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- PDB-5ip9: Structure of RNA Polymerase II-TFIIF complex -

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基本情報

登録情報
データベース: PDB / ID: 5ip9
タイトルStructure of RNA Polymerase II-TFIIF complex
要素
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG
キーワードTRANSCRIPTION
機能・相同性
機能・相同性情報


TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 ...TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / ribosome biogenesis / peroxisome / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / mRNA binding / nucleotide binding / regulation of DNA-templated transcription / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
類似検索 - 分子機能
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / 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 / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / 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 / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / 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 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / 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 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / 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 / 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 / Homeodomain-like / 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 Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/Rpb11 dimerisation domain / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Single Sheet / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6
類似検索 - ドメイン・相同性
DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / 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 RPB7 ...DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / 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 RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.9 Å
データ登録者Plaschka, C. / Hantsche, M. / Dienemann, C. / Burzinski, C. / Plitzko, J. / Cramer, P.
引用ジャーナル: Nature / 年: 2016
タイトル: Transcription initiation complex structures elucidate DNA opening.
著者: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer /
要旨: Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) ...Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.
履歴
登録2016年3月9日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年5月11日Provider: repository / タイプ: Initial release
改定 1.12016年5月25日Group: Database references
改定 1.22016年6月8日Group: Database references
改定 1.32024年1月10日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
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
Q: PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)498,98322
ポリマ－498,43613
非ポリマー5489
水00
1


  • 登録構造と同一
  • ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area66670 Å2
ΔGint-326 kcal/mol
Surface area151010 Å2
手法PISA
単位格子
Length a, b, c (Å)222.820, 392.730, 283.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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要素

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DNA-directed RNA polymerase II subunit ... , 7種, 7分子 ABCDGIK

#1: タンパク質 DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


分子量: 191690.375 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P04050, DNA-directed RNA polymerase
#2: タンパク質 DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


分子量: 138806.109 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P08518, DNA-directed RNA polymerase
#3: タンパク質 DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


分子量: 29921.785 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P16370
#4: タンパク質 DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


分子量: 25451.191 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P20433
#7: タンパク質 DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


分子量: 19081.053 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P34087
#9: 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: 13942.714 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P27999
#11: 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: 13113.989 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P38902

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

#5: 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: 24985.895 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P20434
#6: 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: 10046.682 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P20435
#8: 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: 16394.166 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P20436
#10: 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: 7647.000 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P22139
#12: タンパク質・ペプチド DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


分子量: 5252.261 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P40422

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タンパク質・ペプチド , 1種, 1分子 Q

#13: タンパク質・ペプチド PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG


分子量: 2102.603 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P41895*PLUS

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非ポリマー , 2種, 9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

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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: 6.22 Å3/Da / 溶媒含有率: 80.22 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: peg 6000, sodium acetate, ammonium acetate, hepes, tcep

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06SA / 波長: 0.91889 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2012年7月3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: 0.91889 Å / 相対比: 1
反射解像度: 3.45→50 Å / Num. obs: 112721 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / 冗長度: 7.5 % / Biso Wilson estimate: 99.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.206 / Net I/σ(I): 9.19
反射 シェル
解像度 (Å)最高解像度 (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.45-3.544.0110.631100
3.54-3.642.8270.87199.9
3.64-3.741.8811.31100
3.74-3.861.4371.691100
3.86-3.981.0312.371100
3.98-4.120.6783.451100
4.12-4.280.4894.81100
4.28-4.450.3356.771100
4.45-4.650.2718.331100
4.65-4.880.229.961100
4.88-5.140.20310.731100
5.14-5.450.18711.181100
5.45-5.830.16812.231100
5.83-6.30.14414.231100
6.3-6.90.11316.811100
6.9-7.710.0821.02199.9
7.71-8.910.05626.721100
8.91-10.910.04434.46199.9
10.91-15.430.03838.35199.9
15.430.03242.41195.9

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
BUSTER-TNT2.10.2精密化
PDB_EXTRACT3.2データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 3PO2

3po2


解像度: 3.9→48.93 Å / Cor.coef. Fo:Fc: 0.9248 / Cor.coef. Fo:Fc free: 0.8954 / 交差検証法: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.383
Rfactor反射数%反射Selection details
Rfree0.1937 2265 2.01 %RANDOM
Rwork0.1622 ---
obs0.1628 112717 99.97 %-
原子変位パラメータBiso max: 300 Å2 / Biso mean: 130.08 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.8406 Å20 Å20 Å2
2--25.5238 Å20 Å2
3----29.3644 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
精密化ステップサイクル: final / 解像度: 3.9→48.93 Å
タンパク質核酸リガンド溶媒全体
原子数31330 0 9 0 31339
Biso mean--124.4 --
残基数----3950
拘束条件
Refine-IDタイプ数Restraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d11507SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes859HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4553HARMONIC5
X-RAY DIFFRACTIONt_it31891HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4206SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance38HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37326SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d31891HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg43050HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion23.94
LS精密化 シェル解像度: 3.9→4 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.2915 155 1.88 %
Rwork0.2272 8085 -
all0.2283 8240 -
obs--99.94 %
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)
18.68561.4480.55322.3303-0.35122.1122-0.01150.6308-0.77180.016-0.0786-0.0890.4862-0.31550.0901-0.3162-0.04260.13010.19650.0098-0.353398.481331.7277-37.8527
21.10780.74080.28383.7726-0.76811.6918-0.03650.35780.3214-0.0055-0.17160.2615-0.129-0.19630.2081-0.48780.1722-0.05050.1720.3727-0.068991.513359.4881-40.8573
30.31860.2160.48410.4974-0.18081.27150.03880.09010.15920.2445-0.0949-0.0970.10540.07770.0561-0.177-0.02910.0095-0.07290.0643-0.0512125.82936.63345.1955
41.2563-0.7988-0.35392.6085-0.40750-0.07090.07120.44470.7812-0.15230.1204-0.21450.12020.22320.1958-0.06950.2098-0.2727-0.29320.0029103.53269.365825.3714
52.24220.68990.67660.960.09980.1930.1942-0.04910.33810.1459-0.1143-0.18950.0129-0.0452-0.0799-0.41-0.08990.0864-0.19520.15950.3081140.07266.8794-2.6252
65.7121-3.82180.38721.7538-0.65150.5359-0.2432-0.15230.7280.11760.1192-0.57190.0082-0.0680.124-0.49630.07820.0295-0.4866-0.17370.9119101.954104.570.365
70.12090.11280.74181.29230.30740.34460.09230.3360.6415-0.0812-0.1882-0.05390.1441-0.08590.096-0.37960.06980.1375-0.0720.19850.2408118.98759.1296-18.4193
80.4066-1.2007-0.05730.4765-0.26800.0649-0.1617-0.12580.09110.11571.0227-0.072-0.1231-0.1806-0.43490.05020.3111-0.19780.0360.714666.765644.520910.4976
94.67740.36921.77984.9706-1.03922.0022-0.10210.1098-0.2219-0.16740.22880.24960.0008-0.0229-0.1267-0.48990.23080.1678-0.4411-0.17860.536566.646383.6992-5.8316
101.7099-0.25991.187100.29721.0085-0.12320.20220.3413-0.19470.2860.7447-0.06110.2323-0.1628-0.20160.05910.181-0.21320.03050.355375.072651.69421.5771
110.0124-1.81580.52950.6168-1.03871.1777-0.1397-0.28390.39090.391-0.08380.40430.0397-0.20540.2236-0.19710.26220.4559-0.1886-0.15080.443869.355168.351326.2079
120-1.1113-0.34321.2727-0.6990.2832-0.0844-0.15170.15270.39670.24430.13310.0109-0.0367-0.1599-0.0265-0.02920.3595-0.147-0.12-0.062793.035142.36323.3411
130.07310.8861.73462.93930.61063.957-0.22680.0563-0.0141-0.6760.51070.6559-0.01220.415-0.28390.0393-0.23220.0848-0.22290.0202-0.012786.738317.0139-0.4611
140.4005-0.0610.00010.1217-0.21421.29610.04580.12070.23930.1750.05810.1170.172-0.0242-0.1039-0.07260.02010.1315-0.08960.0028-0.1789108.54138.3982.0771
151.2011-0.00130.11191.1303-0.08130.1989-0.0697-0.297-0.24620.75720.05070.05660.20650.05930.01910.3289-0.00440.1892-0.03720.1795-0.4998110.55816.446236.2838
160.1493-0.0894-0.11831.0362-0.1024.3608-0.0490.3411-0.03560.18510.1054-0.02640.06130.563-0.0564-0.40820.15760.07230.3883-0.092-0.3327135.86529.8736-65.5017
171.2184-0.27910.02763.86080.1160.34380.05790.18030.5267-0.4658-0.1345-0.1336-0.05530.13980.0766-0.3138-0.06980.0802-0.34430.44410.5299126.93592.7723-25.3168
181.369-0.10840.09435.9984-0.54832.53070.05110.130.15670.1530.054-0.51060.20680.2566-0.1051-0.42510.0760.0670.10920.1417-0.0852139.69338.7219-19.8766
190.21330.16141.39870.97291.55365.29450.00420.0553-0.24240.13710.09150.11470.46640.3482-0.0957-0.27750.24640.13660.24780.0089-0.1799126.30723.3184-59.6886
202.28311.64831.44263.93-1.0011.4855-0.1879-0.32750.41720.5085-0.1378-0.6469-0.24890.29690.3257-0.0316-0.3091-0.45590.0424-0.066-0.1398152.24952.35436.373
210.6906-1.51061.47771.4295-2.21162.1602-0.15310.15080.41430.7644-0.05110.4612-0.02180.18340.20410.01170.27390.2978-0.3725-0.26680.651376.888499.312614.1705
223.66681.0445-0.60380.72650.41830.5738-0.03650.09650.29370.61010.08520.28830.11690.2386-0.04870.27220.05260.4208-0.13380.0531-0.268791.164825.841437.5209
231.12610.53620.58082.0994-1.35930-0.06620.3737-0.25480.4154-0.1259-0.31960.11450.2030.19220.10540.1733-0.0821-0.01920.1129-0.3388131.96317.398128.2003
241.46961.44491.26523.22281.18663.54590.12140.0711-0.41330.4871-0.26331.39150.5542-0.0450.1419-0.1156-0.25340.2418-0.25570.22060.457776.35199.64979.1671
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|81 }A3 - 81
2X-RAY DIFFRACTION2{ A|82 - A|323 }A82 - 323
3X-RAY DIFFRACTION3{ A|324 - A|659 }A324 - 659
4X-RAY DIFFRACTION4{ A|660 - A|831 }A660 - 831
5X-RAY DIFFRACTION5{ A|832 - A|1127 }A832 - 1127
6X-RAY DIFFRACTION6{ A|1128 - A|1329 }A1128 - 1329
7X-RAY DIFFRACTION7{ A|1330 - A|1454 }A1330 - 1454
8X-RAY DIFFRACTION8{ B|20 - B|234 }B20 - 234
9X-RAY DIFFRACTION9{ B|235 - B|392 }B235 - 392
10X-RAY DIFFRACTION10{ B|393 - B|539 }B393 - 539
11X-RAY DIFFRACTION11{ B|540 - B|735 }B540 - 735
12X-RAY DIFFRACTION12{ B|736 - B|841 }B736 - 841
13X-RAY DIFFRACTION13{ B|842 - B|974 }B842 - 974
14X-RAY DIFFRACTION14{ B|975 - B|1224 }B975 - 1224
15X-RAY DIFFRACTION15{ C|3 - C|268 }C3 - 268
16X-RAY DIFFRACTION16{ D|4 - D|221 }D4 - 221
17X-RAY DIFFRACTION17{ E|2 - E|215 }E2 - 215
18X-RAY DIFFRACTION18{ F|72 - F|155 }F72 - 155
19X-RAY DIFFRACTION19{ G|1 - G|171 }G1 - 171
20X-RAY DIFFRACTION20{ H|2 - H|146 }H2 - 146
21X-RAY DIFFRACTION21{ I|2 - I|120 }I2 - 120
22X-RAY DIFFRACTION22{ J|1 - J|65 }J1 - 65
23X-RAY DIFFRACTION23{ K|2 - K|114 }K2 - 114
24X-RAY DIFFRACTION24{ L|25 - L|70 }L25 - 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://pdbjlvh1.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