[日本語] English
万見
- PDB-7mni: Crystal structure of the N-terminal domain of NUP88 in complex wi... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7mni
タイトルCrystal structure of the N-terminal domain of NUP88 in complex with NUP98 C-terminal Autoproteolytic Domain
要素
  • Nuclear pore complex protein Nup88
  • Nuclear pore complex protein Nup98
キーワードTRANSPORT PROTEIN / nuclear pore complex component / nucleocytoplasmic transport
機能・相同性
機能・相同性情報


transporter activity / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / 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) ...transporter activity / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / 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) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ / ribosomal large subunit export from nucleus / Regulation of HSF1-mediated heat shock response / mRNA transport / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / Separation of Sister Chromatids / protein import into nucleus / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / cytosol
類似検索 - 分子機能
Nucleoporin Nup88 / Nuclear pore component / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like
類似検索 - ドメイン・相同性
Nuclear pore complex protein Nup98-Nup96 / Nuclear pore complex protein Nup88
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 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

-
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

-
集合体

登録構造単位
A: Nuclear pore complex protein Nup88
B: Nuclear pore complex protein Nup98
C: Nuclear pore complex protein Nup88
D: Nuclear pore complex protein Nup98


分子量 (理論値)分子数
合計 (水以外)143,7934
ポリマ－143,7934
非ポリマー00
水7,512417
1
A: Nuclear pore complex protein Nup88
B: Nuclear pore complex protein Nup98


分子量 (理論値)分子数
合計 (水以外)71,8972
ポリマ－71,8972
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-2 kcal/mol
Surface area26340 Å2
手法PISA
2
C: Nuclear pore complex protein Nup88
D: Nuclear pore complex protein Nup98


分子量 (理論値)分子数
合計 (水以外)71,8972
ポリマ－71,8972
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-3 kcal/mol
Surface area26670 Å2
手法PISA
単位格子
Length a, b, c (Å)59.748, 72.085, 73.042
Angle α, β, γ (deg.)92.530, 103.690, 100.390
Int Tables number1
Space group name H-MP1

-
要素

#1: タンパク質 Nuclear pore complex protein Nup88 / 88 kDa nucleoporin / Nucleoporin Nup88


分子量: 54634.992 Da / 分子数: 2 / 断片: N-terminal domain of NUP88 (UNP residues 1-493) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NUP88 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q99567
#2: タンパク質 Nuclear pore complex protein Nup98


分子量: 17261.568 Da / 分子数: 2
断片: NUP98 C-terminal Autoproteolytic Domain (UNP residues 715-863)
由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: NUP98, ADAR2 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P52948-2, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 417 / 由来タイプ: 天然 / 式: H2O

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.08 Å3/Da / 溶媒含有率: 40.93 %
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: 8.3 / 詳細: 20% w/v PEG4000, 0.22 M sodium chloride, 0.1 M Tris

-
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: 1.00003 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年8月7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: 1.00003 Å / 相対比: 1
反射解像度: 2→20 Å / Num. obs: 76633 / % possible obs: 97.8 % / 冗長度: 6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.056 / Rrim(I) all: 0.143 / Net I/σ(I): 7.5 / Num. measured all: 456229 / Scaling rejects: 251
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.043.60.9841618244720.5130.6041.1571.396.6
10-2070.07837765410.9950.0310.0842386.4

-
解析

ソフトウェア
名称バージョン分類
Aimless0.7.4データスケーリング
PHENIX1.17.1精密化
PDB_EXTRACT3.27データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB entries 5CWW & 1KO6

5cww

1ko6


解像度: 2→20 Å / SU ML: 0.27 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 23.23 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2084 3639 4.76 %
Rwork0.1752 72850 -
obs0.1767 76489 97.69 %
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: 191.54 Å2 / Biso mean: 61.7063 Å2 / Biso min: 21.4 Å2
精密化ステップサイクル: final / 解像度: 2→20 Å
タンパク質核酸リガンド溶媒全体
原子数8852 0 0 418 9270
Biso mean---49.12 -
残基数----1121
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.35251410.2962761290296
2.03-2.050.29851460.28712758290496
2.05-2.080.311340.27992762289696
2.08-2.110.30791490.27382733288296
2.11-2.150.30721540.25682728288296
2.15-2.180.31881610.24882783294497
2.18-2.220.24651290.24492771290097
2.22-2.260.27281350.23362726286197
2.26-2.30.26061630.232808297197
2.3-2.350.26341480.22692772292098
2.35-2.40.26191520.2252797294997
2.4-2.460.26461350.22082780291598
2.46-2.520.23251230.21632850297398
2.52-2.590.22791270.20852815294298
2.59-2.660.26231490.20842792294198
2.66-2.750.25681490.20262796294598
2.75-2.850.2341300.2012863299398
2.85-2.960.26151300.20082812294298
2.96-3.090.25221600.19332770293098
3.09-3.260.21491370.17342858299599
3.26-3.460.1621300.15772866299699
3.46-3.730.16221430.14542825296899
3.73-4.10.17141160.13522842295899
4.1-4.680.1451390.1132850298999
4.68-5.880.15111360.12762873300999
5.88-200.20181230.17352859298299
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)
15.15530.76910.99463.49471.3642.92550.0622-0.15260.30090.2771-0.18560.59690.1162-0.36120.11630.2933-0.03740.02970.2852-0.05580.4523-45.5489-6.1972-35.4936
23.5361.84321.19722.25340.86971.47660.00640.0583-0.1553-0.03450.0409-0.16710.220.0336-0.05340.30060.02960.00880.21950.0070.337-27.9147-9.2881-38.7434
31.43950.52380.23331.7267-0.15172.831-0.0419-0.0732-0.0810.0467-0.0875-0.3712-0.02340.4330.16170.2480.0324-0.050.33390.02520.4239-11.97394.2565-30.5227
44.47750.22211.04044.5657-0.23872.79250.0064-0.128-0.19150.1466-0.01080.2089-0.1734-0.21570.03470.3770.0464-0.03660.2784-0.05310.3295-25.58312.995-21.9112
52.68161.50390.57224.38571.16572.15250.0667-0.05480.19580.2916-0.15380.2891-0.0417-0.14180.09290.37220.0570.02180.3281-0.03050.3836-35.349712.9218-25.345
64.0497-0.2864-0.02645.7271-1.22954.4140.07690.8184-0.4217-0.4713-0.6871-1.27930.66690.91550.51210.63910.11140.05360.76370.1680.68456.9463-20.8554.709
74.0052-0.0189-0.08588.9705-3.74866.54610.0820.4835-0.2162-0.242-0.3423-0.30970.24270.08940.17770.4143-0.0603-0.11510.57770.19850.5598-2.024-16.67955.2267
85.6509-1.07350.33155.5104-0.02613.9480.02941.6859-0.2935-1.1472-0.24640.29490.43970.54120.28510.92630.0937-0.06111.00590.00470.444-3.3855-17.8629-7.2293
91.1907-0.21581.27984.602-2.3292.79730.2162-0.2115-0.2106-0.0008-0.5195-0.41910.09020.25990.26070.4383-0.0173-0.10960.47250.07690.57-9.0696-3.9099-3.8524
102.0109-0.2566-0.12348.3375-2.51682.92360.176-0.3341-0.00120.53740.15670.9531-0.3506-0.409-0.28720.5780.0157-0.18790.58320.08730.6357-14.4806-0.3265-0.0393
113.48340.9475-0.26663.64311.14182.43090.0566-0.01270.43130.1333-0.04190.1018-0.08080.0256-0.02520.2658-0.020.01930.2520.00440.3446-15.44-29.073628.4259
122.57021.43190.71223.17380.9791.6577-0.11420.19560.0175-0.21210.1467-0.30470.0040.11130.00570.2567-0.00680.05840.31470.00120.2865-10.4921-41.060419.4719
131.45470.20260.2071.5238-0.41692.4236-0.03540.2325-0.1441-0.45210.0668-0.12310.1044-0.094-0.03240.3812-0.06350.04460.3286-0.06770.1969-21.2942-54.75678.7499
143.54211.36390.40822.98691.16923.7973-0.0340.07050.0385-0.21110.23540.23330.1331-0.3239-0.14070.2963-0.0691-0.02810.44560.01890.2963-38.8605-50.96813.5648
153.55061.71220.69973.13080.61881.7795-0.02170.11750.1401-0.04910.03890.1860.0618-0.2112-0.03940.27870.03090.04260.4019-0.00280.3266-35.7839-41.272825.3875
162.1198-0.4647-0.1823.6869-3.36484.7896-0.06720.39560.0415-0.2654-0.1847-0.51520.52450.39860.14170.40.05180.01050.3850.02340.423-31.6477-40.0783-34.5224
173.8090.5647-0.87144.1398-2.45015.49970.1219-0.08360.4180.354-0.072-0.1458-0.4291-0.1182-0.08120.31760.0270.00730.2444-0.03050.2785-34.7231-33.8028-29.3016
185.99871.6653-1.47195.44-1.09734.60970.3917-0.61-0.25030.7283-0.5564-0.68570.21870.69270.16760.50330.0144-0.08880.4850.05460.438-26.8116-39.5073-19.4202
192.16560.918-0.3564.3185-3.75735.0570.1063-0.2518-0.03680.1858-0.0147-0.347-0.2023-0.3469-0.06630.3897-0.02160.03180.395-0.05240.2793-36.9335-40.2465-12.5649
202.88450.4906-1.04824.2921-1.99334.21580.3417-0.78570.28420.55330.24460.7576-0.4964-0.7996-0.51260.53170.00760.07680.82920.04470.3614-44.1524-38.2649-8.1924
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 98 )A13 - 98
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 203 )A99 - 203
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 303 )A204 - 303
4X-RAY DIFFRACTION4chain 'A' and (resid 304 through 404 )A304 - 404
5X-RAY DIFFRACTION5chain 'A' and (resid 405 through 493 )A405 - 493
6X-RAY DIFFRACTION6chain 'B' and (resid 714 through 741 )B714 - 741
7X-RAY DIFFRACTION7chain 'B' and (resid 742 through 766 )B742 - 766
8X-RAY DIFFRACTION8chain 'B' and (resid 767 through 791 )B767 - 791
9X-RAY DIFFRACTION9chain 'B' and (resid 792 through 821 )B792 - 821
10X-RAY DIFFRACTION10chain 'B' and (resid 822 through 863 )B822 - 863
11X-RAY DIFFRACTION11chain 'C' and (resid 12 through 108 )C12 - 108
12X-RAY DIFFRACTION12chain 'C' and (resid 109 through 187 )C109 - 187
13X-RAY DIFFRACTION13chain 'C' and (resid 188 through 290 )C188 - 290
14X-RAY DIFFRACTION14chain 'C' and (resid 291 through 372 )C291 - 372
15X-RAY DIFFRACTION15chain 'C' and (resid 373 through 493 )C373 - 493
16X-RAY DIFFRACTION16chain 'D' and (resid 714 through 738 )D714 - 738
17X-RAY DIFFRACTION17chain 'D' and (resid 739 through 768 )D739 - 768
18X-RAY DIFFRACTION18chain 'D' and (resid 769 through 789 )D769 - 789
19X-RAY DIFFRACTION19chain 'D' and (resid 790 through 821 )D790 - 821
20X-RAY DIFFRACTION20chain 'D' and (resid 822 through 863 )D822 - 863

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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