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- PDB-6blp: Pol II elongation complex with an abasic lesion at i+1 position, ... -

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基本情報

登録情報
データベース: PDB / ID: 6blp
タイトルPol II elongation complex with an abasic lesion at i+1 position, soaking AMPCPP
要素
  • (DNA-directed RNA polymerase II subunit ...ポリメラーゼ) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNAポリメラーゼ) x 5
  • DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')
  • RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*G)-3')
キーワードTRANSCRIPTION (転写 (生物学)) / Complex / DNA BINDING PROTEIN (DNA結合タンパク質) / DNA-RNA HYBRID
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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes ...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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA-templated transcription / termination of RNA polymerase III transcription / 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 / RNA polymerase II activity / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / DNA修復 / RNA polymerase I complex / RNA polymerase III complex / transcription by RNA polymerase I / transcription by RNA polymerase III / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / ペルオキシソーム / cytoplasmic stress granule / リボソーム生合成 / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / 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
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 ...Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase 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 / 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 Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Homeodomain-like / Single Sheet / Nucleic acid-binding proteins / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain
類似検索 - ドメイン・相同性
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / デオキシリボ核酸 / DNA (> 10) / リボ核酸 / 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 / デオキシリボ核酸 / DNA (> 10) / リボ核酸 / 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 / 解像度: 3.203 Å
データ登録者Wang, W. / 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)R01 GM102362 米国
引用ジャーナル: Proc. Natl. Acad. Sci. U.S.A. / 年: 2018
タイトル: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
著者: Wang, W. / Walmacq, C. / Chong, J. / Kashlev, M. / Wang, D.
履歴
登録2017年11月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年2月28日Provider: repository / タイプ: Initial release
改定 1.12018年3月14日Group: Database references / カテゴリ: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22018年3月21日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42024年3月13日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
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
T: DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')
R: RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*G)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)482,07223
ポリマ－480,99512
非ポリマー1,07711
水181
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area61650 Å2
ΔGint-398 kcal/mol
Surface area136070 Å2
手法PISA
単位格子
Length a, b, c (Å)169.060, 222.180, 193.200
Angle α, β, γ (deg.)90.00, 101.34, 90.00
Int Tables number5
Space group name H-MC121

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要素

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

#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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150 / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPB2, RPB150, RPO22, YOR151C / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 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 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II ...RNA polymerase II subunit 3 / 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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P16370
#7: 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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPB9, YGL070C / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P27999
#9: 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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPB11 / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P38902

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

#4: 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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPB5, RPA7, RPC9, YBR154C, YBR1204 / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P20434
#5: タンパク質 DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNAポリメラーゼ


分子量: 17931.834 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPO26 / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P20435
#6: 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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPB8, YOR224C, YOR50-14 / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P20436
#8: 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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPB10, YOR210W / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P22139
#10: 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: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 遺伝子: RPC10, RPB12, YHR143W-A, YHR143BW / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P40422

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DNA鎖 / RNA鎖 , 2種, 2分子 TR

#11: DNA鎖 DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')


分子量: 8779.650 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#12: RNA鎖 RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*G)-3')


分子量: 2589.625 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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非ポリマー , 4種, 12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: 2 / 由来タイプ: 合成 / 式: Mg
#15: 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
コメント: AMP-CPP, エネルギー貯蔵分子類似体*YM
#16: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 1 / 由来タイプ: 天然 / 式: H2O

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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: 3.7 Å3/Da / 溶媒含有率: 66.74 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 5.0.1 / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2016年12月18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 Å / 相対比: 1
反射解像度: 3.2→82.9 Å / Num. obs: 99794 / % possible obs: 99.4 % / 冗長度: 3.5 % / Net I/σ(I): 5.3

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解析

ソフトウェア
名称バージョン分類
PHENIX1.8.4_1496精密化
MOSFLMデータ削減
SCALAデータスケーリング
PHASER位相決定
精密化解像度: 3.203→82.88 Å / SU ML: 0.41 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 25.89 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2567 4881 4.89 %
Rwork0.2144 --
obs0.2164 99769 87.04 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.203→82.88 Å
タンパク質核酸リガンド溶媒全体
原子数27808 389 41 1 28239
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00228804
X-RAY DIFFRACTIONf_angle_d0.53138981
X-RAY DIFFRACTIONf_dihedral_angle_d11.62410987
X-RAY DIFFRACTIONf_chiral_restr0.0214381
X-RAY DIFFRACTIONf_plane_restr0.0024973
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.203-3.23940.360290.3109205X-RAY DIFFRACTION6
3.2394-3.27760.3633360.3518646X-RAY DIFFRACTION18
3.2776-3.31750.2945640.30871302X-RAY DIFFRACTION36
3.3175-3.35950.3828870.31471850X-RAY DIFFRACTION51
3.3595-3.40370.30931000.29782346X-RAY DIFFRACTION63
3.4037-3.45040.34181340.29212570X-RAY DIFFRACTION72
3.4504-3.49960.33661650.28242961X-RAY DIFFRACTION82
3.4996-3.55190.351840.28383255X-RAY DIFFRACTION91
3.5519-3.60740.34531900.2833565X-RAY DIFFRACTION99
3.6074-3.66650.31682000.27013595X-RAY DIFFRACTION100
3.6665-3.72980.31371850.25873614X-RAY DIFFRACTION100
3.7298-3.79760.29661940.25413642X-RAY DIFFRACTION100
3.7976-3.87060.29691760.25293663X-RAY DIFFRACTION100
3.8706-3.94960.30491690.24053615X-RAY DIFFRACTION100
3.9496-4.03550.25241850.22663598X-RAY DIFFRACTION100
4.0355-4.12940.3021860.2113640X-RAY DIFFRACTION100
4.1294-4.23260.25771890.20053601X-RAY DIFFRACTION100
4.2326-4.34710.21431930.18883630X-RAY DIFFRACTION100
4.3471-4.4750.24471760.18023597X-RAY DIFFRACTION100
4.475-4.61940.24111900.16973603X-RAY DIFFRACTION100
4.6194-4.78450.22261900.16473641X-RAY DIFFRACTION100
4.7845-4.9760.20961600.17273673X-RAY DIFFRACTION100
4.976-5.20250.21271800.183616X-RAY DIFFRACTION100
5.2025-5.47670.22041920.18863624X-RAY DIFFRACTION100
5.4767-5.81980.22951890.20213625X-RAY DIFFRACTION100
5.8198-6.2690.25211940.20813632X-RAY DIFFRACTION100
6.269-6.89950.25322000.21163596X-RAY DIFFRACTION100
6.8995-7.89730.21011870.18833650X-RAY DIFFRACTION100
7.8973-9.9470.17371870.15953647X-RAY DIFFRACTION99
9.947-82.90750.21841900.20073686X-RAY DIFFRACTION99
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)
10.00730.0030.00360.0347-0.00610.01030.05840.00130.15170.0339-0.03790.1524-0.0185-0.16380.02870.02520.1332-0.01030.3579-0.02580.3761491.29370.3133246.2342
20.1781-0.01150.00290.1145-0.10860.50780.2715-0.0052-0.2836-0.09170.06090.02740.4001-0.05090.97540.08920.12760.0386-0.288-0.2697-0.1409532.9522-25.4847228.9335
30.11840.051-0.00210.10710.09940.09270.01020.05170.0135-0.05610.05650.01680.1154-0.02260.12760.3674-0.062-0.18070.04310.01410.2169517.1668-35.7124216.0393
40.00340.00660.00520.00830.00750.0070.0221-0.0051-0.0002-0.0084-0.0169-0.00190.03550.00840.00090.5950.0505-0.15610.22840.08840.3976507.75795.9853176.0097
50.00760.003-0.00250.00350.0010.0016-0.01350.00070.0081-0.046-0.00670.0120.00750.003-0.05590.2733-0.0928-0.15040.10620.05720.1719514.249-22.9222206.4507
60.00850.00620.00120.0033-0.00050.0007-0.0041-0.03440.0244-0.0233-0.03990.0319-0.0126-0.080700.1460.0094-0.03630.22850.0160.3256497.8252-17.1801237.9987
70.0307-0.0049-0.00220.0050.01320.0392-0.052-0.00520.0470.04580.03280.0295-0.1356-0.0755-0.02610.20060.11420.17390.1071-0.11670.185535.208435.538241.7765
80.02320.0102-0.00310.0489-0.04010.04790.09320.020.0777-0.0673-0.00170.0786-0.0538-0.03070.15870.2110.18290.06520.18070.05240.2333515.47428.1867212.0507
90.015-0.03360.00410.13270.02720.04390.0255-0.00480.00550.00630.03430.0045-0.0036-0.01060.10670.14280.1070.08760.1823-0.07550.2085517.911330.7969243.1756
100.01250.0042-0.03630.0313-0.03690.03470.03530.03040.1205-0.0783-0.0150.0072-0.13540.0566-0.03450.02510.02950.24460.0345-0.0188-0.0426542.117323.701217.576
110.02690.00130.00410.0403-0.07730.1530.118-0.10130.07320.1030.02460.0309-0.0486-0.02330.24330.03040.0890.18870.178-0.20560.0202536.89996.6549259.3642
120.02330.01760.06510.1193-0.00860.1490.0264-0.05190.0265-0.0408-0.00690.09410.0466-0.04270.02190.03010.0680.03070.2867-0.08060.2081526.9355-10.1149246.7282
130.0016-0.00140.00050.00060.00010-0.0197-0.00030.00850.0134-0.0107-0.008-0.00690.0013-00.21990.1601-0.0460.4667-0.00550.3633579.0061-22.7198254.4878
140.0024-0.00260.00220.001-0.00170.00210.00860.0209-0.0480.00310.0065-0.00770.01490.01780.00310.10780.1102-0.04040.1822-0.07630.115561.9505-15.6954262.57
150.0053-0.0036-0.00010.0054-0.00720.00970.00130.0072-0.00150.0122-0.00790.00110.00830.0449-0.02130.05840.0054-0.00370.2334-0.0450.0733558.7881-2.619273.5463
160.00830.01530.00930.02720.01210.01190.0471-0.0445-0.01370.01210.0076-0.01420.03270.02690.0530.04550.0086-0.07090.2212-0.03610.1253563.98773.5518268.5473
170.0006-0.001-0.0004-0.00040.00050.00040.0081-0.01120.0082-0.00760.0081-0.0162-0.00270.01030.01140.13220.12950.04540.2964-0.08850.2194570.9874-21.6443234.7789
180.0193-0.00820.0070.00830.00150.00470.0283-0.0009-0.00150.00620.0097-0.01310.03590.00840.02490.10310.1238-0.05160.20270.02440.1428569.225-28.3279255.994
190.00210.0030.00180.00240.00330.00390.02750.0383-0.0056-0.0223-0.0159-0.02230.0073-0.0256-00.7205-0.184-0.32820.62630.01190.6361492.5356-29.2714185.7244
200.00040.00050.00070.00020.00060.0009-0.00380.0024-0.0026-0.0004-0.00590.00610.0049-0.0057-00.6549-0.0555-0.08220.68970.02060.6976482.2104-36.3205200.1294
210.0011-0.00050.00070.0001-0.00030.0005-0.00210.00630.0041-0.0013-0.0050.0008-0.00620.0002-01.08480.0316-0.04041.11840.0651.1203476.3111-18.633191.2808
220.0019-00.0011-0.000100.00010.0134-0.0040.0065-0.00380.00440.0005-0.00420.006800.6552-0.0204-0.05380.69050.07670.7375481.8468-18.234196.1449
230.00150.0029-0.00050.0001-0.00390.00560.0059-0.03020.02070.0025-0.04230.041-0.0054-0.0428-0.00490.2262-0.167-0.21940.19570.04580.3635492.4724-29.347211.9324
240.00060.00060.00050.0006-0.00050.00050.00060.0041-0.0050.00750.0031-0.0019-0.00210.001-00.5149-0.0874-0.09160.50320.04020.518498.0562-44.8467240.3785
250.0010.00170.00020.00160.00050.0005-0.0072-0.0188-0.0055-0.00010.00470.00730.0061-0.0003-00.35-0.11320.00130.33220.05730.3446509.8408-35.7722254.3837
260.0001-0.0002-0.00050.00030.00020.0010.0059-0.003-0.00170.00550.00760.0024-0.0006-0.004700.5332-0.0514-0.04120.4970.01310.4845515.812-43.6246264.5987
270.00030.00030.00030.0009-0.00020.00020.00440.0021-0.0064-0.0005-0.0018-0.00150.00070.00300.4384-0.09240.04660.3250.0270.3588513.0342-43.9108256.4729
280.0012-0.00010.00070.0008-0.0010.00110.00650.00360.00270.00570.00610.00330.0054-0.005100.39280.00140.00520.41750.0320.4438495.7911-36.5634242.3582
290.009-0.00580.00310.0045-0.00220.00110.0016-0.00210.00030.0004-0.0005-0.00130.00230.00200.6107-0.044-0.01280.58060.02930.6032497.1067-42.6668244.3494
300.00410.002-0.00250.0011-0.00120.00140.0062-0.0076-0-0.00440.0088-0.0070.0068-0.001200.3137-0.0642-0.01830.24550.02820.297509.1209-46.6206245.783
310.0007-0.0006-0.00040.000200-0.00220.01030.0028-0.0017-0.0017-0.00440.00630.005900.49390.12620.04380.4487-0.07470.5068562.2072-55.2667219.1908
320.0002-0.0006-0.00020.001-0.00020.0011-0.0076-0.00140.0095-0.00730.0012-0.00190.00660.0048-00.49840.1349-0.00160.4551-0.04610.5468560.1515-40.745219.4633
330.0023-0.00130.00240.0010.00060.0014-0.02140.00890.0002-0.00580.0091-0.00870.0065-0.0126-00.48550.1625-0.03540.4523-0.07950.5263559.6938-54.1403215.7209
340.0013-0.0012-0.00090.00150.00260.0054-0.00920.0050.00180.00220.0035-0.0063-0.00070.001-00.40320.1008-0.00410.4365-0.06960.4413568.6729-44.3796222.2561
350.0006-0.00160.00050.0017-0.00070.0001-0.00190.0014-0.0176-0.0160.00670.00190.00320.0019-00.34910.09580.01430.2715-0.06670.3534559.0564-55.717235.8349
360-0.0005-0.00050.00060.00150.00530.0067-0.0091-0.0005-0.0013-0.0034-0.0006-0.00070.0025-00.66950.08350.02050.6280.0170.6853566.444-57.8479242.2137
370.0011-0.0021-0.00110.00310.00210.00090.0048-0.0030.0042-0.00410.0128-0.01280.0014-0.0027-00.47720.0896-0.02410.3811-0.16120.4663553.6213-53.2387225.8627
380.0004-0.00040.00080.0010.00050.001-0.01370.0039-0.00730.00660.0014-0.0038-0.0041-0.0032-00.71240.0595-0.05890.6316-0.07050.6685549.2089-56.6672216.9352
390.001-0.0010.00080.0020.00150.0027-0.0028-0.00230.00080.00050.01480.0048-0.0003-0.01-00.48170.1144-0.05780.4463-0.04810.4233553.1426-50.7866220.1399
40-0-0.00030.00020.0003-00.00020.0041-0.0055-0.0102-0.00290.0047-0.0030.0018-0.0051-00.55980.0392-0.00870.4849-0.050.5429549.75-61.3182225.107
410.0088-0.0007-0.00370.00060.00010.0015-0.00410.0033-0.00150.0016-0.00470.0082-0.00280.0088-00.51740.07690.01030.479-0.04760.5204564.8473-55.292227.9353
42-0.0009-0.00110.00160.0031-0.00170.00110.00920.0084-0.007-0.01840.02620.0116-0.0179-0.010600.59470.048-0.10010.28020.13620.4226506.982429.0958179.9691
430.00420.00060.00470.0057-0.00320.00710.00810.0118-0.0063-0.0098-0.0016-0.00010.002-0.00640.00910.18730.01220.07930.2230.05250.0685539.564217.2414190.4234
440.00070.0003-0.00050.0009-0.00010-0.002-0.0032-0.0005-0.00220.00250.0017-0.00180.0082-00.151-0.01050.03960.2746-0.05330.2273561.6224-0.2569254.9565
450.0006000.00020.00010.0004-0.0077-0.00380.0044-0.0061-0.00460.0028-0.009-0.0016-00.2613-0.00940.06230.3408-0.10090.3507570.21310.2647251.7777
460.0025-0.00280.00430.0025-0.00480.0082-0.0182-0.0015-0.0091-0.0008-0.0294-0.0217-0.02230.0268-0.00030.14720.0430.07670.372-0.01610.2541568.51834.4109246.4091
470.0006-0.0003-00.0005-0.00020.00020.00890.0065-0.00420.00490.0111-0.00270.0029-0.000700.0956-0.01420.00430.1935-0.02590.2192553.947420.5938257.3802
480.0035-0.00280.00340.0057-0.00310.0028-0.0083-0.00550.0005-0.0026-0.01510.01330.00090.0109-0.00150.12920.056-0.00620.1533-0.01380.0867544.6211-15.2435264.1677
490.0001-0.00030.0010.000700.00210.0425-0.0127-0.00940.00160.0120.0080.0020.003-00.33030.0509-0.08090.28060.02820.2514548.7875-35.7923264.1091
500.0046-0.00370.00170.0031-0.00050.00130.01680.001-0.0193-0.0040.001-0.01750.02670.02430.01690.18580.1142-0.09990.13610.05580.1872555.5053-38.2533256.1685
510.0019-0.00270.00080.0031-0.0023-0.00070.0363-0.0095-0.00560.00870.04120.00170.05860.0416-00.22280.1304-0.05690.37120.0120.3597574.1101-30.5186262.5999
520.00010.0001-0.00040.00030.00010.00030.00120.0034-0.0004-0.0063-0.0053-0.0023-0.00310.001-00.7765-0.0240.01940.7411-0.09860.7504541.342325.7076274.355
530.01670.0178-0.0250.0201-0.0280.0388-0.00070.00050.0013-0.0013-0.0008-0.0008-0.00070.00101.32670.011-0.01181.3389-0.0031.3287529.850527.5341277.698
540.00550.00230.00390.00120.00110.0048-0.0020.0018-0.0008-0.0006-0.00160.0008-0.0002-0.000700.80090.00470.02090.7748-0.04930.7836540.201734.689271.9165
55-0.0004-0.00140.00070.00080.00110.0021-0.0027-0.0051-0.0033-0.0023-0.00260.0020.00080.0162-00.22770.0212-0.01780.2512-0.01620.1049543.619412.6054271.9013
560.0015-0.00170.00250.0007-0.00110.001-0.00180.00110.00680.02210.005-0.0011-0.0091-0.009900.33560.08270.00020.3653-0.0130.2783520.03174.2455245.7423
570.0004-0.00010.00120.001600.00220.0210.02170.01480.00760.0172-0.003-0.0011-0.0003-00.27090.0630.07530.3726-0.00850.3162522.80375.4543243.0416
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 394 )
2X-RAY DIFFRACTION2chain 'A' and (resid 395 through 946 )
3X-RAY DIFFRACTION3chain 'A' and (resid 947 through 1154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1155 through 1280 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1281 through 1376 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1377 through 1448 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 185 )
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 408 )
9X-RAY DIFFRACTION9chain 'B' and (resid 409 through 487 )
10X-RAY DIFFRACTION10chain 'B' and (resid 488 through 776 )
11X-RAY DIFFRACTION11chain 'B' and (resid 777 through 994 )
12X-RAY DIFFRACTION12chain 'B' and (resid 995 through 1220 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 26 )
14X-RAY DIFFRACTION14chain 'C' and (resid 27 through 51 )
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 104 )
16X-RAY DIFFRACTION16chain 'C' and (resid 105 through 175 )
17X-RAY DIFFRACTION17chain 'C' and (resid 176 through 209 )
18X-RAY DIFFRACTION18chain 'C' and (resid 210 through 268 )
19X-RAY DIFFRACTION19chain 'E' and (resid 3 through 65 )
20X-RAY DIFFRACTION20chain 'E' and (resid 66 through 82 )
21X-RAY DIFFRACTION21chain 'E' and (resid 83 through 103 )
22X-RAY DIFFRACTION22chain 'E' and (resid 104 through 122 )
23X-RAY DIFFRACTION23chain 'E' and (resid 123 through 215 )
24X-RAY DIFFRACTION24chain 'F' and (resid 72 through 86 )
25X-RAY DIFFRACTION25chain 'F' and (resid 87 through 103 )
26X-RAY DIFFRACTION26chain 'F' and (resid 104 through 116 )
27X-RAY DIFFRACTION27chain 'F' and (resid 117 through 132 )
28X-RAY DIFFRACTION28chain 'F' and (resid 133 through 142 )
29X-RAY DIFFRACTION29chain 'F' and (resid 143 through 147 )
30X-RAY DIFFRACTION30chain 'F' and (resid 148 through 155 )
31X-RAY DIFFRACTION31chain 'H' and (resid 3 through 16 )
32X-RAY DIFFRACTION32chain 'H' and (resid 17 through 30 )
33X-RAY DIFFRACTION33chain 'H' and (resid 31 through 43 )
34X-RAY DIFFRACTION34chain 'H' and (resid 44 through 53 )
35X-RAY DIFFRACTION35chain 'H' and (resid 54 through 82 )
36X-RAY DIFFRACTION36chain 'H' and (resid 83 through 92 )
37X-RAY DIFFRACTION37chain 'H' and (resid 93 through 106 )
38X-RAY DIFFRACTION38chain 'H' and (resid 107 through 118 )
39X-RAY DIFFRACTION39chain 'H' and (resid 119 through 127 )
40X-RAY DIFFRACTION40chain 'H' and (resid 128 through 140 )
41X-RAY DIFFRACTION41chain 'H' and (resid 141 through 146 )
42X-RAY DIFFRACTION42chain 'I' and (resid 2 through 52 )
43X-RAY DIFFRACTION43chain 'I' and (resid 53 through 116 )
44X-RAY DIFFRACTION44chain 'J' and (resid 1 through 14 )
45X-RAY DIFFRACTION45chain 'J' and (resid 15 through 26 )
46X-RAY DIFFRACTION46chain 'J' and (resid 27 through 56 )
47X-RAY DIFFRACTION47chain 'J' and (resid 57 through 65 )
48X-RAY DIFFRACTION48chain 'K' and (resid 1 through 9 )
49X-RAY DIFFRACTION49chain 'K' and (resid 10 through 39 )
50X-RAY DIFFRACTION50chain 'K' and (resid 40 through 82 )
51X-RAY DIFFRACTION51chain 'K' and (resid 83 through 114 )
52X-RAY DIFFRACTION52chain 'L' and (resid 27 through 41 )
53X-RAY DIFFRACTION53chain 'L' and (resid 42 through 46 )
54X-RAY DIFFRACTION54chain 'L' and (resid 47 through 51 )
55X-RAY DIFFRACTION55chain 'L' and (resid 52 through 70 )
56X-RAY DIFFRACTION56chain 'T' and (resid 19 through 29 )
57X-RAY DIFFRACTION57chain 'R' and (resid 1 through 8 )

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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