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- PDB-6upy: 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: 6upy
タイトルRNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 2E
要素
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • Non-template strand DNA
  • RNA
  • Template strand DNA
キーワードTRANSCRIPTION/RNA/DNA / RNA polymerase II / 5-guanidinohydantoin / elongation complex / DNA lesion / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex
機能・相同性
機能・相同性情報


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / 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 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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 Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit
類似検索 - ドメイン・相同性
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.4 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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

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


分子量 (理論値)分子数
合計 (水以外)488,02323
ポリマ－486,97013
非ポリマー1,05310
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)168.536, 223.125, 193.062
Angle α, β, γ (deg.)90.000, 100.920, 90.000
Int Tables number5
Space group name H-MC121

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要素

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RNA鎖 , 1種, 1分子 R

#1: RNA鎖 RNA


分子量: 2934.831 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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DNA鎖 , 2種, 2分子 TN

#2: DNA鎖 Template strand DNA


分子量: 8745.599 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: DNA鎖 Non-template strand DNA


分子量: 5663.694 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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DNA-directed RNA polymerase II subunit ... , 5種, 5分子 ABCIK

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


分子量: 191821.578 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P04050, DNA-directed RNA polymerase
#5: タンパク質 DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


分子量: 138937.297 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P08518, DNA-directed RNA polymerase
#6: タンパク質 DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


分子量: 35330.457 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P16370
#10: タンパク質 DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


分子量: 14308.161 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P27999
#12: タンパク質 DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


分子量: 13633.493 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P38902

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

#7: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


分子量: 25117.094 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20434
#8: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


分子量: 17931.834 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20435
#9: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


分子量: 16525.363 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P20436
#11: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


分子量: 8290.732 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P22139
#13: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


分子量: 7729.969 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P40422

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非ポリマー , 3種, 10分子

#14: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn
#15: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg
#16: 化合物 ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE / α,β-メチレンATP


分子量: 505.208 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C11H18N5O12P3 / タイプ: SUBJECT OF INVESTIGATION
コメント: AMP-CPP, エネルギー貯蔵分子類似体*YM

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.66 Å3/Da / 溶媒含有率: 66.39 % / Mosaicity: 0.15 °
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: 8.2.2 / 波長: 1.00003 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2018年9月14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: 1.00003 Å / 相対比: 1
反射解像度: 3.29→49.22 Å / Num. obs: 105549 / % possible obs: 99.6 % / 冗長度: 7.7 % / Biso Wilson estimate: 89.89 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.45 / Rpim(I) all: 0.173 / Rrim(I) all: 0.482 / Net I/σ(I): 6 / Num. measured all: 816457 / Scaling rejects: 8
反射 シェル解像度: 3.29→3.35 Å / 冗長度: 7.8 % / Rmerge(I) obs: 4.436 / Num. measured all: 40606 / Num. unique obs: 5201 / CC1/2: 0.278 / Rpim(I) all: 1.694 / Rrim(I) all: 4.75 / Net I/σ(I) obs: 0.7 / % possible all: 99.3

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
Aimless0.7.2データスケーリング
PDB_EXTRACT3.25データ抽出
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6BLO

6blo


解像度: 3.4→49.218 Å / SU ML: 0.53 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 32.74
Rfactor反射数%反射
Rfree0.2824 1809 1.89 %
Rwork0.2273 --
obs0.2283 95532 99.49 %
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: 393.93 Å2 / Biso mean: 110.0914 Å2 / Biso min: 25.23 Å2
精密化ステップサイクル: final / 解像度: 3.4→49.218 Å
タンパク質核酸リガンド溶媒全体
原子数27957 1016 40 0 29013
Biso mean--171.89 --
残基数----3580
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4-3.49190.40921380.3537712899
3.4919-3.59460.3881380.3324715499
3.5946-3.71060.35631380.3001717199
3.7106-3.84320.35341380.2906715899
3.8432-3.9970.31151400.2699722299
3.997-4.17880.29881380.23637160100
4.1788-4.3990.27271400.21077214100
4.399-4.67440.28141400.19957226100
4.6744-5.0350.25581380.1987186100
5.035-5.54110.28311400.20877241100
5.5411-6.34150.31351400.21977256100
6.3415-7.98410.26181410.20867267100
7.9841-49.2180.20481400.18327340100
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)
13.97362.1679-0.71184.3243-0.81161.2270.61140.2712-0.1687-0.1041-0.4412-0.80010.31020.6207-0.28711.2003-0.0226-0.18310.91160.12731.024913.155812.693839.7283
22.12891.81520.36255.48892.33013.74460.21130.17370.3901-0.50640.2261-0.3473-0.45190.4594-0.54171.8579-0.07830.07291.9892-0.08112.320849.069311.174577.9593
30.01620.0065-0.18070.0127-0.0212.3157-0.2444-0.17120.14090.48920.1692-0.8238-0.43730.7872-0.00982.29540.2136-0.11041.65920.39592.175532.641711.962257.9156
42.27411.9456-0.41264.04980.92350.7679-0.24310.0119-0.1416-0.0814-0.3882-0.4352-0.6815-0.08940.78891.4812-0.2183-0.2280.7922-0.07940.873212.970211.966835.776
51.73081.27962.5461.29371.37364.3606-0.71960.54250.68980.1774-0.12150.47740.00340.4261.12681.9596-0.1587-0.1932.46310.07062.398545.171810.404674.6693
60.5796-0.27410.0390.6027-0.0971.00150.16730.02070.04580.1632-0.05-0.24640.2460.2162-0.10040.9929-0.1224-0.26770.45860.06260.622918.6352-4.253546.5557
70.2031-0.07560.04580.76650.02010.84790.0019-0.07640.03350.24650.1075-0.01280.04710.0899-0.10911.53070.0238-0.47910.6516-0.02050.827522.9361-18.600475.0079
81.2236-0.1980.01371.34360.15921.0748-0.08430.11820.5986-0.57090.1293-0.1127-0.39250.1884-0.01230.9837-0.2409-0.00260.57590.08850.5962-0.337442.350741.6315
90.8878-0.15432.13540.6817-0.03645.2849-0.2679-0.05320.16040.58640.1612-0.3701-0.38050.32460.20191.3143-0.3515-0.08720.6042-0.0010.705310.28830.151155.81
101.73820.02150.63350.6620.88731.7548-0.28230.05470.18360.17980.2808-0.21640.17240.1602-0.02911.1633-0.1989-0.23070.6353-0.06220.764124.260537.232378.7698
110.0339-0.16710.17350.7041-0.09181.1929-0.1116-0.0224-0.0506-0.02380.0495-0.5403-0.50180.49740.1329-0.2845-0.45540.33690.65280.10040.608510.78930.712146.6821
121.38930.30540.76632.44750.52691.75430.365-0.2361-0.01281.0234-0.0912-0.1832-0.1511-0.4163-0.04290.27440.06270.37790.68460.02120.2839-8.732736.64171.4541
130.62790.03810.28311.0590.27711.92680.1330.1917-0.024-0.0365-0.0107-0.1494-0.05790.1372-0.1020.546-0.1498-0.04150.44160.0630.4309-8.19189.762433.7738
141.1041-0.5750.40920.8869-0.00620.71880.19180.30990.291-0.0592-0.1678-0.44980.14690.3633-0.00380.9545-0.1089-0.16940.54050.11010.655323.863-4.890831.746
154.81680.5592-0.79426.4016-2.72574.8082-0.0389-0.4041-0.39670.2421-0.06860.37420.0747-0.1556-0.07680.9643-0.5705-0.14181.0440.16350.7005-44.0649-16.677729.9134
161.49680.28160.98780.74490.00920.6404-0.20020.1258-0.2032-0.66260.24750.11490.35110.00840.01760.9136-0.1863-0.04340.75820.06760.4309-24.886-1.777116.5155
171.85140.3609-0.62322.34350.26211.39620.05130.4355-0.1596-0.5935-0.05820.3543-0.1048-0.2154-0.08931.0450.0779-0.18170.88480.06640.4868-30.3339.841110.5598
180.9065-0.02230.06371.5822-0.50941.06650.3583-0.097-0.3350.1568-0.06780.30060.4194-0.2502-0.30731.2055-0.2877-0.34210.77930.09730.604-32.332-11.755531.9416
192.96561.0732-0.58890.8126-0.34594.5143-0.5569-0.83940.05240.29910.19940.3241-0.00810.03450.3722.51370.3831-0.92571.0871-0.10661.314940.5701-22.497595.2737
200.26670.35640.33860.4790.50060.9375-0.2605-0.89610.46261.2159-0.0389-0.2224-0.72350.06630.39562.90490.6695-1.22111.9349-0.30391.819643.5137-18.3104108.39
211.0983-0.7956-0.70631.19350.82421.0676-0.7628-0.84510.7111.08730.2967-0.5059-0.9049-0.09750.44352.35380.4712-1.1191.4236-0.25041.681852.2442-23.300895.0714
220.8982-1.775-0.82754.26460.93451.6215-1.2034-0.91471.29941.07181.5988-2.3538-0.64221.833-0.79821.79570.1507-0.9541.9125-0.59572.294856.8295-19.200688.0683
232.7880.0105-0.44011.9845-1.13332.77860.3546-0.14310.5364-0.2070.7882-1.1818-0.1491.3681-0.74711.87960.138-0.79721.6646-0.47731.951254.6929-12.096884.9805
242.0496-0.6044-0.03380.43280.82912.406-0.1518-0.25550.11850.42290.1627-0.61160.10230.1128-0.08561.44980.1759-0.61290.6643-0.03931.082340.7879-23.841670.3749
250.93450.21320.52690.04670.11890.2961-0.39650.65340.32440.70010.2359-1.22171.50091.82580.01281.51670.5712-0.20231.2665-0.17161.484846.176-36.896741.8223
261.14020.58910.97780.8916-0.11832.226-0.0510.4797-0.4476-0.00240.2968-0.440.53040.2206-0.31531.79890.3284-0.39380.75320.12430.893330.389-37.348644.4166
272.5331-0.2359-1.97411.91181.2842.1730.04320.4119-0.2009-0.0078-0.2209-0.0865-0.16060.3930.12631.04890.1623-0.17550.686-0.00720.711724.9848-28.999129.835
287.0898-1.3871.03264.62171.61622.1168-0.07570.3425-0.158-0.058-0.28190.0015-0.1189-0.41970.37681.43770.0577-0.14871.0369-0.07790.773418.5314-37.155919.8398
291.18360.6401-0.10029.3493-6.43514.52930.01040.07120.01550.01780.03440.5445-0.3913-0.8653-0.01261.37870.0193-0.32880.9987-0.0010.788918.1673-35.188627.5545
301.9333-0.51250.38060.9175-0.2771.6194-0.1940.25860.7842-0.14980.3365-0.23150.0101-0.0798-0.07442.04150.3051-0.18771.0217-0.20270.949931.9348-35.963733.3264
311.93311.86253.88692.92593.80097.8209-0.38450.3043-0.39340.4247-0.2455-0.4066-0.3085-0.19920.64051.54650.1919-0.09790.7752-0.3311.313139.6896-32.704142.5858
325.16222.63132.77956.5033-3.2495.8839-0.23910.4889-0.9665-0.2653-0.19830.00930.84570.22540.41911.46110.121-0.30080.7081-0.13951.068526.7771-40.750938.3286
331.49180.8826-0.35461.5316-1.34191.3517-0.16940.005-0.66020.32410.11430.12660.3987-0.04030.20061.3593-0.3807-0.02390.84410.51461.3883-26.7856-48.992264.9918
343.17841.51150.03984.33081.20781.9536-0.2609-0.0899-0.28860.0575-0.10330.1652-0.2282-0.05670.1951.3301-0.3373-0.05460.92430.14620.7877-24.7155-33.996265.1976
352.6331-0.2259-0.34620.96031.44692.1956-0.2505-0.4165-0.61860.15920.00750.39710.633-0.02490.19311.4542-0.6015-0.25230.90210.20421.3172-24.8148-47.007169.2363
360.414-0.23510.95954.2764-1.35272.3843-0.3848-0.0209-0.46440.32320.47770.2831-0.3048-0.4649-0.08350.9742-0.3196-0.01050.74030.41571.24-31.7932-42.424962.0607
371.55122.5168-3.4414.2658-5.85988.04770.08010.2325-0.7924-0.90090.0385-0.15890.42250.06450.00581.84340.0718-0.22810.8109-0.06811.18-21.2673-48.279441.705
385.2523.8032-2.22977.1308-2.21421.8315-0.58120.85450.6068-0.88340.40590.4998-0.2202-0.1770.14651.4599-0.873-0.39471.09520.10781.6452-31.9723-50.469245.0556
391.7039-0.30290.22841.8748-0.0372.9373-0.0791-0.1903-0.44070.267-0.1864-0.12120.34290.09840.06121.6415-0.6007-0.2771.10690.46291.2018-16.3369-45.615158.5006
402.5556-2.5379-0.00372.64760.07290.0371-0.0904-0.5292-0.65230.5571-0.002-0.21690.80290.6510.21962.3369-0.6999-0.32671.72830.55821.6004-10.6171-54.698574.6312
411.69730.1966-1.65814.5488-1.39372.2067-0.1738-0.4548-0.62560.5729-0.1637-0.1340.4950.21890.14271.5699-0.6318-0.33010.96420.49680.9199-16.6325-45.095663.6778
422.1176-1.33921.31711.56190.94025.2115-0.5413-0.0252-0.6725-0.4366-0.1421-0.39060.80150.45250.74282.3903-0.3983-0.41611.37740.44541.4257-14.3753-55.513260.3662
430.5875-1.2356-1.62845.53041.80249.4844-0.1726-0.0289-0.5183-0.0083-0.43090.41840.4707-0.39860.48911.2967-0.4542-0.39220.8210.4791.4232-29.7724-48.492356.4788
445.72144.4883-2.01614.6819-2.20683.33760.3413-0.15190.16070.2605-0.0690.09650.04910.208-0.05921.52880.0758-0.18340.7427-0.3980.670426.408642.904299.1559
450.0992-0.4515-0.05732.2298-0.2571.52720.2404-0.1008-0.13590.2073-0.0512-0.26790.04420.0655-0.1081.5854-0.1109-0.27610.7487-0.11190.968529.15334.3089105.1625
461.8557-0.5139-1.79051.36761.2045.58360.3204-0.2604-0.30580.0725-0.42740.1883-0.57220.38130.00861.2703-0.068-0.08270.8631-0.07790.5629-7.644127.14792.7092
475.9833-2.3961-1.3325.9090.42513.22550.3025-0.543-0.0846-0.7605-0.1737-0.1190.10060.19170.04091.705-0.2121-0.26360.96130.06290.6880.119720.97395.223
480.6753-0.6560.42631.0446-0.26390.3134-0.36680.2032-0.1035-0.76240.1627-0.01840.3199-0.1340.19990.2937-0.21040.03390.5810.21740.3764-25.03726.912329.619
493.4193-1.5317-2.42294.20920.57572.21950.39680.21180.4981-0.10040.02310.79960.1509-0.7581-0.09360.4147-0.190.0410.74070.1050.6372-36.296315.803233.8425
502.21220.1576-0.56180.05710.10230.58220.14530.03970.22970.2105-0.16450.3642-0.0087-0.1581-0.1117-0.1108-0.03750.37210.90030.06050.3974-33.85067.145138.1831
511.9789-1.70051.54573.0797-0.42271.70930.07240.23730.1738-0.15380.1315-0.0078-0.16580.05710.0410.1261-0.32870.17880.49010.12010.4541-20.472923.802129.3567
520.5665-0.8985-0.47021.6680.32461.6247-0.11010.3524-0.40470.3705-0.3319-0.4952-0.1014-0.80640.58570.74040.18240.11010.9440.0760.5646-9.5864-8.572820.0851
532.9457-0.31822.72922.0425-0.59342.56840.39310.2477-0.3355-0.2549-0.3606-0.72590.58550.6719-0.20861.2302-0.0574-0.10531.0564-0.0360.7723-12.9432-25.211815.6915
540.88570.687-1.26780.5387-0.97041.84840.1114-0.307-1.18010.3683-0.2374-0.17391.01840.58420.12082.14660.0259-0.51161.16840.10981.2348-11.1878-43.51128.4925
550.5412-0.5142-0.14763.4194-0.43642.06810.28110.1409-0.340.0534-0.19310.55080.5255-0.0434-0.01631.6988-0.1801-0.61240.5998-0.03110.6872-21.6204-27.93526.0737
560.83161.9090.44016.36471.18481.29910.6239-0.252-0.73750.2478-0.17830.7330.8325-0.7096-0.18111.5569-0.446-0.61960.94250.08980.8439-23.1945-36.721230.9438
577.06285.6686-0.70094.67980.13043.76340.25820.0306-0.4085-0.2581-0.0964-0.10460.6065-0.4013-0.16561.3034-0.1427-0.36320.58250.07960.5831-10.1209-18.721428.3751
585.05953.45640.42375.57232.04491.60390.2949-0.0335-1.0384-0.03420.1501-0.27660.7841-0.5526-0.13641.5953-0.2636-0.64260.68470.02880.9923-18.7749-37.535425.9586
592.0716-0.53880.5120.3391-0.43031.11450.28740.1963-0.3229-0.06970.22110.56240.4162-0.5862-0.16880.384-0.4925-0.11540.9005-0.04411.205-39.1185-24.074522.0793
601.993-0.2956-1.42510.35961.74688.45850.8354-0.9711.43120.02830.17260.5726-1.7084-0.8737-0.88492.68210.57550.38561.2416-0.20541.3811-7.499632.533512.2154
611.60171.62332.23593.81490.59414.6912-1.9291.0384-0.2424-1.15531.2966-0.2880.25250.53720.80652.0561-0.68840.01522.12140.75322.0659-1.875836.15257.832
622.70763.33490.5948.0551.02633.6051-0.1241-0.16240.70480.2876-0.32340.0747-2.13460.81920.4032.2779-0.4983-0.44771.22890.35790.8148-2.58833.425915.5313
633.92244.9335-1.95377.3517-3.43054.9727-0.43280.54820.4148-0.75010.05590.0051-0.95760.3460.56790.77750.1921-0.1491.07810.20640.4855-11.523611.249310.0689
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'R' and (resid 1 through 9 )R1 - 9
2X-RAY DIFFRACTION2chain 'T' and (resid 4 through 13 )T4 - 13
3X-RAY DIFFRACTION3chain 'T' and (resid 14 through 18 )T14 - 18
4X-RAY DIFFRACTION4chain 'T' and (resid 20 through 28 )T20 - 28
5X-RAY DIFFRACTION5chain 'N' and (resid 2 through 16 )N2 - 16
6X-RAY DIFFRACTION6chain 'A' and (resid 3 through 844 )A3 - 844
7X-RAY DIFFRACTION7chain 'A' and (resid 845 through 1446 )A845 - 1446
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 191 )B20 - 191
9X-RAY DIFFRACTION9chain 'B' and (resid 192 through 251 )B192 - 251
10X-RAY DIFFRACTION10chain 'B' and (resid 252 through 408 )B252 - 408
11X-RAY DIFFRACTION11chain 'B' and (resid 409 through 545 )B409 - 545
12X-RAY DIFFRACTION12chain 'B' and (resid 546 through 742 )B546 - 742
13X-RAY DIFFRACTION13chain 'B' and (resid 743 through 1071 )B743 - 1071
14X-RAY DIFFRACTION14chain 'B' and (resid 1072 through 1221 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 26 )C2 - 26
16X-RAY DIFFRACTION16chain 'C' and (resid 27 through 88 )C27 - 88
17X-RAY DIFFRACTION17chain 'C' and (resid 89 through 137 )C89 - 137
18X-RAY DIFFRACTION18chain 'C' and (resid 138 through 268 )C138 - 268
19X-RAY DIFFRACTION19chain 'E' and (resid 3 through 38 )E3 - 38
20X-RAY DIFFRACTION20chain 'E' and (resid 39 through 54 )E39 - 54
21X-RAY DIFFRACTION21chain 'E' and (resid 55 through 65 )E55 - 65
22X-RAY DIFFRACTION22chain 'E' and (resid 66 through 103 )E66 - 103
23X-RAY DIFFRACTION23chain 'E' and (resid 104 through 136 )E104 - 136
24X-RAY DIFFRACTION24chain 'E' and (resid 137 through 215 )E137 - 215
25X-RAY DIFFRACTION25chain 'F' and (resid 69 through 78 )F69 - 78
26X-RAY DIFFRACTION26chain 'F' and (resid 79 through 86 )F79 - 86
27X-RAY DIFFRACTION27chain 'F' and (resid 87 through 103 )F87 - 103
28X-RAY DIFFRACTION28chain 'F' and (resid 104 through 116 )F104 - 116
29X-RAY DIFFRACTION29chain 'F' and (resid 117 through 126 )F117 - 126
30X-RAY DIFFRACTION30chain 'F' and (resid 127 through 137 )F127 - 137
31X-RAY DIFFRACTION31chain 'F' and (resid 138 through 147 )F138 - 147
32X-RAY DIFFRACTION32chain 'F' and (resid 148 through 154 )F148 - 154
33X-RAY DIFFRACTION33chain 'H' and (resid 2 through 16 )H2 - 16
34X-RAY DIFFRACTION34chain 'H' and (resid 17 through 30 )H17 - 30
35X-RAY DIFFRACTION35chain 'H' and (resid 31 through 43 )H31 - 43
36X-RAY DIFFRACTION36chain 'H' and (resid 44 through 60 )H44 - 60
37X-RAY DIFFRACTION37chain 'H' and (resid 61 through 82 )H61 - 82
38X-RAY DIFFRACTION38chain 'H' and (resid 83 through 94 )H83 - 94
39X-RAY DIFFRACTION39chain 'H' and (resid 95 through 105 )H95 - 105
40X-RAY DIFFRACTION40chain 'H' and (resid 106 through 111 )H106 - 111
41X-RAY DIFFRACTION41chain 'H' and (resid 112 through 127 )H112 - 127
42X-RAY DIFFRACTION42chain 'H' and (resid 128 through 140 )H128 - 140
43X-RAY DIFFRACTION43chain 'H' and (resid 141 through 146 )H141 - 146
44X-RAY DIFFRACTION44chain 'I' and (resid 2 through 13 )I2 - 13
45X-RAY DIFFRACTION45chain 'I' and (resid 14 through 52 )I14 - 52
46X-RAY DIFFRACTION46chain 'I' and (resid 53 through 87 )I53 - 87
47X-RAY DIFFRACTION47chain 'I' and (resid 88 through 118 )I88 - 118
48X-RAY DIFFRACTION48chain 'J' and (resid 1 through 10 )J1 - 10
49X-RAY DIFFRACTION49chain 'J' and (resid 11 through 31 )J11 - 31
50X-RAY DIFFRACTION50chain 'J' and (resid 32 through 51 )J32 - 51
51X-RAY DIFFRACTION51chain 'J' and (resid 52 through 65 )J52 - 65
52X-RAY DIFFRACTION52chain 'K' and (resid 1 through 9 )K1 - 9
53X-RAY DIFFRACTION53chain 'K' and (resid 10 through 23 )K10 - 23
54X-RAY DIFFRACTION54chain 'K' and (resid 24 through 29 )K24 - 29
55X-RAY DIFFRACTION55chain 'K' and (resid 30 through 52 )K30 - 52
56X-RAY DIFFRACTION56chain 'K' and (resid 53 through 62 )K53 - 62
57X-RAY DIFFRACTION57chain 'K' and (resid 63 through 69 )K63 - 69
58X-RAY DIFFRACTION58chain 'K' and (resid 70 through 82 )K70 - 82
59X-RAY DIFFRACTION59chain 'K' and (resid 83 through 114 )K83 - 114
60X-RAY DIFFRACTION60chain 'L' and (resid 28 through 36 )L28 - 36
61X-RAY DIFFRACTION61chain 'L' and (resid 37 through 51 )L37 - 51
62X-RAY DIFFRACTION62chain 'L' and (resid 52 through 58 )L52 - 58
63X-RAY DIFFRACTION63chain 'L' and (resid 59 through 70 )L59 - 70

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る