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基本情報

登録情報
データベース: PDB / ID: 7mnw
タイトルCrystal Structure of Nup358/RanBP2 Ran-binding domain 1 in complex with Ran-GPPNHP
要素
  • E3 SUMO-protein ligase RanBP2
  • GTP-binding nuclear protein Ran
キーワードTRANSPORT PROTEIN / nuclear pore complex component / nucleocytoplasmic transport / complex (small GTPase-nuclear protein)
機能・相同性
機能・相同性情報


cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / pre-miRNA export from nucleus / RNA nuclear export complex / nuclear pore cytoplasmic filaments / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus ...cytoplasmic periphery of the nuclear pore complex / SUMO ligase complex / SUMO ligase activity / annulate lamellae / pre-miRNA export from nucleus / RNA nuclear export complex / nuclear pore cytoplasmic filaments / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus / nuclear inclusion body / Nuclear Pore Complex (NPC) Disassembly / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Transport of the SLBP independent Mature mRNA / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / Transport of the SLBP Dependant Mature mRNA / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / nuclear export / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / kinase activator activity / 転移酵素; アシル基を移すもの; アミノアシル基を移すもの / GTP metabolic process / SUMO transferase activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / centrosome localization / MicroRNA (miRNA) biogenesis / regulation of gluconeogenesis / Viral Messenger RNA Synthesis / DNA metabolic process / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / dynein intermediate chain binding / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / protein sumoylation / ribosomal large subunit export from nucleus / spermatid development / Regulation of HSF1-mediated heat shock response / mRNA transport / viral process / positive regulation of protein binding / sperm flagellum / nuclear pore / ribosomal subunit export from nucleus / SUMOylation of DNA damage response and repair proteins / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / centriole / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein export from nucleus / SUMOylation of chromatin organization proteins / response to amphetamine / HCMV Late Events / mitotic spindle organization / male germ cell nucleus / hippocampus development / ISG15 antiviral mechanism / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / Separation of Sister Chromatids / Signaling by ALK fusions and activated point mutants / HCMV Early Events / protein import into nucleus / GDP binding / melanosome / nuclear envelope / protein folding / mitotic cell cycle / G protein activity / actin cytoskeleton organization / snRNP Assembly / midbody / nuclear membrane / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding
類似検索 - 分子機能
Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Ran GTPase / Small GTPase Ran-type domain profile. / Zinc finger domain ...Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Ran GTPase / Small GTPase Ran-type domain profile. / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / E3 SUMO-protein ligase RanBP2 / GTP-binding nuclear protein Ran
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Bley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. ...Bley, C.J. / Nie, S. / Mobbs, G.W. / Petrovic, S. / Gres, A.T. / Liu, X. / Mukherjee, S. / Harvey, S. / Huber, F.M. / Lin, D.H. / Brown, B. / Tang, A.W. / Rundlet, E.J. / Correia, A.R. / Chen, S. / Regmi, S.G. / Stevens, T.A. / Jette, C.A. / Dasso, M. / Patke, A. / Palazzo, A.F. / Kossiakoff, A.A. / Hoelz, 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)GM117360 米国
Howard Hughes Medical Institute (HHMI)55108534 米国
Heritage Medical Research Institute 米国
引用ジャーナル: Science / 年: 2022
タイトル: Architecture of the cytoplasmic face of the nuclear pore.
著者: Christopher J Bley / Si Nie / George W Mobbs / Stefan Petrovic / Anna T Gres / Xiaoyu Liu / Somnath Mukherjee / Sho Harvey / Ferdinand M Huber / Daniel H Lin / Bonnie Brown / Aaron W Tang / ...著者: Christopher J Bley / Si Nie / George W Mobbs / Stefan Petrovic / Anna T Gres / Xiaoyu Liu / Somnath Mukherjee / Sho Harvey / Ferdinand M Huber / Daniel H Lin / Bonnie Brown / Aaron W Tang / Emily J Rundlet / Ana R Correia / Shane Chen / Saroj G Regmi / Taylor A Stevens / Claudia A Jette / Mary Dasso / Alina Patke / Alexander F Palazzo / Anthony A Kossiakoff / André Hoelz /
要旨: INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are ...INTRODUCTION The subcellular compartmentalization of eukaryotic cells requires selective transport of folded proteins and protein-nucleic acid complexes. Embedded in nuclear envelope pores, which are generated by the circumscribed fusion of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) are the sole bidirectional gateways for nucleocytoplasmic transport. The ~110-MDa human NPC is an ~1000-protein assembly that comprises multiple copies of ~34 different proteins, collectively termed nucleoporins. The symmetric core of the NPC is composed of an inner ring encircling the central transport channel and outer rings formed by Y‑shaped coat nucleoporin complexes (CNCs) anchored atop both sides of the nuclear envelope. The outer rings are decorated with compartment‑specific asymmetric nuclear basket and cytoplasmic filament nucleoporins, which establish transport directionality and provide docking sites for transport factors and the small guanosine triphosphatase Ran. The cytoplasmic filament nucleoporins also play an essential role in the irreversible remodeling of messenger ribonucleoprotein particles (mRNPs) as they exit the central transport channel. Unsurprisingly, the NPC's cytoplasmic face represents a hotspot for disease‑associated mutations and is commonly targeted by viral virulence factors. RATIONALE Previous studies established a near-atomic composite structure of the human NPC's symmetric core by combining (i) biochemical reconstitution to elucidate the interaction network between symmetric nucleoporins, (ii) crystal and single-particle cryo-electron microscopy structure determination of nucleoporins and nucleoporin complexes to reveal their three-dimensional shape and the molecular details of their interactions, (iii) quantitative docking in cryo-electron tomography (cryo-ET) maps of the intact human NPC to uncover nucleoporin stoichiometry and positioning, and (iv) cell‑based assays to validate the physiological relevance of the biochemical and structural findings. In this work, we extended our approach to the cytoplasmic filament nucleoporins to reveal the near-atomic architecture of the cytoplasmic face of the human NPC. RESULTS Using biochemical reconstitution, we elucidated the protein-protein and protein-RNA interaction networks of the human and cytoplasmic filament nucleoporins, establishing an evolutionarily conserved heterohexameric cytoplasmic filament nucleoporin complex (CFNC) held together by a central heterotrimeric coiled‑coil hub that tethers two separate mRNP‑remodeling complexes. Further biochemical analysis and determination of a series of crystal structures revealed that the metazoan‑specific cytoplasmic filament nucleoporin NUP358 is composed of 16 distinct domains, including an N‑terminal S‑shaped α‑helical solenoid followed by a coiled‑coil oligomerization element, numerous Ran‑interacting domains, an E3 ligase domain, and a C‑terminal prolyl‑isomerase domain. Physiologically validated quantitative docking into cryo-ET maps of the intact human NPC revealed that pentameric NUP358 bundles, conjoined by the oligomerization element, are anchored through their N‑terminal domains to the central stalk regions of the CNC, projecting flexibly attached domains as far as ~600 Å into the cytoplasm. Using cell‑based assays, we demonstrated that NUP358 is dispensable for the architectural integrity of the assembled interphase NPC and RNA export but is required for efficient translation. After NUP358 assignment, the remaining 4-shaped cryo‑ET density matched the dimensions of the CFNC coiled‑coil hub, in close proximity to an outer-ring NUP93. Whereas the N-terminal NUP93 assembly sensor motif anchors the properly assembled related coiled‑coil channel nucleoporin heterotrimer to the inner ring, biochemical reconstitution confirmed that the NUP93 assembly sensor is reused in anchoring the CFNC to the cytoplasmic face of the human NPC. By contrast, two CFNCs are anchored by a divergent mechanism that involves assembly sensors located in unstructured portions of two CNC nucleoporins. Whereas unassigned cryo‑ET density occupies the NUP358 and CFNC binding sites on the nuclear face, docking of the nuclear basket component ELYS established that the equivalent position on the cytoplasmic face is unoccupied, suggesting that mechanisms other than steric competition promote asymmetric distribution of nucleoporins. CONCLUSION We have substantially advanced the biochemical and structural characterization of the asymmetric nucleoporins' architecture and attachment at the cytoplasmic and nuclear faces of the NPC. Our near‑atomic composite structure of the human NPC's cytoplasmic face provides a biochemical and structural framework for elucidating the molecular basis of mRNP remodeling, viral virulence factor interference with NPC function, and the underlying mechanisms of nucleoporin diseases at the cytoplasmic face of the NPC. [Figure: see text].
履歴
登録2021年5月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年6月15日Provider: repository / タイプ: Initial release
改定 1.12022年6月22日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
E: GTP-binding nuclear protein Ran
F: E3 SUMO-protein ligase RanBP2
G: GTP-binding nuclear protein Ran
H: E3 SUMO-protein ligase RanBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)165,33316
ポリマ－163,1478
非ポリマー2,1868
水7,242402
1
A: GTP-binding nuclear protein Ran
B: E3 SUMO-protein ligase RanBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,3334
ポリマ－40,7872
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-43 kcal/mol
Surface area16380 Å2
手法PISA
2
C: GTP-binding nuclear protein Ran
D: E3 SUMO-protein ligase RanBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,3334
ポリマ－40,7872
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-41 kcal/mol
Surface area16270 Å2
手法PISA
3
E: GTP-binding nuclear protein Ran
F: E3 SUMO-protein ligase RanBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,3334
ポリマ－40,7872
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-44 kcal/mol
Surface area16460 Å2
手法PISA
4
G: GTP-binding nuclear protein Ran
H: E3 SUMO-protein ligase RanBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,3334
ポリマ－40,7872
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-43 kcal/mol
Surface area16430 Å2
手法PISA
単位格子
Length a, b, c (Å)137.370, 137.834, 172.934
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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要素

#1: タンパク質
GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


分子量: 24543.182 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAN, ARA24, OK/SW-cl.81 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62826
#2: タンパク質
E3 SUMO-protein ligase RanBP2 / 358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding ...358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding protein 2 / RanBP2 / p270


分子量: 16243.673 Da / 分子数: 4
Fragment: RAN-binding domain 1 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 1171-1306)
由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RANBP2, NUP358 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P49792, 転移酵素; アシル基を移すもの; アミノアシル基を移すもの
#3: 化合物
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Gpp(NH)p


分子量: 522.196 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H17N6O13P3
コメント: GppNHp, GMPPNP, エネルギー貯蔵分子類似体*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: 4 / 由来タイプ: 合成 / 式: Mg
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 402 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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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: 2.51 Å3/Da / 溶媒含有率: 50.97 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 20% w/v PEG3350, 0.2 M potassium sodium tartrate tetrahydrate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-B / 波長: 1 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2020年7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: 2.4→28.96 Å / Num. obs: 64146 / % possible obs: 99.8 % / 冗長度: 13.7 % / Biso Wilson estimate: 36.12 Å2 / Rpim(I) all: 0.082 / Rrim(I) all: 0.306 / Net I/σ(I): 6.7 / Num. measured all: 880269
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.4-2.4914.11.38768962190.752.84798.2
5.16-28.9613.413.98971766870.0340.122100

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解析

ソフトウェア
名称バージョン分類
xia2データスケーリング
PHENIX1.18.2精密化
PDB_EXTRACT3.27データ抽出
PHASER位相決定
Cootモデル構築
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 1RRP

1rrp


解像度: 2.4→28.96 Å / SU ML: 0.34 / 交差検証法: THROUGHOUT / σ(F): 1.97 / 位相誤差: 25.17 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.242 3185 4.97 %
Rwork0.1995 60885 -
obs0.2016 64070 99.71 %
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
原子変位パラメータBiso max: 192.76 Å2 / Biso mean: 60.1529 Å2 / Biso min: 22.5 Å2
精密化ステップサイクル: final / 解像度: 2.4→28.96 Å
タンパク質核酸リガンド溶媒全体
原子数11177 0 180 402 11759
Biso mean--47.35 42.79 -
残基数----1379
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.440.34041120.28952539265196
2.44-2.470.29081490.289726082757100
2.47-2.510.34261230.283626382761100
2.51-2.560.30351340.279726172751100
2.56-2.60.32761380.267326582796100
2.6-2.650.31461500.252825952745100
2.65-2.710.29981220.24626372759100
2.71-2.770.27541390.248226292768100
2.77-2.830.29551470.260326232770100
2.83-2.90.27731330.245726372770100
2.9-2.980.30141400.237626312771100
2.98-3.070.2881380.223526452783100
3.07-3.170.28681420.223926442786100
3.17-3.280.26111410.21926292770100
3.28-3.410.27361520.217826412793100
3.41-3.570.22521550.19626142769100
3.57-3.750.24121410.188426732814100
3.75-3.990.24231330.175626602793100
3.99-4.30.19231270.15626812808100
4.3-4.730.17211360.138126792815100
4.73-5.410.20281390.14527122851100
5.41-6.80.21151630.181826882851100
6.8-28.960.19341310.18542807293899
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)
12.8840.3705-0.65241.6850.17042.57580.0967-0.01950.0022-0.0368-0.1008-0.3163-0.09050.2888-0.00030.2673-0.06760.00170.34210.05890.3569-5.2952-13.0583-25.3619
22.96010.86170.87791.6106-0.9582.27310.1852-0.1737-0.29480.4685-0.1817-0.4830.49110.50500.4169-0.0052-0.10260.6080.08650.60332.2653-22.8651-19.9286
31.55090.12560.06660.57250.77340.90720.0052-0.1929-0.3637-0.0501-0.0756-0.11080.3315-0.2216-0.00090.358-0.0730.00410.39610.06840.3419-15.2513-22.7837-21.3284
46.20371.3555-1.65511.43870.08490.63880.5082.10021.328-1.2336-0.65781.2188-1.1249-0.6986-0.27771.25810.0553-0.08940.95580.25110.9914-29.807-5.8033-49.6226
50.2045-0.541-0.49582.38672.05721.8208-0.4583-0.1197-1.27760.890.4887-0.69291.49790.92180.07020.73850.00320.11230.548-0.12880.9381-15.4673-26.5552-46.4399
60.1789-0.2079-0.07480.2372-0.06560.12280.214-1.13011.16080.7717-0.5883-0.4822-1.390.9044-0.00730.8227-0.16980.03820.8331-0.01810.5325-15.3345-14.9432-6.2599
70.0253-0.0688-0.0180.1656-0.00050.10060.29890.2708-0.1295-0.09710.45510.37180.9769-1.48770.00070.4617-0.1928-0.04730.7568-0.04270.4705-31.678-19.8083-14.1738
80.46380.15270.46720.9895-0.34970.8133-0.0694-0.2605-0.3214-0.0466-0.1120.18370.137-0.377600.2547-0.0340.030.45490.040.3965-34.5372-25.3993-34.5328
94.41470.1504-0.05293.21510.0443.8063-0.1049-0.30570.0788-0.0836-0.058-0.1982-0.2513-0.0587-0.00010.30550.01660.00120.2984-0.00190.2879-28.3955-17.3762-38.8645
102.52561.3875-0.3872.4641-1.70671.5711-0.0630.19980.1973-0.4085-0.1234-0.1175-0.53860.087-00.30210.032-0.00750.36060.05760.3591-26.8658-15.1519-44.8056
111.0851.010.56612.6025-0.07041.79990.44090.4404-0.3416-0.671-0.44620.4847-0.1619-0.3618-0.00030.29060.0299-0.03620.412-0.04830.3805-34.959-25.1423-47.0558
121.63350.27150.32031.99010.33671.27430.0598-0.30410.2310.1019-0.03720.1556-0.2550.1435-0.00050.28170.05570.07030.4393-0.04910.414610.9117-14.0716-56.8492
134.199-0.0192-0.45752.30150.69882.5954-0.0453-0.0168-0.0017-0.199-0.05780.71840.0218-0.5493-0.00070.33730.0597-0.03960.4462-0.09410.7107-1.955-17.1967-60.934
140.0148-0.04330.030.004-0.02-0.00080.39780.2438-0.1161-0.4163-0.22580.4430.57820.3859-0.00011.11890.1912-0.27681.1061-0.22181.2462-3.9505-26.3786-70.4173
152.8539-0.78630.12541.1998-1.0242.0988-0.1470.1819-0.10310.0082-0.0802-0.06830.2690.3059-0.00150.35360.090.0620.3682-0.03440.411118.0905-20.9714-61.1705
161.806-1.5720.94841.418-1.13511.3108-0.3089-0.7956-0.278-0.3965-0.0484-0.3807-0.3646-0.427700.8248-0.02480.16161.0145-0.17890.734724.0026-14.8522-34.3883
170.40010.4509-0.56471.52060.22511.26250.12920.4152-0.02780.00740.1360.3382-1.00090.2466-0.00010.63110.08910.11440.70030.06670.430820.7745-16.4191-75.9998
181.59011.2640.41971.4628-0.5231.20280.1020.322-0.0575-0.3471-0.0975-0.182-0.4349-0.22990.00010.34660.1082-0.01630.5866-0.12860.451731.4025-23.4766-49.3177
190.03530.0413-0.03020.0515-0.02690.006-0.29770.48150.74460.3865-0.3027-0.1577-1.30680.17350.00060.93410.20540.36150.7762-0.14921.322215.9592-8.0141-36.117
201.26740.60441.21432.5365-0.78453.2301-0.16370.46670.1381-0.2937-0.0991-0.0597-0.2049-0.136-0.00570.31190.01320.01410.5026-0.12030.423731.8692-21.0014-48.5224
213.59550.1230.40032.5733-0.15172.4628-0.11870.03330.14880.0694-0.0037-0.0561-0.3111-0.1003-0.00010.32930.06660.00240.4725-0.14110.450529.1915-17.4041-43.0654
220.8108-1.19180.31712.0846-0.76632.28860.128-0.0373-0.0950.3541-0.1825-0.2748-0.18040.0364-0.00010.29750.01850.02610.4061-0.10930.465936.2727-26.9455-39.0416
232.07180.0586-1.15772.151.78432.2206-0.1174-0.0267-0.37610.8232-0.08730.30570.5805-0.6015-0.12830.6939-0.28520.10980.45290.02670.348113.7391-58.5095-14.7527
242.5099-1.1223-0.87072.31450.21492.0757-0.19060.2058-0.95840.05080.11120.30841.149-0.4597-0.07640.8883-0.35250.08040.4427-0.05260.736514.5207-69.8577-20.5573
250.43460.2139-0.28650.40460.06470.2049-0.53990.3865-1.5010.2976-0.2896-0.90331.06020.1422-0.00071.243-0.0710.06781.0797-0.21621.282929.9373-72.9892-20.0729
262.302-0.19341.3142.5339-0.2741.7815-0.1576-0.0194-0.14280.00920.2625-0.22920.02840.060.00970.4483-0.16610.01530.38470.06450.306921.124-51.0765-18.8546
271.71992.2690.91992.85741.01051.4914-0.10570.53770.01351.1477-0.45390.29070.4098-0.50740.00010.7682-0.05760.09020.98580.08260.560814.1928-45.85697.7141
283.5148-0.458-0.71410.1915-0.07920.3775-0.45380.1611-1.0234-1.228-0.260.44980.9531-0.26-0.07651.1217-0.25880.02350.9094-0.12210.548214.9533-55.5544-36.5624
29-0.01950.07310.46570.05220.5113.475-0.16770.39360.373-0.45240.13890.542-2.57450.59120.03620.6039-0.1428-0.02510.59960.01340.511120.5281-37.5906-25.9541
302.3728-1.73090.83062.04910.31723.675-0.0444-0.3385-0.096-0.4528-0.1620.10550.3113-0.1402-0.00090.3964-0.03460.04850.3324-0.04130.299320.8748-42.035-3
312.78460.90010.14422.0258-0.84032.0208-0.20370.08110.1191-0.601-0.04840.02810.0098-0.0281-0.00010.44650.0420.00210.36270.03780.320919.0476-35.5978-6.8626
321.87021.1918-1.56061.53180.12972.8308-0.0838-0.5191-0.43760.1243-0.0790.01190.3629-0.4587-0.00010.3636-0.02190.03370.3443-0.00560.315119.036-41.86582.4683
331.08430.4811-0.06730.5021-0.31330.6461-0.5273-0.4840.93350.73970.2787-0.4257-0.4159-0.573-0.00240.45580.0512-0.01280.4034-0.0650.382924.2568-29.65543.1034
342.5122-0.8064-0.55663.5247-0.05171.6604-0.07-0.12670.28850.79910.0457-0.264-0.01570.26190.00060.5427-0.0888-0.01860.358-0.01630.36957.4199-7.8281-16.5354
351.7237-0.53791.49242.76040.48612.1590.01850.09660.42430.2336-0.1830.3994-0.4753-0.2856-00.6402-0.01650.08570.3357-0.02070.657846.99492.5534-18.8263
361.52140.79390.76742.04051.09660.9610.07590.22790.2888-0.0633-0.14991.019-0.1574-0.4822-0.00220.5295-0.04390.15510.4673-0.03080.656343.6066-7.27-22.659
371.37240.3986-1.19981.78650.30331.3926-0.6034-1.2257-0.08630.6560.1848-0.50220.6816-0.7420.01650.9628-0.02540.1920.55630.01780.72356.7836-31.525-9.8093
380.55680.7168-0.83961.4366-0.46131.90110.22420.5878-1.0691.2716-0.49380.37470.37830.1604-0.00010.8649-0.1085-0.11531.0108-0.15280.878452.3251-21.59248.668
390.5042-0.28930.38530.70920.57340.9237-0.04290.31760.21910.32240.45580.1348-0.22530.2386-0.00010.7392-0.0260.12730.5422-0.03230.443553.0731-21.9918-33.2683
401.2160.66260.09020.6144-0.62030.9703-0.17570.3778-0.4014-1.4215-0.1459-0.04680.1223-0.2099-0.00440.8619-0.055-0.0220.39950.0040.465844.1107-35.4307-9.0479
412.2692-0.8836-1.43311.9199-0.7032.4705-0.3067-0.13240.1019-1.03260.1117-0.4753-0.01740.3394-0.00450.71420.02650.08650.40080.01750.456651.4137-28.5723-2.6222
421.77910.46740.60483.8722-1.03762.04910.0221-0.1303-0.15-0.5305-0.3524-0.7785-0.04050.3942-00.5101-0.00180.03710.46320.04280.465352.6284-28.9243-0.5026
430.20210.0942-0.08990.6511-0.61621.1240.0609-0.2970.8137-0.1978-0.2210.1328-0.4844-0.0449-0.00010.49290.03280.00620.3972-0.05520.411242.2926-26.44614.6335
442.2959-0.7838-0.56271.10260.27941.165-0.451-0.2295-1.34390.52040.26640.69971.46920.2905-0.03320.61460.09710.02490.41480.04840.387946.1829-40.53573.8982
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 102 )A7 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 144 )A103 - 144
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 184 )A145 - 184
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 207 )A185 - 207
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 216 )A208 - 216
6X-RAY DIFFRACTION6chain 'B' and (resid 1172 through 1179 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1180 through 1185 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1186 through 1200 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1201 through 1253 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1254 through 1283 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1284 through 1306 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 8 through 61 )C8 - 61
13X-RAY DIFFRACTION13chain 'C' and (resid 62 through 135 )C62 - 135
14X-RAY DIFFRACTION14chain 'C' and (resid 136 through 144 )C136 - 144
15X-RAY DIFFRACTION15chain 'C' and (resid 145 through 190 )C145 - 190
16X-RAY DIFFRACTION16chain 'C' and (resid 191 through 216 )C191 - 216
17X-RAY DIFFRACTION17chain 'D' and (resid 1172 through 1184 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 1185 through 1205 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 1206 through 1209 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 1210 through 1236 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 1237 through 1283 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 1284 through 1306 )D0
23X-RAY DIFFRACTION23chain 'E' and (resid 7 through 58 )E7 - 58
24X-RAY DIFFRACTION24chain 'E' and (resid 59 through 125 )E59 - 125
25X-RAY DIFFRACTION25chain 'E' and (resid 126 through 144 )E126 - 144
26X-RAY DIFFRACTION26chain 'E' and (resid 145 through 190 )E145 - 190
27X-RAY DIFFRACTION27chain 'E' and (resid 191 through 216 )E191 - 216
28X-RAY DIFFRACTION28chain 'F' and (resid 1172 through 1178 )F0
29X-RAY DIFFRACTION29chain 'F' and (resid 1179 through 1188 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 1189 through 1223 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 1224 through 1253 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 1254 through 1289 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 1290 through 1306 )F0
34X-RAY DIFFRACTION34chain 'G' and (resid 7 through 88 )G7 - 88
35X-RAY DIFFRACTION35chain 'G' and (resid 89 through 132 )G89 - 132
36X-RAY DIFFRACTION36chain 'G' and (resid 133 through 171 )G133 - 171
37X-RAY DIFFRACTION37chain 'G' and (resid 172 through 195 )G172 - 195
38X-RAY DIFFRACTION38chain 'G' and (resid 196 through 216 )G196 - 216
39X-RAY DIFFRACTION39chain 'H' and (resid 1172 through 1184 )H0
40X-RAY DIFFRACTION40chain 'H' and (resid 1185 through 1200 )H0
41X-RAY DIFFRACTION41chain 'H' and (resid 1201 through 1235 )H0
42X-RAY DIFFRACTION42chain 'H' and (resid 1236 through 1279 )H0
43X-RAY DIFFRACTION43chain 'H' and (resid 1280 through 1290 )H0
44X-RAY DIFFRACTION44chain 'H' and (resid 1291 through 1306 )H0

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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

他の情報も見る