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基本情報

登録情報
データベース: PDB / ID: 7mnz
タイトルCrystal Structure of Nup358/RanBP2 Ran-binding domain 4 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 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) / 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 / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / ISG15 antiviral mechanism / 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: 2.35 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
I: GTP-binding nuclear protein Ran
J: E3 SUMO-protein ligase RanBP2
K: GTP-binding nuclear protein Ran
L: E3 SUMO-protein ligase RanBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)246,99024
ポリマ－243,71112
非ポリマー3,27912
水8,521473
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)41,1654
ポリマ－40,6182
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-36 kcal/mol
Surface area17370 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)41,1654
ポリマ－40,6182
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-33 kcal/mol
Surface area17120 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)41,1654
ポリマ－40,6182
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-35 kcal/mol
Surface area17210 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)41,1654
ポリマ－40,6182
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-36 kcal/mol
Surface area17310 Å2
手法PISA
5
I: GTP-binding nuclear protein Ran
J: E3 SUMO-protein ligase RanBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,1654
ポリマ－40,6182
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-36 kcal/mol
Surface area17150 Å2
手法PISA
6
K: GTP-binding nuclear protein Ran
L: E3 SUMO-protein ligase RanBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)41,1654
ポリマ－40,6182
非ポリマー5472
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-36 kcal/mol
Surface area17280 Å2
手法PISA
単位格子
Length a, b, c (Å)142.690, 142.690, 96.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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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: 24430.023 Da / 分子数: 6 / 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: 16188.443 Da / 分子数: 6
Fragment: RAN-binding domain 4 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2911-3045), WHTMKNYY/QNYDNKQV mutant (UNP residues 2962-2969)
Mutation: W2962Q, H2963N, T2964Y, M2965D, K2966N, N2967K, Y2928Q, Y2969V
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: 6 / 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: 6 / 由来タイプ: 合成 / 式: Mg
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 473 / 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: 2.33 Å3/Da / 溶媒含有率: 47.23 %
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 ammonium sulfate, 0.1 M HEPES

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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: 2021年3月2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: 2.35→29.36 Å / Num. obs: 91578 / % possible obs: 99.9 % / 冗長度: 10.2 % / Biso Wilson estimate: 47.55 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.154 / Net I/σ(I): 12.4 / Num. measured all: 935004
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
2.35-2.439.51.88681091700.5911.83599.8
5.06-29.369.930.39064491620.0190.06199.9

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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
PHENIX1.19.1精密化
PDB_EXTRACT3.27データ抽出
Cootモデル構築
PHASER位相決定
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: 2.35→29.36 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 1.97 / 位相誤差: 27.08 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2252 4426 4.84 %
Rwork0.1833 87089 -
obs0.1854 91515 99.87 %
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: 179.4 Å2 / Biso mean: 66.4518 Å2 / Biso min: 26.12 Å2
精密化ステップサイクル: final / 解像度: 2.35→29.36 Å
タンパク質核酸リガンド溶媒全体
原子数16634 0 270 473 17377
Biso mean--44.78 50.65 -
残基数----2060
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.380.40881000.330729793079100
2.38-2.40.3191140.285929053019100
2.4-2.430.3351800.280228963076100
2.43-2.460.28451320.268429313063100
2.46-2.50.26781280.258129253053100
2.5-2.530.30731350.238429423077100
2.53-2.570.31141300.233328512981100
2.57-2.610.26191640.232829383102100
2.61-2.650.27411780.240628613039100
2.65-2.690.27611240.227929503074100
2.69-2.740.28181320.232529263058100
2.74-2.790.2711620.246728613023100
2.79-2.840.30521420.249628562998100
2.84-2.90.31521280.241629123040100
2.9-2.960.27021480.214129293077100
2.96-3.030.26311980.221828813079100
3.03-3.10.27191480.204828833031100
3.11-3.190.23951380.201229433081100
3.19-3.280.27111320.197628983030100
3.28-3.390.23391500.196429073057100
3.39-3.510.24381960.184628463042100
3.51-3.650.22911680.173328863054100
3.65-3.810.21620.159328973059100
3.82-4.020.20121470.15229093056100
4.02-4.270.17321940.137128022996100
4.27-4.590.17381070.128829753082100
4.6-5.050.19091560.132229023058100
5.06-5.780.17061020.162329553057100
5.78-7.270.20061520.185128823034100
7.27-29.360.18661790.15972861304099
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)
12.50560.08570.51752.24561.17751.8013-0.0729-0.1613-0.10970.0415-0.0707-0.0380.23620.1155-00.3323-0.06950.03710.4864-0.06730.3992-28.8623-6.64376.2297
23.49090.2219-0.09312.2860.56743.2053-0.0880.1290.6601-0.3186-0.01140.0926-0.5005-0.0691-00.4252-0.0409-0.01610.4746-0.04990.4994-29.86885.0472-0.8998
30.6484-0.35120.5310.1717-0.20160.832-1.8487-0.17191.36460.09670.58540.3804-1.11180.3283-0.10251.3734-0.241-0.00850.8503-0.15451.1505-20.155215.07612.27
41.2178-1.1014-0.30522.08610.26692.2992-0.1511-0.5060.04830.4066-0.0668-0.2721-0.07180.5978-0.00280.3321-0.0401-0.0070.63-0.1430.4488-21.3059-2.499414.1497
5-0.00050.0131-0.0406-0.0271-0.02710.05530.0491-0.5708-0.7924-0.0079-0.2240.4411.5275-0.25660.00051.1739-0.26630.09110.9611-0.09171.0923-24.1552-36.94514.017
61.4941-0.94930.65350.6038-0.43820.3321-0.5328-0.4282-1.1083-0.75420.8702-0.41960.42530.34690.05870.76340.09630.17510.48640.01220.4734-12.8475-24.9609-4.6321
71.3963-1.9916-0.05658.1066-1.42154.1451-0.26510.39740.31880.0937-0.6031-0.5465-0.5071-0.247-0.26930.5211-0.0612-0.0871.1845-0.29770.5737-31.99917.222523.1851
83.1856-1.1197-0.87145.0017-0.2252.1737-0.3031-0.5234-0.13710.52460.2625-0.30060.1854-0.09040.00010.4575-0.00380.06910.6079-0.02110.4855-14.9792-22.174613.7881
93.20880.25441.1770.80520.89792.0333-0.1124-0.4339-0.10990.6375-0.0311-0.44330.5634-0.3095-0.00020.6161-0.03280.10150.6981-0.04120.5261-16.4177-24.21815.8783
101.7468-0.62762.42792.8356-0.09823.99190.04180.04060.0217-0.254-0.0488-0.14060.8-0.0192-00.5994-0.03240.09560.5568-0.02230.6235-14.8466-26.77936.1259
110.9469-0.30920.58610.42590.12160.6499-0.1484-0.6443-0.65290.1269-0.0762-1.02940.57310.56860.00060.74020.07930.09580.67360.04140.9752-4.0319-31.383813.7373
120.05010.02110.01040.0405-0.04020.08521.0236-0.84871.07570.2730.28430.3883-0.6761-1.1098-0.00080.95370.0397-0.01270.6397-0.11280.8311-59.056-5.454717.6246
133.15040.44570.35951.04990.45060.7066-0.15040.4226-0.0565-0.00340.21590.0574-0.1576-0.04190.00080.3129-0.02360.01360.3657-0.03720.3364-63.0165-13.74221.7175
142.98960.82260.6983.16390.55120.9553-0.18390.6837-0.4877-0.19710.3241-0.38350.10850.35110.00140.3401-0.04810.0530.5642-0.1330.4689-52.1052-17.563-2.3062
15-0.01730.0562-0.02690.183-0.21340.20770.5906-0.0298-1.467-1.133-0.56290.68620.6269-0.1413-0.00130.92440.14620.00991.3119-0.27891.4065-46.8412-30.68361.0265
161.55660.48780.51320.8068-0.05872.1314-0.2454-0.3059-0.33130.36940.06130.00160.32-0.1017-0.00970.3955-0.00330.01890.35410.01220.4652-62.3611-21.159512.2321
172.04681.3725-0.04151.399-0.35252.1326-0.3970.33680.5740.15060.29481.034-0.823-0.5435-0.00040.62830.1477-0.00330.66680.04510.6721-89.99-6.8192-0.5659
180.8123-0.48860.91240.2849-0.53510.9491-0.37770.8752-0.8767-0.3092-0.0443-0.24460.296-0.0743-0.00010.7945-0.05680.04930.6345-0.06420.6744-47.2221-16.372620.1771
195.1901-0.80210.30132.57621.01412.2978-0.0544-0.4216-0.37880.37330.06080.1587-0.01530.1881-0.00010.4323-0.02650.04760.3670.00190.516-81.3318-17.435510.0755
202.8521.18331.17752.62770.23723.0957-0.3605-0.6892-0.26560.54030.23170.1322-0.0738-0.5128-0.00020.43630.04970.04150.5030.03540.4428-84.5472-15.033616.1722
212.3671-0.8254-1.04131.4839-1.23452.8494-0.08730.52950.1610.2655-0.09370.31080.0063-0.3998-0.00010.3352-0.05550.06310.5001-0.06030.5554-87.8188-14.58134.323
222.5602-1.99550.60242.28250.39092.1333-0.12740.1308-1.03120.0786-0.32630.66590.1034-0.6853-0.00870.5021-0.13360.14350.5327-0.07870.6571-92.3222-20.3399.385
230.0653-0.0116-0.04460.0258-0.03180.07220.16120.2891-0.3693-0.0689-0.47070.06440.1926-1.8126-0.00021.0799-0.29540.13841.0344-0.34580.9068-13.8925-33.6024-43.4384
241.4648-0.1027-1.58481.0851-0.18053.4044-0.42490.0783-0.22410.2323-0.16190.21870.8288-0.3787-0.00790.7278-0.06360.19980.4566-0.06690.4799-10.0079-28.2223-25.5104
253.44860.279-1.60932.6047-0.33646.3701-0.1927-0.5149-0.18640.6718-0.1425-0.66630.61181.10830.00790.75840.09470.02720.62740.08710.54753.2219-26.2598-21.5194
260.3162-0.7120.50961.4393-1.37541.19-0.10110.2870.2773-0.2701-0.1969-0.13330.1293-0.0588-0.00030.5683-0.0120.12590.4947-0.140.5031-10.5086-22.2872-39.7128
270.06110.03620.0740.06780.02580.06540.6674-0.1041-0.74860.13480.2271-0.2625-0.01190.229-0.00051.07180.01350.27321.412-0.32451.5596-42.9769-17.8735-25.8407
281.0039-0.49730.43651.32340.01631.18990.10761.3740.32280.5025-0.43080.45951.1231-0.4047-0.01780.5019-0.11420.09350.7001-0.15910.5199-30.2166-10.8354-17.2562
291.7812-0.0231-2.03911.17260.27812.19550.04940.4874-0.0096-0.3131-0.41560.09470.4841-0.1564-0.00640.7733-0.02050.05920.5114-0.09220.4531-9.1657-22.9686-45.4976
302.4253-1.10291.32652.36670.90161.94920.1421-0.3073-0.06680.084-0.1830.23550.70920.1511-00.5115-0.03960.06730.5064-0.12640.4619-23.7908-14.3757-23.973
311.4002-0.3294-0.90572.5999-0.48762.9894-0.01560.14790.1767-0.1863-0.09150.0519-0.1332-0.25200.4671-0.06320.02210.5321-0.14040.4985-26.7669-10.4859-36.0193
321.2365-0.8064-0.26450.7577-0.54042.26060.0046-0.2792-0.26180.5481-0.3765-0.25950.5471-0.28390.00010.4971-0.10280.10260.6096-0.19020.5834-28.5955-14.3327-29.8307
330.61880.0235-0.20170.3075-0.09720.3497-0.09860.17520.9993-0.4462-0.314-0.0796-0.6449-0.57050.00030.5930.0413-0.09210.6067-0.18180.7831-31.9071-0.0358-35.1067
344.76210.93240.60797.82093.90561.9637-0.22291.0659-0.1907-1.4508-0.5186-0.013-0.0121-0.2709-0.19650.40770.03070.2690.7616-0.02470.6333-34.2429-33.089621.993
351.20260.24350.55292.7003-0.09982.05840.1521-0.10210.06970.2048-0.1199-0.01950.14520.036600.3131-0.00820.03310.3211-0.00550.3481-43.0985-36.2537.4043
363.46470.58570.20722.94460.20322.5657-0.0154-0.21830.51510.3103-0.07870.1689-0.32590.0062-00.4461-0.0286-0.00720.3369-0.02950.4782-45.9107-25.023841.5104
370.3819-0.10860.43660.016-0.15990.4983-0.3103-0.09531.61-0.15830.69061.2297-0.8894-0.7826-0.00071.01640.1769-0.04460.7267-0.09831.2907-58.6524-18.768737.7728
381.1485-0.1125-0.30592.00420.36291.88870.05080.1278-0.0947-0.4171-0.24290.099-0.0705-0.31550.00010.36580.0141-0.00630.35290.02070.408-50.0735-35.640426.6641
391.69592.0159-0.22352.37940.09562.2848-0.15750.1282-0.28720.8451-0.0261-1.00480.84370.8775-0.00020.81320.1869-0.12870.65750.03250.6872-39.8696-63.863740.4574
400.4838-0.70760.47150.7466-0.53990.517-0.1011-0.40940.3309-0.1194-0.0677-0.2812-0.46070.13080.00020.8489-0.09950.03770.65240.04340.7457-43.8104-20.256519.1387
412.0195-0.1742-2.29413.48480.63632.5617-0.02790.4048-0.1638-0.11420.12740.1759-0.2467-0.13410.00010.4107-0.0363-0.02670.3813-0.03360.4699-48.6472-53.666229.4464
420.77150.7535-0.11260.7476-0.13720.4628-0.24440.819-0.6423-0.6675-0.03740.2680.30570.1190.00050.5748-0.03590.0420.6264-0.140.5783-48.4295-61.899615.3779
431.30540.9777-0.89482.0255-0.434.1439-0.04370.06690.01940.3938-0.05370.05010.29550.020700.4364-0.00460.00140.3976-0.010.481-47.0631-57.869330.031
442.1278-2.37240.6612.5514-0.70112.2783-0.3579-0.1426-0.39550.1921-0.06620.90520.7436-0.2001-0.00030.6109-0.12880.14030.4884-0.06720.6194-52.7048-64.372129.519
450.6427-0.39690.43881.7423-0.80211.26810.0178-0.02520.09150.1677-0.1422-0.1533-0.49850.601900.5118-0.1389-0.03470.52570.01120.4279-41.67442.2357-25.9485
460.8202-0.27480.95011.32580.49581.5663-0.3545-0.32540.45010.4302-0.1021-0.455-0.81410.5576-0.00910.7992-0.2254-0.11550.66340.06130.6254-39.320751.6342-18.9655
473.1213-1.32111.73452.6517-0.29432.1016-0.4639-0.25410.9423-0.05490.1334-0.0294-0.8054-0.25700.6638-0.0001-0.08240.6104-0.090.5941-51.694455.0045-21.3599
480.4191-0.29430.29130.2946-0.31250.2106-0.16820.1746-0.0097-0.6576-0.14720.1755-0.2777-0.3737-0.00010.7336-0.111-0.070.5125-0.01180.5232-48.639749.0289-37.5207
490.2007-0.39130.27550.3872-0.22280.4579-0.36020.50250.1556-0.70090.6466-0.40260.07740.6503-0.01060.6771-0.16880.14590.6485-0.20470.7509-42.926526.7881-41.0103
501.28110.49250.63270.69990.68961.5511-0.0981-0.1685-0.18950.40420.4804-0.62950.69491.01890.00130.73540.1013-0.04910.6652-0.06560.6763-42.572614.374-20.2643
510.3781-0.0924-0.44090.27820.00130.41270.1657-0.47190.10131.0067-0.62390.57690.4667-0.7487-00.8033-0.11710.08710.7912-0.03760.7553-41.631357.6926-42.3901
521.18140.4729-0.35760.8944-0.60190.32420.07940.96390.2798-1.04620.30060.4871-0.2933-0.6980.00020.9359-0.1153-0.04160.6707-0.05470.6656-53.625325.3275-42.8665
532.2278-0.2684-0.38144.3601-0.08942.46560.01790.2689-0.0343-0.55110.1234-0.0657-0.02250.237900.4986-0.02990.02880.4951-0.0420.5331-48.671322.5549-32.7808
541.5449-0.66871.18082.40451.12263.5254-0.1422-0.11030.0840.12140.21990.1230.52010.1698-00.4646-0.0022-0.0280.4998-0.04510.6192-49.821818.7007-26.5168
550.6328-0.33920.02020.949-0.49720.4820.03190.5518-0.8773-0.26180.01131.46870.738-0.1693-0.0020.6795-0.1288-0.08310.5138-0.0730.9428-58.882511.7808-34.1317
568.08061.5798-8.37980.3266-1.73199.32081.1144-1.3462-0.01440.88880.2005-0.6108-1.26890.39630.68170.6960.1629-0.24160.85090.31580.8951-51.146410.200920.8076
571.56490.7354-0.35631.21320.05451.4276-0.1826-0.01790.1157-0.02380.06890.0827-0.2540.0204-0.00010.49650.0837-0.01890.26840.03450.408-54.775417.42015.7613
580.70030.4604-0.54322.36010.56981.193-0.24550.3629-0.1324-0.34730.32510.33280.2114-0.2881-0.00010.5689-0.0058-0.02930.44420.03830.529-62.378310.3441-1.5946
592.7536-0.71250.00053.0447-0.5273.0450.01150.0993-0.0317-0.15090.20521.4776-0.3144-0.7161-0.00220.52390.0969-0.06770.54270.08280.7458-70.310116.92862.7904
600.63350.9183-0.10330.9128-0.16731.9217-0.0523-0.95250.65680.5769-0.21260.3983-0.4143-0.1486-0.00620.69490.10610.01650.50960.04520.4737-57.808521.35419.469
610.12870.48840.04672.0818-0.05311.803-0.1526-0.3898-0.28990.02920.0625-0.59990.26251.27900.73260.0225-0.03141.00660.06910.7798-32.827634.1161.5524
621.4337-0.4443-0.80110.8321-0.51661.2664-0.5235-0.0708-0.1563-0.85260.18770.4358-0.665-0.09370.00020.95260.06470.05790.58590.08150.5895-63.715410.868924.5954
633.60971.16080.57552.452-1.67872.92310.1272-0.25140.42560.545-0.14580.1960.24850.082-0.00020.62390.0647-0.0330.3991-0.04360.5236-44.405736.456115.1638
640.6368-0.9208-0.17841.76450.71122.228-0.0625-0.00660.26040.45250.16470.18690.16090.26850.00010.5480.084-0.02810.44380.05040.4835-43.099735.3414.2142
652.41270.5829-0.81211.63191.94113.326-0.148-0.00210.1366-0.3481-0.02890.37690.38640.533700.56670.0827-0.04670.46640.0370.5082-40.984836.85587.076
660.56080.176-0.38740.92520.00680.8349-0.64870.41441.78820.732-0.01830.6054-0.79190.38170.00040.7633-0.0255-0.06950.52550.06860.9974-41.72349.171514.3859
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 61 )A6 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 130 )A62 - 130
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 144 )A131 - 144
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 185 )A145 - 185
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 203 )A186 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 211 )A204 - 211
7X-RAY DIFFRACTION7chain 'B' and (resid 2907 through 2922 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 2923 through 2966 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 2967 through 2992 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 2993 through 3025 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 3026 through 3044 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 7 through 10 )C7 - 10
13X-RAY DIFFRACTION13chain 'C' and (resid 11 through 58 )C11 - 58
14X-RAY DIFFRACTION14chain 'C' and (resid 59 through 131 )C59 - 131
15X-RAY DIFFRACTION15chain 'C' and (resid 132 through 144 )C132 - 144
16X-RAY DIFFRACTION16chain 'C' and (resid 145 through 185 )C145 - 185
17X-RAY DIFFRACTION17chain 'C' and (resid 186 through 211 )C186 - 211
18X-RAY DIFFRACTION18chain 'D' and (resid 2907 through 2921 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 2922 through 2960 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 2961 through 2992 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 2993 through 3015 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 3016 through 3044 )D0
23X-RAY DIFFRACTION23chain 'E' and (resid 6 through 9 )E6 - 9
24X-RAY DIFFRACTION24chain 'E' and (resid 10 through 69 )E10 - 69
25X-RAY DIFFRACTION25chain 'E' and (resid 70 through 156 )E70 - 156
26X-RAY DIFFRACTION26chain 'E' and (resid 157 through 188 )E157 - 188
27X-RAY DIFFRACTION27chain 'E' and (resid 189 through 199 )E189 - 199
28X-RAY DIFFRACTION28chain 'E' and (resid 200 through 211 )E200 - 211
29X-RAY DIFFRACTION29chain 'F' and (resid 2907 through 2934 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 2935 through 2954 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 2955 through 3001 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 3002 through 3025 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 3026 through 3044 )F0
34X-RAY DIFFRACTION34chain 'G' and (resid 7 through 10 )G7 - 10
35X-RAY DIFFRACTION35chain 'G' and (resid 11 through 58 )G11 - 58
36X-RAY DIFFRACTION36chain 'G' and (resid 59 through 131 )G59 - 131
37X-RAY DIFFRACTION37chain 'G' and (resid 132 through 144 )G132 - 144
38X-RAY DIFFRACTION38chain 'G' and (resid 145 through 186 )G145 - 186
39X-RAY DIFFRACTION39chain 'G' and (resid 187 through 211 )G187 - 211
40X-RAY DIFFRACTION40chain 'H' and (resid 2907 through 2921 )H0
41X-RAY DIFFRACTION41chain 'H' and (resid 2922 through 2957 )H0
42X-RAY DIFFRACTION42chain 'H' and (resid 2958 through 2968 )H0
43X-RAY DIFFRACTION43chain 'H' and (resid 2969 through 3014 )H0
44X-RAY DIFFRACTION44chain 'H' and (resid 3015 through 3044 )H0
45X-RAY DIFFRACTION45chain 'I' and (resid 8 through 62 )I8 - 62
46X-RAY DIFFRACTION46chain 'I' and (resid 63 through 94 )I63 - 94
47X-RAY DIFFRACTION47chain 'I' and (resid 95 through 156 )I95 - 156
48X-RAY DIFFRACTION48chain 'I' and (resid 157 through 175 )I157 - 175
49X-RAY DIFFRACTION49chain 'I' and (resid 176 through 187 )I176 - 187
50X-RAY DIFFRACTION50chain 'I' and (resid 188 through 211 )I188 - 211
51X-RAY DIFFRACTION51chain 'J' and (resid 2907 through 2921 )J0
52X-RAY DIFFRACTION52chain 'J' and (resid 2922 through 2939 )J0
53X-RAY DIFFRACTION53chain 'J' and (resid 2940 through 2991 )J0
54X-RAY DIFFRACTION54chain 'J' and (resid 2992 through 3025 )J0
55X-RAY DIFFRACTION55chain 'J' and (resid 3026 through 3044 )J0
56X-RAY DIFFRACTION56chain 'K' and (resid 7 through 10 )K7 - 10
57X-RAY DIFFRACTION57chain 'K' and (resid 11 through 63 )K11 - 63
58X-RAY DIFFRACTION58chain 'K' and (resid 64 through 99 )K64 - 99
59X-RAY DIFFRACTION59chain 'K' and (resid 100 through 156 )K100 - 156
60X-RAY DIFFRACTION60chain 'K' and (resid 157 through 186 )K157 - 186
61X-RAY DIFFRACTION61chain 'K' and (resid 187 through 211 )K187 - 211
62X-RAY DIFFRACTION62chain 'L' and (resid 2907 through 2924 )L0
63X-RAY DIFFRACTION63chain 'L' and (resid 2925 through 2973 )L0
64X-RAY DIFFRACTION64chain 'L' and (resid 2974 through 2994 )L0
65X-RAY DIFFRACTION65chain 'L' and (resid 2995 through 3024 )L0
66X-RAY DIFFRACTION66chain 'L' and (resid 3025 through 3044 )L0

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万見について

-
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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