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- PDB-6uq1: 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: 6uq1
タイトルRNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 6
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/DNA/RNA / RNA polymerase II / 5-guanidinohydantoin / elongation complex / DNA lesion / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex
機能・相同性
機能・相同性情報


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / transcription by RNA polymerase III / transcription by RNA polymerase I / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / : / : / : / : / : / : / 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 / metal ion binding / nucleus / cytoplasm
類似検索 - 分子機能
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit ...Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / 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 / Homeodomain-like / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit
類似検索 - ドメイン・相同性
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 / 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: 3.6 Å
データ登録者Oh, J. / Wang, D.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102362 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2020
タイトル: RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
著者: Oh, J. / Fleming, A.M. / Xu, J. / Chong, J. / Burrows, C.J. / Wang, D.
履歴
登録2019年10月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年6月10日Provider: repository / タイプ: Initial release
改定 1.12023年10月11日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
改定 1.22024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
R: RNA
T: Template strand DNA
N: Non-template strand DNA
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)488,45922
ポリマ－487,91213
非ポリマー5489
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)170.502, 223.508, 194.943
Angle α, β, γ (deg.)90.000, 101.580, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11I-82-

GLU

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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: 3876.368 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 , 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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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.73 Å3/Da / 溶媒含有率: 67.02 % / Mosaicity: 0.2 °
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: 0.9767 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: 0.9767 Å / 相対比: 1
反射解像度: 3.54→49.521 Å / Num. obs: 86875 / % possible obs: 100 % / 冗長度: 7 % / Biso Wilson estimate: 93.24 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.491 / Rpim(I) all: 0.2 / Rrim(I) all: 0.531 / Net I/σ(I): 5.1
反射 シェル解像度: 3.54→3.6 Å / 冗長度: 7.2 % / Rmerge(I) obs: 3.695 / Num. measured all: 33112 / Num. unique obs: 4609 / CC1/2: 0.251 / Rpim(I) all: 1.481 / Rrim(I) all: 3.984 / Net I/σ(I) obs: 0.6 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
Aimless0.7.3データスケーリング
PHENIX1.13_2998精密化
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: 3.6→49.521 Å / SU ML: 0.4 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 32.72
Rfactor反射数%反射
Rfree0.2874 1900 2.3 %
Rwork0.2398 --
obs0.2409 82539 99.88 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 328.22 Å2 / Biso mean: 110.9463 Å2 / Biso min: 14.34 Å2
精密化ステップサイクル: final / 解像度: 3.6→49.521 Å
タンパク質核酸リガンド溶媒全体
原子数27992 1097 9 0 29098
Biso mean--164.24 --
残基数----3596
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
3.6-3.690.38121340.34845730
3.69-3.78970.37121360.33355753
3.7897-3.90120.33021350.31795748
3.9012-4.02710.40241350.29855709
4.0271-4.17090.31811360.27525751
4.1709-4.33780.30251350.24895718
4.3378-4.53510.29271360.23035792
4.5351-4.77410.26111350.2195699
4.7741-5.07290.2881360.21945788
5.0729-5.46410.31041360.23275757
5.4641-6.01320.32941360.23845745
6.0132-6.88130.25251360.23275794
6.8813-8.66210.23941370.2015810
8.6621-49.5210.21671370.19145845
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)
10.01860.05040.04480.16190.10630.0972-0.67430.3884-0.26820.34810.271-0.46890.11910.17650.00311.3371-0.08550.26081.5858-0.04851.285211.354510.560342.1729
20.02150.01910.00160.03670.00570.04440.29890.18240.4412-0.20160.08170.11890.2172-0.2440.00061.774-0.02160.1022.4918-0.38192.78951.094111.436381.2201
30.01160.00050.00990.02080.00930.01190.10130.0219-0.08240.0311-0.03260.0543-0.04140.00460.00022.4487-0.2009-0.2152.06930.55081.673534.292614.207961.429
40.0208-0.0165-0.01050.04170.00390.00570.0572-0.25460.0922-0.0009-0.1815-0.22710.0134-0.03890.00292.2665-0.03750.00391.5923-0.18341.327116.75054.160845.3839
50.00360.0056-0.00350.0063-0.00530.0036-0.05650.1735-0.05580.0212-0.07240.3311-0.0533-0.2498-0.00151.87920.2931-0.16551.1242-0.08691.146112.687219.800932.835
60.01560.0032-0.0120.0186-0.0060.01030.22710.12490.16690.03840.127-0.09950.0518-0.1330.00361.9937-0.5802-0.16932.47390.07232.282327.80098.838764.9027
70.01550.0161-0.00230.03960.02750.04660.0469-0.0936-0.09530.1025-0.05330.094-0.0912-0.013-0.00012.22170.2704-0.20192.9828-0.10022.550344.643913.454569.9603
80.0268-0.00490.01150.0009-0.00320.0167-0.01750.12140.1179-0.0349-0.05740.0543-0.05540.0369-0.00072.66950.6106-0.16212.86620.03732.325951.939910.263686.4057
90.0314-0.3336-0.05333.94370.70790.14050.02930.07120.01820.0029-0.00350.0810.0007-0.01020.00592.62320.3333-0.18042.16170.24192.383564.72497.725789.0996
100.2887-0.021-0.08440.34320.11240.24960.1470.15660.3382-0.24360.0141-0.15550.26290.4032-0.00020.6106-0.141-0.05510.92240.10861.133952.20969.644342.3425
110.55230.13850.01130.0955-0.13340.23610.21640.21270.0482-0.0103-0.0010.01490.48070.08810.15350.9142-0.1063-0.31970.39620.06810.583510.9065-12.387134.6327
120.2322-0.0989-0.2230.68230.21140.19710.0653-0.2695-0.02640.26720.0286-0.11260.2116-0.19920.01930.9662-0.3676-0.12030.38590.22630.3774-5.9952-6.742366.8747
130.1343-0.2222-0.08110.5369-0.05350.1390.0347-0.0412-0.03240.12690.1364-0.04250.17670.10020.02851.0346-0.0025-0.33640.2434-0.01840.575322.2763-18.854275.4043
140.10210.0417-0.02830.0222-0.0059-0-0.1063-0.47790.33570.0070.0236-0.034-0.35670.185-0.00860.7594-0.1899-0.00190.4229-0.03640.6172-0.866943.449851.7636
150.5090.17130.06170.59630.36780.2306-0.03780.2110.18190.19320.0963-0.33840.06630.0850.01040.8144-0.1148-0.10610.41990.06760.65477.93236.65448.4163
160.5587-0.10180.36280.29390.24160.512-0.1098-0.0480.1210.2121-0.03990.086-0.14420.022-0.00060.3033-0.12170.07250.35570.01520.49620.625938.394565.7604
170.1362-0.08160.17280.8608-0.2520.4149-0.0188-0.15640.0520.51590.157-0.2903-0.2907-0.0970.02730.1692-0.15020.22380.39080.03130.2174-7.806430.115864.9628
180.09640.06870.04460.11590.0010.02090.02460.1928-0.0699-0.1955-0.1083-0.0711-0.06210.1048-0.1645-0.2963-0.33610.36910.31260.25490.1484-5.31989.786628.4106
190.190.0093-0.01350.14680.01270.065-0.0144-0.13670.11080.0495-0.031-0.19460.1952-0.0176-0.00780.0456-0.10280.1590.4720.13860.432614.6259-3.105636.0757
200.13180.08720.12030.2107-0.00340.1352-0.0218-0.1384-0.0738-0.1526-0.15120.28340.2659-0.1172-0.00010.8252-0.2092-0.14140.75430.04320.5285-35.8904-12.74525.7403
210.0168-0.01040.020.13470.0470.0333-0.25950.22830.0565-0.1892-0.14450.44970.3292-0.0025-0.01740.5735-0.13980.01680.55580.09860.3094-23.59252.538511.0894
220.0978-0.0834-0.0750.10590.01460.12990.17480.3941-0.0333-0.3709-0.25950.2254-0.0153-0.035-0.01921.09990.1087-0.29860.82040.05160.5117-29.071210.645415.3293
230.03850.0127-0.01770.06880.00760.01650.0598-0.33180.0402-0.067-0.0725-0.089-0.244-0.1684-0.00031.1021-0.2964-0.16130.92680.08210.6122-36.59-15.104650.2178
240.2938-0.18410.19540.2598-0.21590.1950.15310.1598-0.1670.11920.24460.08760.3076-0.10490.06180.8288-0.3617-0.2290.8080.03620.522-34.3851-21.491428.2521
250.11960.0479-0.05610.0463-0.0230.0543-0.0664-0.1992-0.30930.19160.1884-0.09670.0748-0.0960.00491.91870.0961-0.69920.9418-0.04631.265240.0714-22.628497.9062
260.08170.0114-0.03530.0005-0.00220.0117-0.16770.20220.17270.53010.1723-0.374-0.4097-0.1338-0.00021.95320.2202-0.58721.1985-0.17341.604850.9859-21.50994.0987
270.00150.01080.00440.09530.0260.0093-0.01530.0156-0.2292-0.07290.0705-0.03330.0623-0.0093-0.01311.0214-0.424-0.32382.2146-0.60232.950261.7782-12.664291.0518
280.3746-0.2594-0.20010.17150.12810.18120.08930.05770.26960.23830.0995-0.32530.29910.23270.00470.80240.0713-0.45280.6113-0.06430.822544.2987-20.424475.0336
290.0283-0.0395-0.02270.07030.07150.07960.07950.1432-0.09330.05250.0839-0.49670.20530.0770.00011.01670.1583-0.32270.544-0.03470.730730.9924-33.191537.1802
300.0150.00290.00110.00520.00760.0223-0.31790.0525-0.1822-0.049-0.2385-0.0977-0.00580.0382-0.00470.78150.19-0.0680.7841-0.12270.611818.9571-35.943523.3683
310.02210.02920.0150.03970.02020.0430.1513-0.04720.2568-0.13980.1563-0.02520.00370.06530.00131.47580.04680.00560.8663-0.17010.837335.5542-32.902137.76
320.05-0.02390.00520.0441-0.03050.02560.1963-0.0389-0.04840.02930.35810.4865-0.0584-0.04250.00370.89140.0028-0.25040.8731-0.11190.944931.8956-38.416839.2565
330.0522-0.0479-0.05420.06180.03390.0588-0.1484-0.0502-0.0715-0.16230.16050.38290.47190.03060.00080.636-0.1991-0.0430.46190.12170.8527-26.8454-44.043561.7578
340.0712-0.0242-00.30830.09710.0303-0.17190.102-0.2798-0.09040.03860.0719-0.02330.0382-0.34551.3407-0.613-0.23510.73090.24571.1429-24.6098-48.088551.2383
350.0355-0.03360.02630.0527-0.0210.022-0.1655-0.0498-0.73780.32550.02190.12070.54120.13560.00121.5079-0.2946-0.15940.87530.32310.977-18.0567-50.504462.7963
360.55830.1416-0.48560.0455-0.13540.43830.35530.0196-0.05970.01220.1426-0.27470.00290.12440.15621.404-0.1956-0.36880.7893-0.27290.902630.046239.5668106.3183
370.00520.0020.00030.049-0.0170.00450.368-0.17440.0318-0.1179-0.18910.03530.31250.2084-0.00011.0411-0.0424-0.17090.6136-0.00350.806124.249433.0265103.1335
380.0545-0.0142-0.01160.01720.03690.0802-0.07330.026-0.2082-0.130.17220.26790.11650.15030.0030.9208-0.056-0.15550.7848-0.00370.548-8.799227.401993.4719
390.11350.04020.04530.1233-0.05750.06540.15010.0911-0.2139-0.3934-0.1094-0.013-0.0909-0.0614-0.00151.2320.0624-0.37640.67990.02320.6536-0.972921.0996.2429
400.1553-0.06810.06760.12780.02830.06220.0683-0.09270.0854-0.04260.1068-0.0015-0.07860.11770.31590.3799-0.04570.18250.52350.15070.2543-25.2577.243929.745
410.25270.1652-0.06370.1418-0.04410.19110.0866-0.01570.14450.0524-0.02460.1342-0.0113-0.06070.49580.1263-0.1971-0.08910.4436-0.07040.5251-36.611116.327233.8863
420.0348-0.0195-0.09570.05080.0360.2616-0.00790.0142-0.0179-0.0142-0.0304-0.05850.01540.0399-0.2170.3253-0.1370.24990.77850.09980.6413-38.12588.584338.2323
430.09030.0268-0.00760.03490.04930.10150.28680.1105-0.18170.03870.0757-0.05890.1310.24590.01670.2665-0.1135-0.0630.6478-0.00530.3587-27.99379.299537.4599
440.0756-0.00710.01860.25330.09930.04450.01650.01820.1108-0.04950.0820.0124-0.0673-0.01940.11980.4136-0.20420.24470.7313-0.03230.6792-19.43927.014427.6757
450.26670.18380.48380.13540.33570.84110.18310.1728-0.07740.13390.0489-0.68140.459-0.07740.06980.3606-0.02010.01940.74610.09340.4489-11.5376-22.920419.5098
460.63370.3328-0.29540.2925-0.16060.13790.34090.10460.0324-0.11720.11930.29580.2269-0.09950.04220.67140.1209-0.13230.4325-0.01650.3206-21.9029-27.723225.8453
470.1047-0.1017-0.02630.1468-0.00790.02830.3601-0.278-0.3106-0.28950.024-0.2771-0.035-0.29060.00240.8918-0.3156-0.13660.56330.03780.7169-17.5253-28.53429.2817
480.0220.11930.11190.73030.87331.26680.26760.0183-0.03620.2606-0.01570.04710.340.06580.34940.4112-0.3392-0.11780.44280.02790.5657-33.7838-28.269822.8968
490.0213-0.0277-0.0250.04090.03440.02880.0434-0.1499-0.1130.13230.23080.1407-0.1052-0.1079-0.00031.80540.0534-0.01940.9168-0.08241.4973-7.914933.155212.9142
500.0024-0.0007-0.00230.0111-0.00390.0041-0.06780.0031-0.008-0.03640.06940.0139-0.03710.0635-0.00011.7767-0.001-0.08171.73320.46921.7332-4.261433.21615.8946
510.0197-0.0193-0.06260.04460.0720.2020.02660.00910.07270.0281-0.0725-0.02550.01230.0057-0.00091.487-0.47340.40161.5742-0.45151.60914.54435.79466.8173
520.03030.02780.00290.0273-0.00270.01660.1236-0.042-0.02020.02550.1583-0.0247-0.04930.0117-0.00441.7428-0.18750.05381.2650.48641.44-5.006141.151612.0212
53-0-0.0017-0.00140.0160.00960.00610.02310.00180.03590.07330.05580.0051-0.0664-0.04850.00171.4636-0.2984-0.33241.40740.1490.7705-2.833633.956515.8515
54-0.00090.0011-0.001-0.001-0.00060.00040.01780.2040.1449-0.1823-0.076-0.0434-0.1791-0.0509-0.00011.0345-0.0292-0.18250.79880.18510.3749-11.453511.689910.1949
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 12 )R2 - 12
2X-RAY DIFFRACTION2chain 'T' and (resid 2 through 11 )T2 - 11
3X-RAY DIFFRACTION3chain 'T' and (resid 12 through 16 )T12 - 16
4X-RAY DIFFRACTION4chain 'T' and (resid 17 through 22 )T17 - 22
5X-RAY DIFFRACTION5chain 'T' and (resid 23 through 27 )T23 - 27
6X-RAY DIFFRACTION6chain 'N' and (resid 2 through 6 )N2 - 6
7X-RAY DIFFRACTION7chain 'N' and (resid 7 through 11 )N7 - 11
8X-RAY DIFFRACTION8chain 'N' and (resid 12 through 16 )N12 - 16
9X-RAY DIFFRACTION9chain 'N' and (resid 17 through 17 )N17
10X-RAY DIFFRACTION10chain 'A' and (resid 3 through 278 )A3 - 278
11X-RAY DIFFRACTION11chain 'A' and (resid 279 through 590 )A279 - 590
12X-RAY DIFFRACTION12chain 'A' and (resid 591 through 845 )A591 - 845
13X-RAY DIFFRACTION13chain 'A' and (resid 846 through 1446 )A846 - 1446
14X-RAY DIFFRACTION14chain 'B' and (resid 20 through 97 )B20 - 97
15X-RAY DIFFRACTION15chain 'B' and (resid 98 through 269 )B98 - 269
16X-RAY DIFFRACTION16chain 'B' and (resid 270 through 494 )B270 - 494
17X-RAY DIFFRACTION17chain 'B' and (resid 495 through 796 )B495 - 796
18X-RAY DIFFRACTION18chain 'B' and (resid 797 through 1038 )B797 - 1038
19X-RAY DIFFRACTION19chain 'B' and (resid 1039 through 1221 )B0
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 51 )C2 - 51
21X-RAY DIFFRACTION21chain 'C' and (resid 52 through 96 )C52 - 96
22X-RAY DIFFRACTION22chain 'C' and (resid 97 through 176 )C97 - 176
23X-RAY DIFFRACTION23chain 'C' and (resid 177 through 209 )C177 - 209
24X-RAY DIFFRACTION24chain 'C' and (resid 210 through 268 )C210 - 268
25X-RAY DIFFRACTION25chain 'E' and (resid 3 through 46 )E3 - 46
26X-RAY DIFFRACTION26chain 'E' and (resid 47 through 89 )E47 - 89
27X-RAY DIFFRACTION27chain 'E' and (resid 90 through 103 )E90 - 103
28X-RAY DIFFRACTION28chain 'E' and (resid 104 through 215 )E104 - 215
29X-RAY DIFFRACTION29chain 'F' and (resid 70 through 102 )F70 - 102
30X-RAY DIFFRACTION30chain 'F' and (resid 103 through 127 )F103 - 127
31X-RAY DIFFRACTION31chain 'F' and (resid 128 through 142 )F128 - 142
32X-RAY DIFFRACTION32chain 'F' and (resid 143 through 154 )F143 - 154
33X-RAY DIFFRACTION33chain 'H' and (resid 2 through 81 )H2 - 81
34X-RAY DIFFRACTION34chain 'H' and (resid 82 through 105 )H82 - 105
35X-RAY DIFFRACTION35chain 'H' and (resid 106 through 146 )H106 - 146
36X-RAY DIFFRACTION36chain 'I' and (resid 2 through 28 )I2 - 28
37X-RAY DIFFRACTION37chain 'I' and (resid 29 through 52 )I29 - 52
38X-RAY DIFFRACTION38chain 'I' and (resid 53 through 87 )I53 - 87
39X-RAY DIFFRACTION39chain 'I' and (resid 88 through 119 )I88 - 119
40X-RAY DIFFRACTION40chain 'J' and (resid 1 through 10 )J1 - 10
41X-RAY DIFFRACTION41chain 'J' and (resid 11 through 31 )J11 - 31
42X-RAY DIFFRACTION42chain 'J' and (resid 32 through 43 )J32 - 43
43X-RAY DIFFRACTION43chain 'J' and (resid 44 through 55 )J44 - 55
44X-RAY DIFFRACTION44chain 'J' and (resid 56 through 65 )J56 - 65
45X-RAY DIFFRACTION45chain 'K' and (resid 1 through 29 )K1 - 29
46X-RAY DIFFRACTION46chain 'K' and (resid 30 through 52 )K30 - 52
47X-RAY DIFFRACTION47chain 'K' and (resid 53 through 70 )K53 - 70
48X-RAY DIFFRACTION48chain 'K' and (resid 71 through 114 )K71 - 114
49X-RAY DIFFRACTION49chain 'L' and (resid 28 through 36 )L28 - 36
50X-RAY DIFFRACTION50chain 'L' and (resid 37 through 41 )L37 - 41
51X-RAY DIFFRACTION51chain 'L' and (resid 42 through 46 )L42 - 46
52X-RAY DIFFRACTION52chain 'L' and (resid 47 through 51 )L47 - 51
53X-RAY DIFFRACTION53chain 'L' and (resid 52 through 58 )L52 - 58
54X-RAY DIFFRACTION54chain 'L' and (resid 59 through 70 )L59 - 70

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る