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- PDB-7mo3: Crystal Structure of the ZnF3 of Nucleoporin NUP153 in complex wi... -

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基本情報

登録情報
データベース: PDB / ID: 7mo3
タイトルCrystal Structure of the ZnF3 of Nucleoporin NUP153 in complex with Ran-GDP, resolution 2.05 Angstrom
要素
  • GTP-binding nuclear protein Ran
  • Nuclear pore complex protein Nup153
キーワードTRANSPORT PROTEIN / nuclear pore complex component / nucleocytoplasmic transport / complex (small GTPase-nuclear protein) / zinc finger
機能・相同性
機能・相同性情報


nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins ...nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / negative regulation of RNA export from nucleus / annulate lamellae / Regulation of HSF1-mediated heat shock response / nuclear pore complex assembly / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / nuclear inclusion body / nuclear pore nuclear basket / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear localization sequence binding / DNA metabolic process / dynein intermediate chain binding / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / mRNA transport / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / nuclear pore / protein-membrane adaptor activity / centriole / protein export from nucleus / viral process / nuclear periphery / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / 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 / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / double-stranded DNA binding / nuclear membrane / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
類似検索 - 分子機能
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / small GTPase Ran family profile. / Ran GTPase / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / small GTPase Ran family profile. / Ran GTPase / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / Nuclear pore complex protein Nup153 / GTP-binding nuclear protein Ran
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Rattus norvegicus (ドブネズミ)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.05 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 1.22024年5月22日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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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: Nuclear pore complex protein Nup153
C: GTP-binding nuclear protein Ran
D: Nuclear pore complex protein Nup153
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,94210
ポリマ－57,8764
非ポリマー1,0666
水1,49583
1
A: GTP-binding nuclear protein Ran
B: Nuclear pore complex protein Nup153
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,4715
ポリマ－28,9382
非ポリマー5333
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-29 kcal/mol
Surface area11950 Å2
手法PISA
2
C: GTP-binding nuclear protein Ran
D: Nuclear pore complex protein Nup153
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,4715
ポリマ－28,9382
非ポリマー5333
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-28 kcal/mol
Surface area12330 Å2
手法PISA
単位格子
Length a, b, c (Å)68.970, 62.550, 70.650
Angle α, β, γ (deg.)90.000, 105.120, 90.000
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 / タンパク質・ペプチド , 2種, 4分子 ACBD

#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: 24483.086 Da / 分子数: 2 / 変異: F35S / 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・ペプチド Nuclear pore complex protein Nup153 / 153 kDa nucleoporin / Nucleoporin Nup153


分子量: 4455.060 Da / 分子数: 2 / Fragment: ZINC FINGER 3 of NUP153 (UNP residues 781-817) / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Nup153 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P49791

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非ポリマー , 4種, 89分子

#3: 化合物 ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / コメント: GDP, 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: 2 / 由来タイプ: 合成 / 式: Mg
#5: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 83 / 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: 2.54 Å3/Da / 溶媒含有率: 51.61 %
結晶化温度: 294 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: 20% w/v PEG3350, 0.1 M Bis-Tris

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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: SSRL / ビームライン: BL12-2 / 波長: 1.03317 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2020年10月29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: 1.03317 Å / 相対比: 1
反射解像度: 2.05→29.39 Å / Num. obs: 66213 / % possible obs: 93.2 % / 冗長度: 7.2 % / Biso Wilson estimate: 48.68 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Net I/σ(I): 15.7
反射 シェル

Diffraction-ID: 1 / % possible all: 93.7

解像度 (Å)冗長度 (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
2.05-2.127.11.12429634150.7251.976
4.41-29.396.943.42418735220.0140.037

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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
Cootモデル構築
AutoSol位相決定
XDSデータ削減
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.05→29.39 Å / SU ML: 0.3 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 30.63 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2282 3136 4.74 %
Rwork0.204 63077 -
obs0.2052 66213 92.56 %
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: 249.83 Å2 / Biso mean: 98.6589 Å2 / Biso min: 38.43 Å2
精密化ステップサイクル: final / 解像度: 2.05→29.39 Å
タンパク質核酸リガンド溶媒全体
原子数3853 0 84 83 4020
Biso mean--68.12 65.37 -
残基数----487
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.080.38761670.42822731289887
2.08-2.120.41361770.392850302794
2.12-2.150.35821320.36612968310095
2.15-2.190.40551290.34942887301694
2.19-2.230.29091210.32012950307194
2.23-2.280.25911230.3042908303194
2.28-2.330.34251620.28612865302793
2.33-2.380.31081720.2942845301793
2.38-2.440.31741550.2772801295691
2.44-2.510.31391480.26592627277585
2.51-2.580.29821540.2612759291391
2.58-2.670.24911170.25493009312696
2.67-2.760.24331290.24542997312696
2.76-2.870.32971250.24232974309996
2.87-30.30121290.23652938306794
3-3.160.22761580.22412876303494
3.16-3.360.26041380.21652858299692
3.36-3.620.22691550.21942609276485
3.62-3.980.20531570.18392838299592
3.98-4.550.16811320.15882986311896
4.55-5.730.1928980.15712978307694
5.73-29.390.1861580.16342823298192
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8998-0.67730.54820.7504-0.42650.4466-0.0263-0.40071.4868-0.0284-0.2607-1.5067-0.31771.0723-0.02140.75860.06150.00430.628-0.0870.610617.6826.6321-26.7996
22.8775-0.61361.55034.10250.66642.6033-0.0590.2420.2988-0.3387-0.0944-0.1822-0.09920.254300.5497-0.03140.05330.44050.03480.457910.048417.8369-27.4836
30.6895-0.05511.27082.0574-0.33352.43840.3290.582-0.1879-1.374-0.23090.50160.6222-0.123-0.00270.81960.032-0.07690.55850.02130.5452.825815.3384-35.8786
43.014-1.88530.33384.7341-0.53884.01370.22040.2224-0.3544-0.71430.07190.79760.6855-0.70790.00220.7095-0.1737-0.11730.60570.01170.6889-2.893510.1133-28.4649
52.11890.68362.2130.725-0.07173.10760.7714-1.0947-1.26150.40050.12570.48890.9367-1.28140.25170.6072-0.2248-0.0810.81930.14760.9761-10.060412.6724-18.6886
60.0108-0.0009-0.00970.0043-0.00520.0131-0.04860.2682-0.69961.2732-0.3598-0.56981.48540.88940.00571.4460.2785-0.07491.0468-0.10250.996118.957-3.8694-19.5181
70.1265-0.0780.00180.10310.08440.1414-0.4583-1.20310.88970.4289-0.4486-0.77220.58461.4770.00331.63850.1645-0.02931.1982-0.08321.26424.8751-0.543-29.5769
84.6064-0.35735.27771.85540.21356.31390.5685-0.1691-0.44670.1784-0.2402-0.15931.36530.6361.0020.91330.18720.37951.03550.03540.842525.405710.9083-34.2199
90.4826-0.05620.44030.612-0.26790.84490.25170.61680.0088-0.7331-0.3141-0.75190.01890.82820.00031.03660.14230.27741.01470.06740.779724.405611.681-39.7696
100.1312-0.2603-0.04810.52640.07170.00990.42591.4074-0.4691-1.70290.4721-0.36020.04261.21390.02610.9195-0.1377-0.12810.83420.03730.917127.375824.3718-11.8452
113.8775-0.56860.94654.62680.33945.5454-0.4716-0.36160.1660.78690.2463-1.04310.27140.7750.00140.61830.1144-0.08850.593-0.04580.682928.812914.1835-1.9965
123.3096-0.75871.35253.5812-0.24155.3546-0.8003-1.03230.42991.22470.3962-0.6481-0.3752-0.1219-0.00561.06960.2345-0.29030.8401-0.12330.727722.987820.95416.2928
132.72510.3921.53930.80130.67161.1192-0.6168-1.46460.73460.71360.06620.0316-0.7387-1.5278-0.03981.30490.1893-0.06751.2048-0.15180.462811.760516.071410.4595
140.1490.0443-0.00320.06940.00980.01420.7953-0.2298-0.28450.3720.06450.3422-1.23270.3306-0.00271.56760.2129-0.41611.6319-0.22781.471630.696425.2226.3017
151.036-0.452-0.40840.27860.6112.14071.54460.26880.27770.9894-0.54270.03520.73350.52060.07641.0288-0.16860.05590.91720.09491.282725.210234.0977-14.805
166.15174.28541.27723.40382.63617.66750.0436-0.87371.8914-0.2214-0.4185-0.1858-1.44021.106-0.65620.7932-0.34970.19311.3111-0.12081.666936.869925.7687-19.2303
170.2007-0.13240.20030.1124-0.02050.25380.61340.10091.23650.5629-0.6863-0.67710.50271.0456-0.00020.81410.04630.05151.11660.12811.192340.844221.8035-16.2031
182.26931.78130.77293.0941.16492.61310.722-0.98510.50350.0011-0.1561-0.6069-0.1937-0.03760.82730.86210.13910.37141.60420.27271.200142.532716.9451-18.1064
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 12 )A7 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 72 )A13 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 95 )A73 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 178 )A96 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 210 )A179 - 210
6X-RAY DIFFRACTION6chain 'B' and (resid 780 through 785 )B780 - 785
7X-RAY DIFFRACTION7chain 'B' and (resid 786 through 790 )B786 - 790
8X-RAY DIFFRACTION8chain 'B' and (resid 791 through 797 )B791 - 797
9X-RAY DIFFRACTION9chain 'B' and (resid 798 through 817 )B798 - 817
10X-RAY DIFFRACTION10chain 'C' and (resid 7 through 13 )C7 - 13
11X-RAY DIFFRACTION11chain 'C' and (resid 14 through 103 )C14 - 103
12X-RAY DIFFRACTION12chain 'C' and (resid 104 through 178 )C104 - 178
13X-RAY DIFFRACTION13chain 'C' and (resid 179 through 208 )C179 - 208
14X-RAY DIFFRACTION14chain 'C' and (resid 209 through 213 )C209 - 213
15X-RAY DIFFRACTION15chain 'D' and (resid 780 through 788 )D780 - 788
16X-RAY DIFFRACTION16chain 'D' and (resid 789 through 795 )D789 - 795
17X-RAY DIFFRACTION17chain 'D' and (resid 796 through 810 )D796 - 810
18X-RAY DIFFRACTION18chain 'D' and (resid 811 through 817 )D811 - 817

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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://pdbjlvh1.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