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- PDB-5u5q: 12 Subunit RNA Polymerase II at Room Temperature collected using SFX -

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基本情報

登録情報
データベース: PDB / ID: 5u5q
タイトル12 Subunit RNA Polymerase II at Room Temperature collected using SFX
要素
  • (DNA-directed RNA polymerase II subunit ...ポリメラーゼ) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNAポリメラーゼ) x 5
キーワードTRANSFERASE (転移酵素) / DNA-DIRECTED RNA POLYMERASE (ポリメラーゼ) / TRANSCRIPTION (転写 (生物学)) / Serial Femtosecond Crystallography
機能・相同性
機能・相同性情報


RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 ...RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase II transcription / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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 / termination of RNA polymerase III transcription / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / 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 / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / DNA修復 / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / cytoplasmic stress granule / ペルオキシソーム / single-stranded DNA binding / リボソーム生合成 / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / 核小体 / ミトコンドリア / DNA binding / zinc ion binding / 核質 / metal ion binding / 細胞核 / 細胞質
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 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain ...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 / 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. / 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 / HRDC-like superfamily / 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 / DNA directed RNA polymerase, 7 kDa subunit / DNA-directed RNA polymerase subunit Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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, 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. / 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 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily
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
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / 自由電子レーザー / 解像度: 3.8 Å
データ登録者Bushnell, D.A. / Oberthur, D. / Mariani, V. / Yefanov, O. / Tolstikova, A. / Barty, A.
資金援助 米国, 1件
組織認可番号国
National Science Foundation (NSF, United States)NSF-1231306 米国
引用ジャーナル: Sci Rep / 年: 2017
タイトル: Double-flow focused liquid injector for efficient serial femtosecond crystallography.
著者: Oberthuer, D. / Knoska, J. / Wiedorn, M.O. / Beyerlein, K.R. / Bushnell, D.A. / Kovaleva, E.G. / Heymann, M. / Gumprecht, L. / Kirian, R.A. / Barty, A. / Mariani, V. / Tolstikova, A. / ...著者: Oberthuer, D. / Knoska, J. / Wiedorn, M.O. / Beyerlein, K.R. / Bushnell, D.A. / Kovaleva, E.G. / Heymann, M. / Gumprecht, L. / Kirian, R.A. / Barty, A. / Mariani, V. / Tolstikova, A. / Adriano, L. / Awel, S. / Barthelmess, M. / Dorner, K. / Xavier, P.L. / Yefanov, O. / James, D.R. / Nelson, G. / Wang, D. / Calvey, G. / Chen, Y. / Schmidt, A. / Szczepek, M. / Frielingsdorf, S. / Lenz, O. / Snell, E. / Robinson, P.J. / Sarler, B. / Belsak, G. / Macek, M. / Wilde, F. / Aquila, A. / Boutet, S. / Liang, M. / Hunter, M.S. / Scheerer, P. / Lipscomb, J.D. / Weierstall, U. / Kornberg, R.D. / Spence, J.C. / Pollack, L. / Chapman, H.N. / Bajt, S.
履歴
登録2016年12月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年3月29日Provider: repository / タイプ: Initial release
改定 1.12017年9月6日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22017年11月1日Group: Author supporting evidence / カテゴリ: pdbx_struct_assembly_auth_evidence
改定 1.32018年2月14日Group: Data collection / カテゴリ: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
改定 1.42018年9月19日Group: Data collection / カテゴリ: diffrn_detector / Item: _diffrn_detector.detector
改定 1.52019年11月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)514,70621
ポリマ－514,15812
非ポリマー5489
水0
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
Buried area65200 Å2
ΔGint-320 kcal/mol
Surface area167290 Å2
単位格子
Length a, b, c (Å)223.400, 396.800, 287.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
詳細Assembly confirmed by gel filtration

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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 / ポリメラーゼ / 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, ポリメラーゼ
#2: タンパク質 DNA-directed RNA polymerase II subunit RPB2 / ポリメラーゼ / 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, ポリメラーゼ
#3: タンパク質 DNA-directed RNA polymerase II subunit RPB3 / ポリメラーゼ / 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
#4: タンパク質 DNA-directed RNA polymerase II subunit RPB4 / ポリメラーゼ / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20433
#7: タンパク質 DNA-directed RNA polymerase II subunit RPB7 / ポリメラーゼ / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P34087
#9: タンパク質 DNA-directed RNA polymerase II subunit RPB9 / ポリメラーゼ / 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
#11: タンパク質 DNA-directed RNA polymerase II subunit RPB11 / ポリメラーゼ / 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

#5: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNAポリメラーゼ / 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
#6: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNAポリメラーゼ / 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
#8: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNAポリメラーゼ / 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
#10: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNAポリメラーゼ / 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
#12: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNAポリメラーゼ / 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 , 2種, 9分子

#13: 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
#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

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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: 6.2 Å3/Da / 溶媒含有率: 80.18 %
結晶化温度: 289.65 K / 手法: microdialysis / pH: 6.3
詳細: 21-22% PEG 400, 5% PEG 5%, 100 mM Ammonium Phosphate pH 6.3, 100 mM NaCl, 1 mM ZnCl2 and 10 mM DTT

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データ収集

回折平均測定温度: 293.15 K
放射光源由来: 自由電子レーザー / サイト: SLAC LCLS / ビームライン: CXI / 波長: 1.55 Å
検出器タイプ: CS-PAD CXI-2 / 検出器: PIXEL / 日付: 2015年5月26日 / 詳細: 90 150 nm2 FWHM (V H) with Kirkpatrick-Baez mirrors
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.55 Å / 相対比: 1
反射解像度: 3.8→40.611 Å / Num. obs: 123899 / % possible obs: 99 % / 冗長度: 54.9 % / Biso Wilson estimate: 140.9 Å2 / Net I/σ(I): 2.41

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解析

ソフトウェア
名称バージョン分類
PHENIX(dev_2356: ???)精密化
CrystFELデータ削減
CrystFELデータスケーリング
Cootモデル構築
精密化解像度: 3.8→40.611 Å / SU ML: 0.75 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 32.45
Rfactor反射数%反射
Rfree0.2706 2493 2.01 %
Rwork0.2179 --
obs0.219 123899 98.91 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3.8→40.611 Å
タンパク質核酸リガンド溶媒全体
原子数31625 0 9 0 31634
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00332198
X-RAY DIFFRACTIONf_angle_d0.61643479
X-RAY DIFFRACTIONf_dihedral_angle_d18.0712257
X-RAY DIFFRACTIONf_chiral_restr0.0434882
X-RAY DIFFRACTIONf_plane_restr0.0045654
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.87310.42221400.39146080X-RAY DIFFRACTION90
3.8731-3.9520.43331000.37956383X-RAY DIFFRACTION94
3.952-4.03790.39211330.36596614X-RAY DIFFRACTION98
4.0379-4.13170.36261600.34746685X-RAY DIFFRACTION99
4.1317-4.2350.36261200.3266770X-RAY DIFFRACTION99
4.235-4.34930.37811440.30456700X-RAY DIFFRACTION100
4.3493-4.47720.27081160.27246827X-RAY DIFFRACTION100
4.4772-4.62150.30271510.26936758X-RAY DIFFRACTION100
4.6215-4.78640.31781560.25766769X-RAY DIFFRACTION100
4.7864-4.97770.31561550.25196778X-RAY DIFFRACTION100
4.9777-5.20380.29471450.25326794X-RAY DIFFRACTION100
5.2038-5.47760.29231340.24316812X-RAY DIFFRACTION100
5.4776-5.81990.29281500.23416815X-RAY DIFFRACTION100
5.8199-6.26770.2791290.22036829X-RAY DIFFRACTION100
6.2677-6.89570.24461550.19776845X-RAY DIFFRACTION100
6.8957-7.88720.24261370.16626883X-RAY DIFFRACTION100
7.8872-9.91310.17621460.13696927X-RAY DIFFRACTION100
9.9131-40.61290.21281220.14837137X-RAY DIFFRACTION100
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)
11.4648-0.5850.30571.20741.19834.0391-0.14260.5946-0.5685-0.1481-0.2576-0.04030.2352-0.3238-01.1388-0.04650.12811.4913-0.01221.071399.281632.3005-38.59
2-0.2137-0.58660.9160.8892-0.7324-0.1913-0.36410.1236-0.2452-0.02920.13520.0629-0.5837-0.0589-0.00011.51520.24040.01541.72030.35241.578697.899369.1884-46.6354
30.73770.79320.16470.7220.69151.3751-0.20550.3526-0.33510.45970.35370.70880.3665-0.645-0.00020.9025-0.0393-0.0621.65010.24091.239184.081844.8068-33.2941
41.00922.0395-0.89691.0196-1.2111.63460.50590.20840.49450.04670.3429-0.9740.1346-0.44540.30740.8834-0.01570.20970.80210.26540.1202117.231231.1112-7.3468
51.234-0.39310.46820.21230.16160.39650.18410.04990.8555-0.1737-0.08720.08680.51390.0155-00.9285-0.0036-0.06910.85820.17720.7619119.379712.1864-13.6064
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941.77161.3193-0.46971.42080.00330.2168-1.082-1.0936-1.35071.2588-0.4256-0.1461.0247-0.7652-0.05491.50540.0748-0.59112.0388-0.11721.3526152.198449.123441.8781
952.43152.207-1.86051.9798-1.5872.3939-1.6508-0.8898-0.4779-2.0854-1.1799-2.16280.14290.287-0.47641.71560.173-0.33922.04680.46221.919155.274632.326435.3119
961.0883-0.62-0.8970.15030.30490.63250.47580.35630.1217-1.1761-0.21062.34720.6651.2715-01.7707-0.0342-0.5011.759-0.07181.1686154.095853.355632.7865
971.7046-1.1226-0.79510.84530.56330.25370.5835-0.00552.54140.5321-0.4725-0.92590.43610.67530.26222.03540.0614-0.7381.61270.37251.3319154.155759.447830.3398
980.09360.0690.0292-0.00860.00540.0553-0.3361-1.33230.27670.58430.2388-1.4003-0.39322.5978-01.74450.0241-0.38462.5459-0.1392.4293158.53460.900733.7348
990.0216-0.0211-0.03780.07210.04710.03690.14160.8781-0.5968-0.5317-0.16291.1312-0.434-2.2178-01.46130.2315-0.05342.7709-0.57832.0199161.233351.648426.2787
1000.2072-0.09720.14610.32230.01870.08650.7674-0.4765-0.14970.1366-0.0113-0.6771-0.11080.19920.28932.1480.0551-0.92731.8576-0.5710.4365155.609847.501941.8201
1011.3357-0.14411.75791.6090.38582.573-0.4301-0.2605-0.2251-0.6689-0.91180.5282-0.6947-0.0931-1.19520.5170.832-0.82880.6889-0.06192.867469.2863106.10142.0386
1020.1848-0.2294-0.95490.251.06954.54860.91820.0961-0.6849-0.4052-1.42641.21822.6155-2.8761-0.02471.16790.13940.33981.30130.10551.502461.0761105.6518-4.16
1035.0482-1.2539-1.68531.60031.09986.8854-0.72220.3981-0.56330.6296-1.204-0.30360.418-0.4895-2.82140.46550.2650.09051.10510.52011.972771.488119.2071-8.4339
1040.13270.00580.15780.0142-0.00130.0841-0.2385-1.13112.6792-0.6221-0.2078-1.4034-1.2916-0.820401.2596-0.01470.10331.2285-0.17172.194364.2235110.3418-8.2831
1050.05990.0852-0.01360.0924-0.03320.0169-0.6409-0.93830.9142-0.07140.43660.3634-0.5123-0.5035-0.00011.01890.05810.28921.315-0.1481.28168.9863115.8581-0.1713
1060.05420.12770.12630.22150.21870.18011.56690.52320.59951.12120.3357-0.4141-0.20870.0391-01.47710.1631-0.17271.4319-0.11.617784.4737103.79414.5037
107-0.0308-0.0132-0.01380.0397-0.07190.0829-0.23420.095-0.4518-0.24620.80610.4742-0.35740.036101.70860.18460.59191.2572-0.06891.515176.368491.117521.9227
1080.7264-0.1470.05380.00420.0229-0.0328-0.7671-0.1467-1.08520.63260.70561.32-0.95131.73770.01781.90010.10420.48551.4064-0.14331.455482.336991.140433.5756
1090.24680.4128-0.33170.4044-0.30090.2221-0.7750.51990.3405-0.0899-0.8092-0.3232-0.8118-0.593801.87620.19650.10311.3460.00421.83986.774393.7722.7898
1100.0602-0.01830.06450.0071-0.01240.0539-0.11560.14040.87670.16491.64030.98060.97180.10430.00012.49050.21730.8261.61520.41923.529486.9502103.220322.4717
1110.0715-0.0441-0.11330.0028-0.00160.17380.21960.52780.4059-0.9237-0.40270.4056-0.4994-0.18930.00011.3889-0.0564-0.2161.0593-0.19490.742595.658922.280331.2264
1120.0043-0.0063-0.0291-0.00050.02540.0595-0.2304-0.12430.0939-1.1265-1.3055-0.9428-0.68051.71620.00011.9479-0.22430.00111.23880.09331.2261102.126223.151535.4213
1130.1083-0.58030.04552.8071-0.29690.0140.99230.05290.1494-1.2680.27321.81361.5821-0.3048-0.00212.2046-0.03260.59451.74230.1451.0989.621423.225940.9778
1140.0187-0.0342-0.02320.0280.03420.0168-0.13150.35-0.85370.45960.0729-0.0244-0.2304-0.403401.7033-0.03990.69061.7013-0.10031.178584.079326.893747.6897
1150.43160.56820.05760.75570.06740.00730.3388-0.20430.97960.95040.29950.07470.84242.50350.04771.5353-0.13631.04472.7702-0.7470.82290.98732.284847.8862
1160.0698-0.17660.00980.5873-0.31150.25471.2139-0.00672.1601-0.3013-0.4658-0.83340.79460.5152-0.01291.9033-0.1244-0.00892.0518-0.38051.2472100.818628.526544.575
1170.092-0.02720.05470.02290.00620.0351-0.8592-0.3440.4327-1.10591.1498-0.28940.17560.6826-0.00011.6882-0.08290.01291.44360.0691.694299.454230.135237.3154
1180.08030.065-0.05980.0485-0.02170.08260.45760.3220.66120.5632-0.1893-0.997-0.45430.958501.92670.05440.03781.4302-0.16351.102990.503530.384433.1396
1190.18620.08990.10730.63370.24220.1224-0.2470.1987-0.4074-0.75770.0338-0.8270.2588-0.70360.00191.8185-0.60310.46411.70570.09260.383582.039525.379127.0393
1200.90870.09870.26890.16840.18150.26420.529-0.8358-1.88490.82011.66640.5279-1.2503-2.40340.12811.5137-0.24730.55461.68340.37791.677875.083521.091322.6437
1210.1055-0.0843-0.093-0.00880.0370.08930.19161.3085-0.70670.8088-0.7511-0.25180.16910.8194-01.55330.0750.12511.47580.08990.9491115.88815.652615.7324
122-0.0036-0.0150.00310.0071-0.0141-0.01640.4985-0.7142-1.57730.75760.86321.56942.4732-1.2693-01.1383-0.1421-0.2141.75590.0331.2049130.313410.559815.5754
1231.51650.35021.08122.74560.49096.9878-0.5687-0.0343-0.2793-0.6559-2.1949-0.12010.3821-0.2026-6.62311.3042-0.08280.37210.48490.9189-1.3927139.179519.425119.343
1240.01520.08480.07290.22390.30160.3155-0.0344-0.1906-0.43971.78481.0135-0.1118-1.04981.02370.00861.45520.2525-0.19590.80110.23390.486132.749621.386431.7089
125-0.006-0.00230.00020.0191-0.04970.02490.6405-1.8234-1.128-0.3143-0.56710.30270.8683-0.2208-01.65110.14550.05061.76360.07361.6809146.387122.603734.9289
1260.2499-0.781-0.48332.21421.33192.7398-0.43840.6415-0.3471.5991-0.7537-0.56450.3201-1.1225-1.54071.6960.2906-0.72871.14930.32960.3873130.949626.321220.9184
1270.10930.1991-0.08660.1631-0.11790.03470.87360.3165-0.028-1.2572-0.8784-0.3281.55071.27110.00121.24620.21230.11631.33020.18261.119134.669521.943420.8337
1280.3270.2841-0.13751.35040.07970.11151.1521-1.18540.79081.5663-0.1401-3.0368-0.61720.14360.01261.37410.2736-0.1791.65120.06581.1098147.000215.088429.2255
1290.0167-0.0030.016-0.0101-0.00140.0046-0.3891-0.0587-0.7170.1092-0.7938-0.13340.1168-0.265802.02170.1210.09691.48740.13210.9845134.245912.045239.3026
1300.11060.0193-0.08050.2524-0.14260.0820.321-0.52661.29710.7599-1.056-0.85921.6583-0.742801.7504-0.1217-0.18742.23850.33171.1587120.541610.838252.5386
1310.0444-0.02360.58340.0067-0.27247.1868-1.15251.41611.2820.1499-0.7734-0.1008-0.43091.6959-1.65991.29110.44230.60650.54872.79392.508675.46194.31916.9839
1320.5202-0.29450.54340.99190.04920.722-0.62980.6068-0.1911-0.1233-1.3658-0.82540.96791.4949-0.12942.4057-1.33841.26992.7386-0.82172.393270.391313.734512.9703
1330.07630.1069-0.01990.4678-0.02380.00680.8952-0.202-0.03140.124-0.86450.7673-0.75891.30030.00141.6851-0.2865-0.52972.0630.12470.7471.34226.55950.4415
1340.0725-0.06820.0070.04270.01650.0433-0.0622-0.0051-1.33951.4717-1.76452.3149-0.1268-1.5455-0.00061.2156-0.52840.34242.1305-0.4161.98964.668113.0455.5437
1350.7453-0.568-0.29950.6674-0.36171.58880.1960.07470.17630.405-0.25450.4698-0.6932-0.7358-0.10911.1116-0.16610.53071.2828-0.79522.571968.22918.3016.3257
1360.5693-0.00420.56230.58170.90131.80070.8177-0.3210.0983-0.29452.18150.38790.11220.8250.16171.9162-0.3344-0.28011.13230.23021.163285.42077.09219.8981
1370.0251-0.01270.02360.05360.03820.0156-0.0875-0.7152-0.71090.43960.2216-1.40390.17270.4570.00011.73610.1067-0.07951.35880.27181.1396100.575511.505117.9905
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:83)
2X-RAY DIFFRACTION2(chain A and resid 84:240)
3X-RAY DIFFRACTION3(chain A and resid 241:327)
4X-RAY DIFFRACTION4(chain A and resid 328:391)
5X-RAY DIFFRACTION5(chain A and resid 392:432)
6X-RAY DIFFRACTION6(chain A and resid 433:482)
7X-RAY DIFFRACTION7(chain A and resid 483:541)
8X-RAY DIFFRACTION8(chain A and resid 542:613)
9X-RAY DIFFRACTION9(chain A and resid 614:684)
10X-RAY DIFFRACTION10(chain A and resid 685:755)
11X-RAY DIFFRACTION11(chain A and resid 756:900)
12X-RAY DIFFRACTION12(chain A and resid 901:975)
13X-RAY DIFFRACTION13(chain A and resid 976:1063)
14X-RAY DIFFRACTION14(chain A and resid 1064:1144)
15X-RAY DIFFRACTION15(chain A and resid 1145:1207)
16X-RAY DIFFRACTION16(chain A and resid 1208:1243)
17X-RAY DIFFRACTION17(chain A and resid 1244:1265)
18X-RAY DIFFRACTION18(chain A and resid 1266:1313)
19X-RAY DIFFRACTION19(chain A and resid 1314:1387)
20X-RAY DIFFRACTION20(chain A and resid 1388:1455)
21X-RAY DIFFRACTION21(chain B and resid 20:53)
22X-RAY DIFFRACTION22(chain B and resid 54:118)
23X-RAY DIFFRACTION23(chain B and resid 119:170)
24X-RAY DIFFRACTION24(chain B and resid 171:225)
25X-RAY DIFFRACTION25(chain B and resid 226:252)
26X-RAY DIFFRACTION26(chain B and resid 253:323)
27X-RAY DIFFRACTION27(chain B and resid 324:355)
28X-RAY DIFFRACTION28(chain B and resid 356:409)
29X-RAY DIFFRACTION29(chain B and resid 410:467)
30X-RAY DIFFRACTION30(chain B and resid 468:484)
31X-RAY DIFFRACTION31(chain B and resid 485:510)
32X-RAY DIFFRACTION32(chain B and resid 511:643)
33X-RAY DIFFRACTION33(chain B and resid 644:707)
34X-RAY DIFFRACTION34(chain B and resid 708:723)
35X-RAY DIFFRACTION35(chain B and resid 724:738)
36X-RAY DIFFRACTION36(chain B and resid 739:861)
37X-RAY DIFFRACTION37(chain B and resid 862:969)
38X-RAY DIFFRACTION38(chain B and resid 970:1102)
39X-RAY DIFFRACTION39(chain B and resid 1103:1134)
40X-RAY DIFFRACTION40(chain B and resid 1135:1224)
41X-RAY DIFFRACTION41(chain C and resid 3:45)
42X-RAY DIFFRACTION42(chain C and resid 46:70)
43X-RAY DIFFRACTION43(chain C and resid 71:79)
44X-RAY DIFFRACTION44(chain C and resid 80:96)
45X-RAY DIFFRACTION45(chain C and resid 97:107)
46X-RAY DIFFRACTION46(chain C and resid 108:158)
47X-RAY DIFFRACTION47(chain C and resid 159:185)
48X-RAY DIFFRACTION48(chain C and resid 186:223)
49X-RAY DIFFRACTION49(chain C and resid 224:246)
50X-RAY DIFFRACTION50(chain C and resid 247:268)
51X-RAY DIFFRACTION51(chain D and resid 3:21)
52X-RAY DIFFRACTION52(chain D and resid 22:33)
53X-RAY DIFFRACTION53(chain D and resid 34:44)
54X-RAY DIFFRACTION54(chain D and resid 45:64)
55X-RAY DIFFRACTION55(chain D and resid 65:74)
56X-RAY DIFFRACTION56(chain D and resid 75:130)
57X-RAY DIFFRACTION57(chain D and resid 131:145)
58X-RAY DIFFRACTION58(chain D and resid 146:163)
59X-RAY DIFFRACTION59(chain D and resid 164:189)
60X-RAY DIFFRACTION60(chain D and resid 190:221)
61X-RAY DIFFRACTION61(chain E and resid 1:14)
62X-RAY DIFFRACTION62(chain E and resid 15:41)
63X-RAY DIFFRACTION63(chain E and resid 42:77)
64X-RAY DIFFRACTION64(chain E and resid 78:105)
65X-RAY DIFFRACTION65(chain E and resid 106:125)
66X-RAY DIFFRACTION66(chain E and resid 126:148)
67X-RAY DIFFRACTION67(chain E and resid 149:158)
68X-RAY DIFFRACTION68(chain E and resid 159:183)
69X-RAY DIFFRACTION69(chain E and resid 184:202)
70X-RAY DIFFRACTION70(chain E and resid 203:215)
71X-RAY DIFFRACTION71(chain F and resid 69:73)
72X-RAY DIFFRACTION72(chain F and resid 74:84)
73X-RAY DIFFRACTION73(chain F and resid 85:93)
74X-RAY DIFFRACTION74(chain F and resid 94:106)
75X-RAY DIFFRACTION75(chain F and resid 107:113)
76X-RAY DIFFRACTION76(chain F and resid 114:122)
77X-RAY DIFFRACTION77(chain F and resid 123:132)
78X-RAY DIFFRACTION78(chain F and resid 133:143)
79X-RAY DIFFRACTION79(chain F and resid 144:150)
80X-RAY DIFFRACTION80(chain F and resid 151:155)
81X-RAY DIFFRACTION81(chain G and resid 1:6)
82X-RAY DIFFRACTION82(chain G and resid 7:21)
83X-RAY DIFFRACTION83(chain G and resid 22:57)
84X-RAY DIFFRACTION84(chain G and resid 58:79)
85X-RAY DIFFRACTION85(chain G and resid 80:97)
86X-RAY DIFFRACTION86(chain G and resid 98:116)
87X-RAY DIFFRACTION87(chain G and resid 117:128)
88X-RAY DIFFRACTION88(chain G and resid 129:149)
89X-RAY DIFFRACTION89(chain G and resid 150:159)
90X-RAY DIFFRACTION90(chain G and resid 160:171)
91X-RAY DIFFRACTION91(chain H and resid 2:14)
92X-RAY DIFFRACTION92(chain H and resid 15:27)
93X-RAY DIFFRACTION93(chain H and resid 28:38)
94X-RAY DIFFRACTION94(chain H and resid 39:67)
95X-RAY DIFFRACTION95(chain H and resid 76:91)
96X-RAY DIFFRACTION96(chain H and resid 92:108)
97X-RAY DIFFRACTION97(chain H and resid 109:121)
98X-RAY DIFFRACTION98(chain H and resid 122:131)
99X-RAY DIFFRACTION99(chain H and resid 132:139)
100X-RAY DIFFRACTION100(chain H and resid 140:146)
101X-RAY DIFFRACTION101(chain I and resid 2:6)
102X-RAY DIFFRACTION102(chain I and resid 7:14)
103X-RAY DIFFRACTION103(chain I and resid 15:25)
104X-RAY DIFFRACTION104(chain I and resid 26:34)
105X-RAY DIFFRACTION105(chain I and resid 35:41)
106X-RAY DIFFRACTION106(chain I and resid 42:51)
107X-RAY DIFFRACTION107(chain I and resid 52:64)
108X-RAY DIFFRACTION108(chain I and resid 65:86)
109X-RAY DIFFRACTION109(chain I and resid 87:115)
110X-RAY DIFFRACTION110(chain I and resid 116:120)
111X-RAY DIFFRACTION111(chain J and resid 1:7)
112X-RAY DIFFRACTION112(chain J and resid 8:15)
113X-RAY DIFFRACTION113(chain J and resid 16:22)
114X-RAY DIFFRACTION114(chain J and resid 23:28)
115X-RAY DIFFRACTION115(chain J and resid 29:37)
116X-RAY DIFFRACTION116(chain J and resid 38:44)
117X-RAY DIFFRACTION117(chain J and resid 45:50)
118X-RAY DIFFRACTION118(chain J and resid 51:55)
119X-RAY DIFFRACTION119(chain J and resid 56:60)
120X-RAY DIFFRACTION120(chain J and resid 61:65)
121X-RAY DIFFRACTION121(chain K and resid 1:12)
122X-RAY DIFFRACTION122(chain K and resid 13:20)
123X-RAY DIFFRACTION123(chain K and resid 21:39)
124X-RAY DIFFRACTION124(chain K and resid 40:50)
125X-RAY DIFFRACTION125(chain K and resid 51:57)
126X-RAY DIFFRACTION126(chain K and resid 58:67)
127X-RAY DIFFRACTION127(chain K and resid 68:76)
128X-RAY DIFFRACTION128(chain K and resid 77:90)
129X-RAY DIFFRACTION129(chain K and resid 91:99)
130X-RAY DIFFRACTION130(chain K and resid 100:115)
131X-RAY DIFFRACTION131(chain L and resid 25:29)
132X-RAY DIFFRACTION132(chain L and resid 30:36)
133X-RAY DIFFRACTION133(chain L and resid 37:44)
134X-RAY DIFFRACTION134(chain L and resid 45:51)
135X-RAY DIFFRACTION135(chain L and resid 52:56)
136X-RAY DIFFRACTION136(chain L and resid 57:65)
137X-RAY DIFFRACTION137(chain L and resid 66:70)

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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