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- PDB-6sb0: cryo-EM structure of mTORC1 bound to PRAS40-fused active RagA/C G... -

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基本情報

登録情報
データベース: PDB / ID: 6sb0
タイトルcryo-EM structure of mTORC1 bound to PRAS40-fused active RagA/C GTPases
要素
  • (Ras-related GTP-binding protein ...) x 2
  • Proline-rich AKT1 substrate 1
  • Regulatory-associated protein of mTOR
  • Target of rapamycin complex subunit LST8MTOR
  • mTOR,Serine/threonine-protein kinase mTOR,mTOR,Serine/threonine-protein kinase mTOR
キーワードSIGNALING PROTEIN / small GTPases (低分子量GTPアーゼ) / mTORC1 activator / roadblock domain / GTPase domain (GTPアーゼ)
機能・相同性
機能・相同性情報


Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation ...Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TORC2 complex / regulation of TORC1 signaling / regulation of membrane permeability / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / protein localization to lysosome / regulation of autophagosome assembly / nucleus localization / TORC1 signaling / voluntary musculoskeletal movement / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / regulation of TOR signaling / positive regulation of keratinocyte migration / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / energy reserve metabolic process / Energy dependent regulation of mTOR by LKB1-AMPK / ruffle organization / protein serine/threonine kinase inhibitor activity / negative regulation of cell size / positive regulation of osteoclast differentiation / cellular response to osmotic stress / protein localization to membrane / enzyme-substrate adaptor activity / anoikis / negative regulation of protein localization to nucleus / cardiac muscle cell development / negative regulation of TOR signaling / positive regulation of transcription by RNA polymerase III / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / regulation of cell size / negative regulation of macroautophagy / オートファジー / small GTPase-mediated signal transduction / positive regulation of oligodendrocyte differentiation / lysosome organization / positive regulation of actin filament polymerization / protein kinase inhibitor activity / positive regulation of myotube differentiation / protein kinase activator activity / behavioral response to pain / oligodendrocyte differentiation / mTORC1-mediated signalling / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / social behavior / CD28 dependent PI3K/Akt signaling / positive regulation of phosphoprotein phosphatase activity / neurotrophin TRK receptor signaling pathway / cellular response to nutrient levels / HSF1-dependent transactivation / MTOR / positive regulation of TOR signaling / neuronal action potential / regulation of macroautophagy / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of translational initiation / 細胞内膜系 / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lamellipodium assembly / positive regulation of epithelial to mesenchymal transition / regulation of neuron apoptotic process / positive regulation of lipid biosynthetic process / regulation of cellular response to heat / heart morphogenesis / protein-membrane adaptor activity / cardiac muscle contraction / phagocytic vesicle / positive regulation of stress fiber assembly / negative regulation of TORC1 signaling / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / positive regulation of TORC1 signaling / cytoskeleton organization / tumor necrosis factor-mediated signaling pathway / T cell costimulation / cellular response to amino acid starvation / cellular response to starvation / positive regulation of glycolytic process
類似検索 - 分子機能
Proline-rich AKT1 substrate 1 protein / Proline-rich AKT1 substrate 1 / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / RagA/B / Gtr1/RagA G protein / RagC/D / Gtr1/RagA G protein conserved region ...Proline-rich AKT1 substrate 1 protein / Proline-rich AKT1 substrate 1 / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / RagA/B / Gtr1/RagA G protein / RagC/D / Gtr1/RagA G protein conserved region / Target of rapamycin complex subunit LST8 / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / HEATリピート / HEATリピート / Rapamycin binding domain / PIK-related kinase, FAT / FAT domain / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40リピート / WD40リピート / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / グアノシン三リン酸 / Serine/threonine-protein kinase mTOR / Ras-related GTP-binding protein A / Regulatory-associated protein of mTOR / Proline-rich AKT1 substrate 1 / Target of rapamycin complex subunit LST8 / Ras-related GTP-binding protein C
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 5.5 Å
データ登録者Anandapadamanaban, M. / Berndt, A. / Masson, G.R. / Perisic, O. / Williams, R.L.
資金援助 英国, 3件
組織認可番号国
Medical Research Council (United Kingdom)MC_U105184308 英国
Cancer Research UKC14801/A21211 英国
European Molecular Biology Organizationlong-term fellowship 英国
引用ジャーナル: Science / 年: 2019
タイトル: Architecture of human Rag GTPase heterodimers and their complex with mTORC1.
著者: Madhanagopal Anandapadamanaban / Glenn R Masson / Olga Perisic / Alex Berndt / Jonathan Kaufman / Chris M Johnson / Balaji Santhanam / Kacper B Rogala / David M Sabatini / Roger L Williams /
要旨: The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag ...The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo-electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagA/RagC nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.
履歴
登録2019年7月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年10月16日Provider: repository / タイプ: Initial release
改定 1.12019年10月23日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年5月22日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-10132
  • 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: mTOR,Serine/threonine-protein kinase mTOR,mTOR,Serine/threonine-protein kinase mTOR
B: mTOR,Serine/threonine-protein kinase mTOR,mTOR,Serine/threonine-protein kinase mTOR
E: Target of rapamycin complex subunit LST8
C: Ras-related GTP-binding protein A
D: Ras-related GTP-binding protein C
Y: Regulatory-associated protein of mTOR
T: Proline-rich AKT1 substrate 1
H: Target of rapamycin complex subunit LST8
I: Ras-related GTP-binding protein A
J: Ras-related GTP-binding protein C
N: Regulatory-associated protein of mTOR
O: Proline-rich AKT1 substrate 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,162,77216
ポリマ－1,160,83912
非ポリマー1,9334
水0
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: mass spectrometry, HDX-MS, SEC-MALLS provides evidence of this mTORC1-RagA/C complex and a dimer in solution.
タイプ名称対称操作数
identity operation1_5551
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
12E
22H
13C
23I
14D
24J
15Y
25N
16T
26O

NCSドメイン領域:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A17 - 2549
2111B17 - 2549
1121E8 - 324
2121H8 - 324
1131C4 - 301
2131I4 - 301
1141D60 - 369
2141J60 - 369
1151Y18 - 1331
2151N18 - 1331
1161T126 - 232
2161O126 - 232

NCSアンサンブル:
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2given(-0.999997, 0.001994, 0.001637), (-0.002012, -0.999938, -0.010928), (0.001616, -0.010931, 0.999939)245.82762, 324.9903, 1.60697
3given(1), (1), (1)
4given(-0.999969, -0.004555, 0.006344), (0.004541, -0.999987, -0.002191), (0.006353, -0.002162, 0.999977)246.28407, 323.00888, -0.42714
5given(1), (1), (1)
6given(-0.999964, 0.008184, 0.002374), (-0.008169, -0.999948, 0.006068), (0.002423, 0.006048, 0.999979)245.66022, 324.25351, -0.12096
7given(1), (1), (1)
8given(-0.999939, 0.01074, -0.002714), (-0.01068, -0.999717, -0.021261), (-0.002942, -0.021231, 0.99977)246.24002, 327.26749, 1.7088
9given(1), (1), (1)
10given(-0.999951, 0.008513, 0.004968), (-0.008602, -0.999796, -0.01827), (0.004811, -0.018312, 0.999821)244.95395, 325.72314, 1.34705
11given(1), (1), (1)
12given(-0.999919, -0.008862, 0.009142), (0.008979, -0.999877, 0.012848), (0.009027, 0.01293, 0.999876)246.33859, 321.48648, -2.15536

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要素

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タンパク質 , 4種, 8分子 ABEHYNTO

#1: タンパク質 mTOR,Serine/threonine-protein kinase mTOR,mTOR,Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1


分子量: 287012.031 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: P42345, non-specific serine/threonine protein kinase
#2: タンパク質 Target of rapamycin complex subunit LST8 / MTOR / TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 ...TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 protein 8 / mLST8


分子量: 35910.090 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MLST8, GBL, LST8 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9BVC4
#5: タンパク質 Regulatory-associated protein of mTOR / Raptor / p150 target of rapamycin (TOR)-scaffold protein


分子量: 149200.016 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RPTOR, KIAA1303, RAPTOR / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8N122
#6: タンパク質 Proline-rich AKT1 substrate 1 / 40 kDa proline-rich AKT substrate


分子量: 27412.293 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AKT1S1, PRAS40 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q96B36

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Ras-related GTP-binding protein ... , 2種, 4分子 CIDJ

#3: タンパク質 Ras-related GTP-binding protein A / RagA / Adenovirus E3 14.7 kDa-interacting protein 1 / FIP-1


分子量: 36600.195 Da / 分子数: 2 / Mutation: Q66L / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RRAGA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q7L523
#4: タンパク質 Ras-related GTP-binding protein C / RagC / GTPase-interacting protein 2 / TIB929


分子量: 44284.832 Da / 分子数: 2 / Mutation: T90N / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RRAGC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9HB90

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非ポリマー , 2種, 4分子

#7: 化合物 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP / グアノシン三リン酸


分子量: 523.180 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: GTP, エネルギー貯蔵分子*YM
#8: 化合物 ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP / グアノシン二リン酸


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: GDP, エネルギー貯蔵分子*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: 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
ID名称タイプEntity IDParent-ID由来
1cryoEM structure of mTORC1 bound to RagA/C complexCOMPLEX#1-#60MULTIPLE SOURCES
2mTORC1COMPLEX#1-#2, #51RECOMBINANT
3RagA/CCOMPLEX#3-#4, #61RECOMBINANT
分子量値: 1.09 MDa / 実験値: YES
由来(天然)
IDEntity assembly-ID生物種Ncbi tax-ID
12Homo sapiens (ヒト)9606
23Homo sapiens (ヒト)9606
由来(組換発現)
IDEntity assembly-ID生物種Ncbi tax-ID
12Homo sapiens (ヒト)9606
23Escherichia coli (大腸菌)562
緩衝液pH: 7 / 詳細: 50mM HEPES pH 7.0, 100mM NaCl, 2mM MgCl2, 1mM TCEP
試料濃度: 0.05 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
詳細: mTORC1 (mTOR complex 1) is a dimer consists of three proteins: mTOR, mLST8 and RAPTOR. The interacting partner, PRAS40-fused-RagA/C (referred as RagA/C here) forms complex with mTORC1 for its ...詳細: mTORC1 (mTOR complex 1) is a dimer consists of three proteins: mTOR, mLST8 and RAPTOR. The interacting partner, PRAS40-fused-RagA/C (referred as RagA/C here) forms complex with mTORC1 for its activation. We solved the cryo-EM structure of mTORC1 bound to RagA/C.
試料支持グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/2
急速凍結装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 95 %

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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: FEI TITAN 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 FIELDBright-field microscopy / Cs: 2.7 mm
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影平均露光時間: 1.8 sec. / 電子線照射量: 40 e/Å2 / 検出モード: COUNTING
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
画像スキャン横: 3838 / 縦: 3710 / 動画フレーム数/画像: 22 / 利用したフレーム数/画像: 1-22

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解析

ソフトウェア名称: REFMAC / バージョン: 5.8.0238 / 分類: 精密化
EMソフトウェア
ID名称バージョンカテゴリ
1RELION3.0.3粒子像選択
2EPU1.10.0.77REL画像取得
4Gctf1.18CTF補正
7REFMAC5.8.0238モデルフィッティング
9REFMAC5.8.0238モデル精密化
10RELION3.0.6初期オイラー角割当
11RELION3.0.6最終オイラー角割当
12RELION3.0.6分類
13RELION3.0.6３次元再構成
画像処理詳細: The selected images were processed using MotionCor2 within the RELION-3.0.6 package.
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 580707
対称性点対称性: C1 (非対称)
3次元再構成解像度: 5.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 90809 / アルゴリズム: FOURIER SPACE
詳細: For the final reconstruction of mTORC1-RagA/C structure we used a strategy taking advantage of the relion particle symmetry expand program, and duplicated the C2-refined particles and applied ...詳細: For the final reconstruction of mTORC1-RagA/C structure we used a strategy taking advantage of the relion particle symmetry expand program, and duplicated the C2-refined particles and applied the appropriate rotation and translation to generate a set of monomers. We performed mTORC1-RagA/C 'pseudo-monomer' focussed classification with signal subtraction and obtained a reconstruction of 5.5 A resolution map. This cryo-EM density corresponded to the mTORC1-RagA/C pseudomonomer, where the previously published structure for apo-mTORC1 (PDB ID 6BCX) and our high-resolution crystal structure of RagA/C (6S6A) were fitted with great confidence from our experimental analysis including Pulldown assays, mutational at per-residue level in the binding interface and HDX-Mass Spectrometry.
クラス平均像の数: 1 / 対称性のタイプ: POINT
原子モデル構築B value: 283 / プロトコル: RIGID BODY FIT / 空間: REAL
詳細: Cryo-EM model of mTORC1-RagA/C was refined using REFMAC5 program in CCPEM package, with a composite map of the 3D reconstruction of mTORC1-RagA/C pseudo-monomer (as mentioned in ...詳細: Cryo-EM model of mTORC1-RagA/C was refined using REFMAC5 program in CCPEM package, with a composite map of the 3D reconstruction of mTORC1-RagA/C pseudo-monomer (as mentioned in Reconstruction section) of one protomer together with the generated map for the other second protomer of mTORC1-RagA/C. This second protomer of mTORC1-RagA/C map was generated by simply aligning the first 3D reconstructed pseudomonomer map onto the mTORC1 dimer consensus C2 map and then obtained the rotation-translation matrix with CHIMERA and then used Maputils program in CCP4i. From the resulting mTORC1-RagA/C dimer map, the model of mTORC1-RagA/C was built by using previously published structure of apo-mTORC1 (PDB ID 6BCX) and our crystal structure of RagA/C was fitted (PDB ID 6S6A, unreleased). The entire mTORC1-RagA/C final model was refined using REFMAC5 program using the restraints from the crystal structure of RagA/C and previously published mTORC1 structure. Side chains were removed before refinement, since these were not evident in the cryo-EM densities. Separate model refinements were performed against single half-maps, and the resulting models were compared with the other half-maps to confirm the absence of overfitting.
原子モデル構築
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameタイプ
16BCX

6bcx

16BCX1PDBexperimental model
26S6A

6s6a

16S6A2PDBexperimental model
精密化解像度: 5.5→321.75 Å / Cor.coef. Fo:Fc: 0.895 / SU B: 104.924 / SU ML: 1.049
立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES
Rfactor反射数%反射
Rwork0.36707 --
obs0.36707 146374 100 %
溶媒の処理溶媒モデル: PARAMETERS FOR MASK CACLULATION
原子変位パラメータBiso mean: 288.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.31 Å20.36 Å20.22 Å2
2---0.39 Å22.09 Å2
3---4.7 Å2
精密化ステップサイクル: 1 / 合計: 66022
拘束条件
Refine-IDタイプDev idealDev ideal target数
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01267371
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.8791.62991357
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.42658227
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.53621.9213530
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.2351511760
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.74715481
ELECTRON MICROSCOPYr_chiral_restr0.1320.28873
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0250728
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it36.70728.54133124
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it60.21642.59241279
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it45.94829.51634247
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined277422
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / タイプ: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-ID数Rms dev position (Å)
11A17344
22E245622.54
33C242830.31
44D216731.76
55Y824322.13
66T25024.99
LS精密化 シェル解像度: 5.5→5.643 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0 0 -
Rwork0.8 10792 -
obs--100 %

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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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