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- PDB-9nut: SsoPfMCM:DNA class 1a from DNA 2 -

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基本情報

登録情報
データベース: PDB / ID: 9nut
タイトルSsoPfMCM:DNA class 1a from DNA 2
要素
  • DNA (60-MER)
  • Minichromosome maintenance protein MCM, Cell division control protein 21,Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
キーワードREPLICATION / DNA replication / helicase / MCM
機能・相同性
機能・相同性情報


MCM complex / DNA 3'-5' helicase / DNA helicase activity / single-stranded DNA binding / DNA replication / ATP hydrolysis activity / ATP binding / identical protein binding
類似検索 - 分子機能
MCM protein C-terminal winged helix-turn-helix domain / : / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain ...MCM protein C-terminal winged helix-turn-helix domain / : / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family C-terminal AAA(+) ATPase domain (MCM-CTD) profile. / minichromosome maintenance proteins / MCM domain / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Minichromosome maintenance protein MCM
類似検索 - 構成要素
生物種Saccharolobus solfataricus P2 (古細菌)
synthetic construct (人工物)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.93 Å
データ登録者Enemark, E.J. / Rasouli, S. / Myasnikov, A.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136313 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM152281 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103429 米国
引用
ジャーナル: To Be Published
タイトル: SsoPfMCM:DNA class 1a from DNA 2
著者: Enemark, E.J. / Rasouli, S. / Myasnikov, A.
#1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2025年3月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02026年4月1日Provider: repository / タイプ: Initial release
改定 1.02026年4月1日Data content type: EM metadata / Data content type: EM metadata / Provider: repository / タイプ: Initial release
改定 1.02026年4月1日Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / タイプ: Initial release
改定 1.02026年4月1日Data content type: FSC / Data content type: FSC / Provider: repository / タイプ: Initial release
改定 1.02026年4月1日Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / タイプ: Initial release
改定 1.02026年4月1日Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / タイプ: Initial release
改定 1.02026年4月1日Data content type: Image / Data content type: Image / Provider: repository / タイプ: Initial release
改定 1.02026年4月1日Data content type: Primary map / Data content type: Primary map / Provider: repository / タイプ: Initial release

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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: Minichromosome maintenance protein MCM, Cell division control protein 21,Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
B: Minichromosome maintenance protein MCM, Cell division control protein 21,Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
C: Minichromosome maintenance protein MCM, Cell division control protein 21,Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
D: Minichromosome maintenance protein MCM, Cell division control protein 21,Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
E: Minichromosome maintenance protein MCM, Cell division control protein 21,Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
F: Minichromosome maintenance protein MCM, Cell division control protein 21,Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
X: DNA (60-MER)
Y: DNA (60-MER)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)456,92326
ポリマ－453,8228
非ポリマー3,10118
水43224
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: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_555x,y,z1

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要素

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タンパク質 / DNA鎖 , 2種, 8分子 ABCDEFXY

#1: タンパク質
Minichromosome maintenance protein MCM, Cell division control protein 21,Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase


分子量: 69472.336 Da / 分子数: 6 / 由来タイプ: 組換発現
詳細: N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus ...詳細: N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966)
由来: (組換発現) Saccharolobus solfataricus P2 (古細菌)
遺伝子: MCM, SSO0774, PF0482 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9UXG1, DNA helicase
#2: DNA鎖 DNA (60-MER)


分子量: 18493.824 Da / 分子数: 2 / 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, 42分子

#3: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: ADP, エネルギー貯蔵分子*YM
#4: 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: 6 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 24 / 由来タイプ: 天然 / 式: H2O

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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 modificationN

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Complex of MCM hexamer with DNA and Mg/ATP-gammaS / タイプ: COMPLEX
詳細: MCM is a Chimeric fusion of Saccharolobus solfataricus MCM N-terminal domain with Pyrococcus furious MCM ATPase domain
Entity ID: #1-#2 / 由来: RECOMBINANT
分子量実験値: NO
由来(天然)生物種: Saccharolobus solfataricus P2 (古細菌)
由来(組換発現)生物種: Escherichia coli (大腸菌)
緩衝液pH: 7.6
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: TFS KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 1800 nm / 最小 デフォーカス（公称値）: 800 nm
撮影電子線照射量: 78.22 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

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解析

EMソフトウェア名称: PHENIX / バージョン: 1.21.2_5419 / カテゴリ: モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 2.93 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 60755 / 対称性のタイプ: POINT
原子モデル構築PDB-ID: 4R7Y

4r7y


Accession code: 4R7Y / Source name: PDB / タイプ: experimental model
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 164.52 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.003830080
ELECTRON MICROSCOPYf_angle_d0.594840893
ELECTRON MICROSCOPYf_chiral_restr0.04334706
ELECTRON MICROSCOPYf_plane_restr0.00365054
ELECTRON MICROSCOPYf_dihedral_angle_d13.10484512

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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

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