0.02430.721939.2299-29.657441.7882
334.71510.6916-0.4490.8464-0.66631.81250.2922-0.057-0.0406-0.14820.2022-0.0226-0.0110.6818-0.2440.31960.20820.09840.625-0.17330.810432.0125-38.120839.0465
340.8098-0.185-0.27522.1415-0.1640.6925-0.0029-0.1998-0.37090.2885-0.08730.05670.5752-0.01730.06550.7507-0.2339-0.16560.6370.40990.9974-26.335-42.112263.6809
351.4329-1.00730.5751.6583-0.7961.99190.2535-0.4724-0.15670.69760.13820.3738-0.0937-0.185-0.06940.5715-0.39790.13270.459-0.03360.6774-28.1747-42.488166.6463
360.71050.2020.84651.954-0.76081.562-0.18140.2146-0.4309-0.317-0.0569-0.21190.2530.0830.12951.3777-0.3827-0.30390.64290.12670.8-23.8612-49.107248.9314
371.447-0.0074-1.24316.3812-7.01648.79710.07590.636-0.4147-0.5311-0.10980.07370.8124-0.1919-0.05481.3354-0.5858-0.00950.9563-0.23551.2232-31.1196-50.406140.5457
383.5041-0.6594-1.30344.59330.59164.8321-0.01760.2234-0.4596-0.0214-0.09550.29490.3213-0.50640.07340.7287-0.2188-0.140.64330.18141.1628-28.0135-46.074553.4155
392.6836-0.9927-0.29910.36650.10420.6377-0.1724-0.3005-0.52570.34320.23460.04850.63460.1629-0.02941.3133-0.3095-0.43620.59750.26740.6232-14.2942-47.362265.2618
402.3832-1.09961.48562.40250.06221.2784-0.2576-0.136-0.1091-0.0137-0.09160.11930.1830.01530.17521.0998-0.1097-0.07520.98220.26130.821-15.2208-55.758260.1417
411.0794-0.62420.091.0819-0.1132.81250.0208-0.1147-0.1586-0.2466-0.07720.16730.0753-0.3178-0.30171.0354-0.0361-0.26660.88480.49590.9703-29.9969-48.409856.3355
420.12450.1201-0.26431.591-0.05880.57440.0833-0.09070.13980.15320.18650.1065-0.05140.3238-0.12111.22880.0083-0.19260.5208-0.14880.721627.51136.3336104.938
432.1973-0.4989-0.31742.04330.24171.97470.3839-0.4494-0.4235-0.1054-0.14750.1086-0.16110.2844-0.18650.9134-0.0766-0.24760.66480.04320.4814-4.653924.311494.6897
440.57690.0194-0.19270.1439-0.44321.39280.1733-0.07910.1882-0.11340.05230.04340.0456-0.32140.41350.32450.01950.18610.53520.26330.2567-25.09297.421529.5666
451.69611.1692-0.38312.38280.16011.90190.2420.22750.53150.01590.08490.2966-0.248-0.07910.0654-0.0058-0.0441-0.03090.22860.07040.2753-35.143215.474332.0939
460.2049-0.04070.01930.10080.03550.1054-0.0365-0.04640.04280.0113-0.0090.01610.0111-0.0532-0.76910.1645-0.11940.28060.56010.02030.4493-38.908711.733439.056
470.0845-0.0770.08420.1367-0.06120.08550.12940.0710.21940.02880.0320.0514-0.03160.05330.37980.07880.18460.10680.4417-0.06780.2628-27.77929.381737.437
482.4379-0.94321.56074.7537-1.32021.65970.13660.15550.424-0.18240.1593-0.0837-0.15510.09730.03930.31280.08760.16130.37740.040.53-19.265326.991227.5806
490.0259-0.10450.10970.4126-0.42850.4433-0.00460.2824-0.0379-0.1269-0.1584-0.26750.00730.0659-0.06440.14790.18660.17480.42810.0980.5275-9.7427-8.120420.0602
501.48660.29880.38123.3416-0.42171.36870.2166-0.1165-0.0265-0.14760.0982-0.4004-0.05790.23540.44670.13630.11990.16030.54080.00950.1372-13.7615-28.976520.0598
510.9471-0.8540.50172.69120.57952.1038-0.08860.1765-0.00570.1756-0.20020.45790.1981-0.12240.03580.934-0.261-0.19630.4761-0.05280.4677-26.3119-28.043328.8412
521.3058-0.2282-0.60281.33590.21440.6420.2630.2022-0.1386-0.20470.24420.10710.3958-0.27820.01120.8051-0.1526-0.2680.52090.04040.3984-17.9287-28.883329.5763
531.6974-0.5402-0.33760.6097-0.38130.60540.2860.2493-0.28110.12740.01940.20270.5139-0.48050.09620.5982-0.3397-0.37680.4648-0.01850.5365-33.0376-27.85422.89
540.5592-0.1697-0.40130.05210.12260.28790.0345-0.33190.13170.34180.19180.3132-0.2365-0.4938-0.0681.6944-0.0463-0.22010.82010.11951.1688-7.857433.263511.9393
554.5404-2.64240.59221.73520.41974.93140.1219-0.17480.6779-0.01850.0884-0.1781-0.32240.345-0.07271.6678-0.22820.29241.98230.51641.87672.288933.84144.103
561.36281.09850.90824.5218-1.02951.5763-0.01580.54860.1964-0.17930.3579-0.2793-0.7813-0.1375-0.07370.743-0.0564-0.04911.07390.22740.7024-2.429237.047713.4244
570.74830.4058-0.90511.5661-0.4511.1272-0.1170.51050.4835-0.4246-0.1682-0.1381-0.04410.1261-0.28610.8730.105-0.33140.88510.28010.5279-11.579411.987510.2755
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'R' and (resid 2 through 11 )R2 - 11
2X-RAY DIFFRACTION2chain 'T' and (resid 2 through 16 )T2 - 16
3X-RAY DIFFRACTION3chain 'T' and (resid 17 through 27 )T17 - 27
4X-RAY DIFFRACTION4chain 'N' and (resid 2 through 11 )N2 - 11
5X-RAY DIFFRACTION5chain 'N' and (resid 12 through 17 )N12 - 17
6X-RAY DIFFRACTION6chain 'A' and (resid 3 through 260 )A3 - 260
7X-RAY DIFFRACTION7chain 'A' and (resid 261 through 590 )A261 - 590
8X-RAY DIFFRACTION8chain 'A' and (resid 591 through 844 )A591 - 844
9X-RAY DIFFRACTION9chain 'A' and (resid 845 through 1106 )A845 - 1106
10X-RAY DIFFRACTION10chain 'A' and (resid 1107 through 1208 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 1209 through 1316 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 1317 through 1446 )A0
13X-RAY DIFFRACTION13chain 'B' and (resid 20 through 212 )B20 - 212
14X-RAY DIFFRACTION14chain 'B' and (resid 213 through 269 )B213 - 269
15X-RAY DIFFRACTION15chain 'B' and (resid 270 through 494 )B270 - 494
16X-RAY DIFFRACTION16chain 'B' and (resid 495 through 748 )B495 - 748
17X-RAY DIFFRACTION17chain 'B' and (resid 749 through 1051 )B749 - 1051
18X-RAY DIFFRACTION18chain 'B' and (resid 1052 through 1221 )B0
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 51 )C2 - 51
20X-RAY DIFFRACTION20chain 'C' and (resid 52 through 96 )C52 - 96
21X-RAY DIFFRACTION21chain 'C' and (resid 97 through 175 )C97 - 175
22X-RAY DIFFRACTION22chain 'C' and (resid 176 through 268 )C176 - 268
23X-RAY DIFFRACTION23chain 'E' and (resid 3 through 38 )E3 - 38
24X-RAY DIFFRACTION24chain 'E' and (resid 39 through 89 )E39 - 89
25X-RAY DIFFRACTION25chain 'E' and (resid 90 through 136 )E90 - 136
26X-RAY DIFFRACTION26chain 'E' and (resid 137 through 215 )E137 - 215
27X-RAY DIFFRACTION27chain 'F' and (resid 69 through 73 )F69 - 73
28X-RAY DIFFRACTION28chain 'F' and (resid 74 through 86 )F74 - 86
29X-RAY DIFFRACTION29chain 'F' and (resid 87 through 102 )F87 - 102
30X-RAY DIFFRACTION30chain 'F' and (resid 103 through 116 )F103 - 116
31X-RAY DIFFRACTION31chain 'F' and (resid 117 through 132 )F117 - 132
32X-RAY DIFFRACTION32chain 'F' and (resid 133 through 142 )F133 - 142
33X-RAY DIFFRACTION33chain 'F' and (resid 143 through 154 )F143 - 154
34X-RAY DIFFRACTION34chain 'H' and (resid 2 through 23 )H2 - 23
35X-RAY DIFFRACTION35chain 'H' and (resid 24 through 53 )H24 - 53
36X-RAY DIFFRACTION36chain 'H' and (resid 54 through 81 )H54 - 81
37X-RAY DIFFRACTION37chain 'H' and (resid 82 through 91 )H82 - 91
38X-RAY DIFFRACTION38chain 'H' and (resid 92 through 99 )H92 - 99
39X-RAY DIFFRACTION39chain 'H' and (resid 100 through 127 )H100 - 127
40X-RAY DIFFRACTION40chain 'H' and (resid 128 through 140 )H128 - 140
41X-RAY DIFFRACTION41chain 'H' and (resid 141 through 146 )H141 - 146
42X-RAY DIFFRACTION42chain 'I' and (resid 2 through 52 )I2 - 52
43X-RAY DIFFRACTION43chain 'I' and (resid 53 through 119 )I53 - 119
44X-RAY DIFFRACTION44chain 'J' and (resid 1 through 10 )J1 - 10
45X-RAY DIFFRACTION45chain 'J' and (resid 11 through 27 )J11 - 27
46X-RAY DIFFRACTION46chain 'J' and (resid 28 through 43 )J28 - 43
47X-RAY DIFFRACTION47chain 'J' and (resid 44 through 55 )J44 - 55
48X-RAY DIFFRACTION48chain 'J' and (resid 56 through 65 )J56 - 65
49X-RAY DIFFRACTION49chain 'K' and (resid 1 through 9 )K1 - 9
50X-RAY DIFFRACTION50chain 'K' and (resid 10 through 39 )K10 - 39
51X-RAY DIFFRACTION51chain 'K' and (resid 40 through 52 )K40 - 52
52X-RAY DIFFRACTION52chain 'K' and (resid 53 through 69 )K53 - 69
53X-RAY DIFFRACTION53chain 'K' and (resid 70 through 114 )K70 - 114
54X-RAY DIFFRACTION54chain 'L' and (resid 28 through 38 )L28 - 38
55X-RAY DIFFRACTION55chain 'L' and (resid 39 through 43 )L39 - 43
56X-RAY DIFFRACTION56chain 'L' and (resid 44 through 58 )L44 - 58
57X-RAY DIFFRACTION57chain '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

他の情報も見る