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- EMDB-7076: Mechanisms of Opening and Closing of the Bacterial Replicative He... -

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基本情報

登録情報
データベース: EMDB / ID: EMD-7076
タイトルMechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex
マップデータDnaB-LambdaP helicase-helicase loader complex from single particle cryoEM at 4.1A. The suggested viewing thresholds are 0.0276 (Chimera) or an isomesh level of 6 (PyMol).
試料
  • 複合体: DnaB helicase - Lambda P helicase loader DNA replication complex
    • 複合体: E coli DnaB helicase
      • タンパク質・ペプチド: Replicative DNA helicase
    • 複合体: Lambda P helicase loader
      • タンパク質・ペプチド: Replication protein PDNA複製
  • リガンド: ADENOSINE-5'-DIPHOSPHATE
キーワードHelicase Loader / Helicase (ヘリカーゼ) / DNA replication (DNA複製) / ATPase (ATPアーゼ) / DNA Replication Initiation / Bacteriophage Lambda / REPLICATION (DNA複製)
機能・相同性
機能・相同性情報


DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DNA helicase complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / bidirectional double-stranded viral DNA replication / replisome / DNA replication, synthesis of primer ...DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DNA helicase complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / bidirectional double-stranded viral DNA replication / replisome / DNA replication, synthesis of primer / DNA duplex unwinding / response to ionizing radiation / replication fork processing / DNA unwinding involved in DNA replication / DNA replication initiation / DNA helicase activity / helicase activity / ヘリカーゼ / DNA複製 / hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / 細胞質基質
類似検索 - 分子機能
Replication P / Replication protein P / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. ...Replication P / Replication protein P / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / 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
Replicative DNA helicase / Replication protein P / Replicative DNA helicase
類似検索 - 構成要素
生物種Escherichia coli (大腸菌) / Enterobacteria phage lambda (λファージ) / Escherichia coli O111:NM (大腸菌) / Escherichia phage lambda (λファージ)
手法単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.1 Å
データ登録者Chase J / Catalano A
資金援助 米国, 12件
OrganizationGrant number国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM084162 米国
National Science Foundation (NSF, United States)MCB 1818255 米国
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)5G12MD007603-30 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM109824 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103314 米国
Other governmentPA200A150068 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM128303 米国
Other privateSF349247 (Simons Foundation) 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 米国
Other privateF00316 (Agouron Institute) 米国
National Institutes of Health/Office of the DirectorOD019994 米国
Other privateSM-2015-289297 (Silicon Mechanics/Research Cluster Grant program) 米国
引用ジャーナル: Elife / 年: 2018
タイトル: Mechanisms of opening and closing of the bacterial replicative helicase.
著者: Jillian Chase / Andrew Catalano / Alex J Noble / Edward T Eng / Paul Db Olinares / Kelly Molloy / Danaya Pakotiprapha / Martin Samuels / Brian Chait / Amedee des Georges / David Jeruzalmi /
要旨: Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and ...Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
履歴
登録2017年10月18日-
ヘッダ(付随情報) 公開2019年3月6日-
マップ公開2019年3月6日-
更新2024年3月13日-
現状2024年3月13日処理サイト: RCSB / 状態: 公開

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構造の表示

ムービー
  • 表面図（断面を密度値に従い着色）
  • 表面レベル: 0.03
  • UCSF Chimeraによる作画
  • ダウンロード
  • 表面図（円筒半径に従い着色）
  • 表面レベル: 0.03
  • UCSF Chimeraによる作画
  • ダウンロード
  • あてはめたモデルとの重ね合わせ
  • 原子モデル: PDB-6bbm
  • 表面レベル: 0.03
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューアEMマップ:
SurfViewMolmilJmol/JSmol
添付画像

emd_7076.png

ダウンロードとリンク

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マップ

ファイルダウンロード / ファイル: emd_7076.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈DnaB-LambdaP helicase-helicase loader complex from single particle cryoEM at 4.1A. The suggested viewing thresholds are 0.0276 (Chimera) or an isomesh level of 6 (PyMol).
ボクセルのサイズX=Y=Z: 1.07 Å
密度
表面レベル登録者による: 0.0276 / ムービー #1: 0.03
最小 - 最大-0.09008105 - 0.161977
平均 (標準偏差)0.000051110845 (±0.0061288467)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ256256256
Spacing256256256
セルA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4マップ ヘッダ情報:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-163-114-126
NX/NY/NZ210124170
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0900.1620.000

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添付データ

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試料の構成要素

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全体 : DnaB helicase - Lambda P helicase loader DNA replication complex

全体名称: DnaB helicase - Lambda P helicase loader DNA replication complex
要素
  • 複合体: DnaB helicase - Lambda P helicase loader DNA replication complex
    • 複合体: E coli DnaB helicase
      • タンパク質・ペプチド: Replicative DNA helicase
    • 複合体: Lambda P helicase loader
      • タンパク質・ペプチド: Replication protein PDNA複製
  • リガンド: ADENOSINE-5'-DIPHOSPHATE

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超分子 #1: DnaB helicase - Lambda P helicase loader DNA replication complex

超分子名称: DnaB helicase - Lambda P helicase loader DNA replication complex
タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2
詳細: pET24a containing full-length DnaB was co-expressed with pCDFDuet containing full-length LambdaP in BL21(DE3) cells. The resolution of the LambdaP portion of our EM map did not permit the ...詳細: pET24a containing full-length DnaB was co-expressed with pCDFDuet containing full-length LambdaP in BL21(DE3) cells. The resolution of the LambdaP portion of our EM map did not permit the unambiguous assignment of the amino acid sequence to the structure. As such, the model for LambdaP was built as a poly alanine model. Additionally, only half of LambdaP was observed in our maps due to the intrinsic flexibility of the amino and carboxy terminal domains of LambdaP. Subsequent experiments determined that the observed portion of LambdaP in our maps corresponds to the C-terminal domain.
由来(天然)生物種: Escherichia coli (大腸菌)

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超分子 #2: E coli DnaB helicase

超分子名称: E coli DnaB helicase / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1
詳細: E coli DnaB helicase is observed as an open-spiral hexamer, in which one of the interfaces is breached. Five ADP molecules are observed at the five intact ATP binding sites. Additionally, ...詳細: E coli DnaB helicase is observed as an open-spiral hexamer, in which one of the interfaces is breached. Five ADP molecules are observed at the five intact ATP binding sites. Additionally, clear density is observed for five of six linkers permitting unambiguous assignment of NTD to parent CTD domain.
由来(天然)生物種: Escherichia coli (大腸菌)

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超分子 #3: Lambda P helicase loader

超分子名称: Lambda P helicase loader / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2
詳細: Five lambda P molecules were observed bound to the five intact DnaB subunit interfaces. Unambiguous assignment of side chain density for lambda P was not possible due to the resolution of ...詳細: Five lambda P molecules were observed bound to the five intact DnaB subunit interfaces. Unambiguous assignment of side chain density for lambda P was not possible due to the resolution of this region of the EM map. Instead, a polyalanine model was built for each lambda P molecule. Additionally, density for approximately half of the expected 233 residues of lambda P was observed owing to flexibility between domains. Subsequent experiments confirmed that the observed region of Lambda P is the C-terminal domain, which interacts with DnaB.
由来(天然)生物種: Enterobacteria phage lambda (λファージ)

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分子 #1: Replicative DNA helicase

分子名称: Replicative DNA helicase / タイプ: protein_or_peptide / ID: 1 / コピー数: 6 / 光学異性体: LEVO / EC番号: ヘリカーゼ
由来(天然)生物種: Escherichia coli O111:NM (大腸菌)
分子量理論値: 52.450945 KDa
組換発現生物種: Escherichia coli BL21(DE3) (大腸菌)
配列文字列: MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF YTRPHRHIFT EMARLQESGS PIDLITLAE SLERQGQLDS VGGFAYLAEL SKNTPSAANI SAYADIVRER AVVREMISVA NEIAEAGFDP QGRTSEDLLD L AESRVFKI ...文字列:
MAGNKPFNKQ QAEPRERDPQ VAGLKVPPHS IEAEQSVLGG LMLDNERWDD VAERVVADDF YTRPHRHIFT EMARLQESGS PIDLITLAE SLERQGQLDS VGGFAYLAEL SKNTPSAANI SAYADIVRER AVVREMISVA NEIAEAGFDP QGRTSEDLLD L AESRVFKI AESRANKDEG PKNIADVLDA TVARIEQLFQ QPHDGVTGVN TGYDDLNKKT AGLQPSDLII VAARPSMGKT TF AMNLVEN AAMLQDKPVL IFSLEMPSEQ IMMRSLASLS RVDQTKIRTG QLDDEDWARI SGTMGILLEK RNIYIDDSSG LTP TEVRSR ARRIAREHGG IGLIMIDYLQ LMRVPALSDN RTLEIAEISR SLKALAKELN VPVVALSQLN RSLEQRADKR PVNS DLRES GSIEQDADLI MFIYRDEVYH ENSDLKGIAE IIIGKQRNGP IGTVRLTFNG QWSRFDNYAG PQYDDE

UniProtKB: Replicative DNA helicase

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分子 #2: Replication protein P

分子名称: Replication protein P / タイプ: protein_or_peptide / ID: 2 / コピー数: 5 / 光学異性体: LEVO
由来(天然)生物種: Escherichia phage lambda (λファージ)
分子量理論値: 23.141221 KDa
組換発現生物種: Escherichia coli BL21(DE3) (大腸菌)
配列文字列: MKNIAAQMVN FDREQMRRIA NNMPEQYDEK PQVQQVAQII NGVFSQLLAT FPASLANRDQ NEVNEIRRQW VLAFRENGIT TMEQVNAGM RVARRQNRPF LPSPGQFV(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK) ...文字列:
MKNIAAQMVN FDREQMRRIA NNMPEQYDEK PQVQQVAQII NGVFSQLLAT FPASLANRDQ NEVNEIRRQW VLAFRENGIT TMEQVNAGM RVARRQNRPF LPSPGQFV(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)

UniProtKB: Replication protein P

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分子 #3: ADENOSINE-5'-DIPHOSPHATE

分子名称: ADENOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 3 / コピー数: 5 / 式: ADP
分子量理論値: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP / ADP, エネルギー貯蔵分子*YM / アデノシン二リン酸

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実験情報

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構造解析

手法クライオ電子顕微鏡法
解析単粒子再構成法
試料の集合状態particle

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試料調製

濃度0.48 mg/mL
緩衝液pH: 7.5
構成要素:
濃度式名称
20.0 mMNa-HEPESSodium HEPES
450.0 mMNaCl塩化ナトリウムSodium Chloride塩化ナトリウム
2.0 mMDTTDithiothreitolジチオトレイトール
0.5 mMMgCl2Magnesium Chloride
0.5 mMATPアデノシン三リン酸Adenosine triphosphateアデノシン三リン酸

詳細: Concentrated BP sample (18mg/mL) was diluted with freshly prepared buffer to desired concentration (~1.5 micromolar) for grid preparation.
グリッドモデル: Quantifoil R0.6/1 / 材質: GOLD / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: PLASMA CLEANING / 前処理 - 時間: 60 sec. / 前処理 - 雰囲気: OTHER
詳細: The grid was coated with 50 nm of evaporated gold prior to use. All remaining carbon was removed by plasma cleaning for 5 minutes in a Gatan Solarus plasma cleaner.
凍結凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV
詳細: 3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane..
詳細The sample was monodisperse. Side views were more electron weak than top or bottom views creating challenges for particle picking. This issue was overcome with cryo-electron tomography techniques used for 1) initial model generation and 2) template generation for particle picking.

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電子顕微鏡法

顕微鏡FEI TITAN KRIOS
電子線加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN
電子光学系C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス（公称値）: -0.003 µm / 最小 デフォーカス（公称値）: -0.001 µm / 倍率（公称値）: 22500
特殊光学系球面収差補正装置: The Krios this data was collected on has a Cs of 2.7.
試料ステージ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
ホルダー冷却材: NITROGEN
温度最低: 70.0 K / 最高: 70.0 K
詳細Preliminary grid screening was performed prior to Krios data collections. All microscope alignments were completed by the New York Structural Biology SEMC team.
撮影フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
検出モード: COUNTING / デジタル化 - サイズ - 横: 3838 pixel / デジタル化 - サイズ - 縦: 3710 pixel / デジタル化 - 画像ごとのフレーム数: 1-50 / 撮影したグリッド数: 3 / 実像数: 2426 / 平均露光時間: 10.0 sec. / 平均電子線量: 8.0 e/Å2
詳細: Single particle movies were recorded at a pixel size of 1.07 angstroms/pixel. Three 24-hour sessions produced 2,426 micrograph movies. In addition, five tilt series were collected from the ...詳細: Single particle movies were recorded at a pixel size of 1.07 angstroms/pixel. Three 24-hour sessions produced 2,426 micrograph movies. In addition, five tilt series were collected from the same grids bi-directionally over a tilt range of -45 degrees to +45 degrees in 3 degree increments at a dose of 2.57 to 3.3 electrons per angstrom squared (total accumulated dose of 90 electrons per angstrom squared). Tilt series were collected at a pixel size of 1.76 angstroms and at defocus values of -2.8um, -6.1um and -9.3um.
実験機器
モデル: Titan Krios / 画像提供: FEI Company

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画像解析

初期モデルモデルのタイプ: ORTHOGONAL TILT / Orthogonal tilt - Number images: 1000 / Orthogonal tilt - Tilt angle1: -45 degrees / Orthogonal tilt - Tilt angle2: 45 degrees
詳細: Three tilt series were collected from same single-particle grids at a pixel size of 1.76 angstroms per pixel and defocus values of -2.8um, -6.1um and -9.3um. Tilt series were collected bi- ...詳細: Three tilt series were collected from same single-particle grids at a pixel size of 1.76 angstroms per pixel and defocus values of -2.8um, -6.1um and -9.3um. Tilt series were collected bi-directionally over a tilt range of -45 degrees to +45 degrees in 3 degree increments, with a dose of 2.57 to 3.3 electrons per angstrom squared per tilt increment (subdivided over seven to nine frames.) A low resolution initial model was generated from ~1,000 particles picked from three tilt series. These tilt series were first aligned using a fiducial-less algorithm implemented in Appion-Portomo, then reconstructed using Tomo3D. 1,000 particles were picked from resulting tomograms (binned 4 x 4) to generate a ~40 angstrom initial model. Resolution was estimated by filtering procedures. The resulting volume served as an initial model and was projected to generate templates for template-based particle picking of single particle micrographs.
最終 再構成解像度のタイプ: BY AUTHOR / 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF
ソフトウェア:
名称詳細
RELIONAuto refine and post processing was performed in Relion.
DynamoDynamo was used to generate sub-tomogram average, later used as initial model.

詳細: Relion was used to independently refine half sets using 0.143 gold-standard to a resolution of 4.1A. A total of 90,883 particles went into this reconstruction.
使用した粒子像数: 90883
詳細Images collected were CTF corrected and selected based on CTF estimates of less than 10 angstrom at a confidence cutoff of 0.8 for subsequent processing.
FSC曲線 (解像度の算出)

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原子モデル構築 1

初期モデル
PDB IDChain

2r5u

residue_range: 1-173, source_name: PDB, initial_model_type: experimental model

3bh0

residue_range: 203-441, source_name: PDB, initial_model_type: experimental model
詳細The initial fitting was done with the 2R5U and 3BH0 models onto which the E. coli amino sequence had been built. The linker segments that connected these segments were built by hand. PHENIX real_space_refine was used to refine the complete model for the B6P5 entity.
精密化空間: REAL / プロトコル: FLEXIBLE FIT
得られたモデル

PDB-6bbm:
Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex

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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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