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- PDB-7nqa: Crystal structure of Nucleoporin-98 nanobody MS98-6 complex solve... -

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基本情報

登録情報
データベース: PDB / ID: 7nqa
タイトルCrystal structure of Nucleoporin-98 nanobody MS98-6 complex solved at 2.2A resolution
要素
  • Anti-Nup98 Nanobody MS98-6
  • Nuclear pore complex protein Nup98-Nup96
キーワードNUCLEAR PROTEIN / Nup98 / Nanobody / complex
機能・相同性
機能・相同性情報


structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport / nuclear membrane
類似検索 - 分子機能
Nucleoporin FG repeat / Nucleoporin FG repeat region / 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
類似検索 - 構成要素
生物種Xenopus tropicalis (ネッタイツメガエル)
Vicugna pacos (アルパカ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者Sola-Colom, M. / Trakhanov, S. / Goerlich, D.
引用ジャーナル: EMBO J / 年: 2024
タイトル: A checkpoint function for Nup98 in nuclear pore formation suggested by novel inhibitory nanobodies.
著者: Mireia Solà Colom / Zhenglin Fu / Philip Gunkel / Thomas Güttler / Sergei Trakhanov / Vasundara Srinivasan / Kathrin Gregor / Tino Pleiner / Dirk Görlich /
要旨: Nuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from ...Nuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from frog to human. We also report a simplified assay that directly tracks postmitotic NPC assembly with added fluorophore-labeled anti-Nup nanobodies. During interphase, NPCs are inserted into a pre-existing nuclear envelope. Monitoring this process is challenging because newly assembled NPCs are indistinguishable from pre-existing ones. We overcame this problem by inserting Xenopus-derived NPCs into human nuclear envelopes and using frog-specific anti-Nup nanobodies for detection. We further asked whether anti-Nup nanobodies could serve as NPC assembly inhibitors. Using a selection strategy against conserved epitopes, we obtained anti-Nup93, Nup98, and Nup155 nanobodies that block Nup-Nup interfaces and arrest NPC assembly. We solved structures of nanobody-target complexes and identified roles for the Nup93 α-solenoid domain in recruiting Nup358 and the Nup214·88·62 complex, as well as for Nup155 and the Nup98 autoproteolytic domain in NPC scaffold assembly. The latter suggests a checkpoint linking pore formation to the assembly of the Nup98-dominated permeability barrier.
履歴
登録2021年3月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年7月21日Provider: repository / タイプ: Initial release
改定 1.12022年9月28日Group: Database references / Structure summary / カテゴリ: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
改定 1.22023年8月2日Group: Database references / Source and taxonomy / Structure summary
カテゴリ: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024年4月3日Group: Database references / Structure summary
カテゴリ: entity / entity_name_com ...entity / entity_name_com / pdbx_database_related / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_database_related.content_type ..._entity.pdbx_description / _pdbx_database_related.content_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
改定 1.52024年5月22日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: Nuclear pore complex protein Nup98-Nup96
D: Anti-Nup98 Nanobody MS98-6
B: Nuclear pore complex protein Nup98-Nup96
C: Anti-Nup98 Nanobody MS98-6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,6848
ポリマ－61,4934
非ポリマー1914
水5,837324
1
A: Nuclear pore complex protein Nup98-Nup96
D: Anti-Nup98 Nanobody MS98-6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)30,8924
ポリマ－30,7462
非ポリマー1452
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-16 kcal/mol
Surface area13500 Å2
手法PISA
2
B: Nuclear pore complex protein Nup98-Nup96
C: Anti-Nup98 Nanobody MS98-6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)30,7924
ポリマ－30,7462
非ポリマー462
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-31 kcal/mol
Surface area13410 Å2
手法PISA
単位格子
Length a, b, c (Å)83.760, 96.630, 100.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

#1: タンパク質 Nuclear pore complex protein Nup98-Nup96


分子量: 17275.402 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Xenopus tropicalis (ネッタイツメガエル)
遺伝子: nup98 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): NEB Express / 参照: UniProt: A0A6I8SCP2
#2: 抗体 Anti-Nup98 Nanobody MS98-6


分子量: 13471.062 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): NEB Express
#3: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H12NO3 / タイプ: SUBJECT OF INVESTIGATION / コメント: pH緩衝剤*YM
#4: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Na / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 324 / 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Y

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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: 3.32 Å3/Da / 溶媒含有率: 58 % / 解説: Rods
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 9
詳細: 2.5% (w/v) PEG 6000, 25% (v/v) PEG MME 500, 0.1 M Tris-HCl pH 9.0

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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: SLS / ビームライン: X10SA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年11月12日 / 詳細: Dynamically bendable mirrow
放射モノクロメーター: Si(111) / 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→48.3 Å / Num. obs: 49105 / % possible obs: 87.7 % / 冗長度: 13.2 % / Biso Wilson estimate: 39.94 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.9
反射 シェル解像度: 2→2.05 Å / 冗長度: 4.98 % / Num. unique obs: 1808 / CC1/2: 0.32 / % possible all: 44

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
PHENIX1.16_3549精密化
XDSデータ削減
XSCALEデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5E0Q

5e0q


解像度: 2.2→29.69 Å / SU ML: 0.2527 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 25.2197
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
詳細: We processed data at 2A resolution but used 30-2.2A shell for refinement
Rfactor反射数%反射
Rfree0.226 2066 5 %
Rwork0.1764 39262 -
obs0.1789 41328 97.93 %
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 mean: 56.2 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→29.69 Å
タンパク質核酸リガンド溶媒全体
原子数4322 0 11 324 4657
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00674413
X-RAY DIFFRACTIONf_angle_d0.8065975
X-RAY DIFFRACTIONf_chiral_restr0.0537652
X-RAY DIFFRACTIONf_plane_restr0.0046780
X-RAY DIFFRACTIONf_dihedral_angle_d3.2712637
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.31431240.29182348X-RAY DIFFRACTION89.24
2.25-2.310.27541340.25862538X-RAY DIFFRACTION97.48
2.31-2.370.29941370.24982602X-RAY DIFFRACTION97.82
2.37-2.440.27321320.24222550X-RAY DIFFRACTION97.74
2.44-2.520.33171370.23412609X-RAY DIFFRACTION97.76
2.52-2.610.32141380.21642611X-RAY DIFFRACTION98.39
2.61-2.710.25841360.21912588X-RAY DIFFRACTION98.13
2.71-2.840.29221380.20152615X-RAY DIFFRACTION98.64
2.84-2.990.23621380.2092628X-RAY DIFFRACTION98.47
2.99-3.170.26031380.20322618X-RAY DIFFRACTION98.82
3.17-3.420.231400.19052652X-RAY DIFFRACTION99.11
3.42-3.760.18981400.16542668X-RAY DIFFRACTION98.98
3.76-4.30.20021410.14342676X-RAY DIFFRACTION99.23
4.3-5.420.18521430.12732722X-RAY DIFFRACTION99.44
5.42-29.690.19071500.14472837X-RAY DIFFRACTION99.53
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)
14.510166832252.645246283890.7841446186313.256867053692.766064254014.25168751801-0.07026846282550.695050301946-0.695758688863-0.3827675686180.259637711531-1.140118149980.04244236550312.13724291885-0.2581814199720.3685077016150.004300519487370.1075080073060.9228434278990.08072716336490.6350115800342.295504183365.93364359594-10.9262525105
23.521421893930.4229583768430.5657021777064.538717417550.02430705236140.3289041548110.02687126503030.1634742846630.3130391206610.244380568032-0.0527117896897-0.87444072088-0.3694310255641.448563941620.01207919196120.431699754041-0.2458514415160.006341116585580.9185199599250.05045771737680.5093966393721.7792339758115.3606182588-8.19697928641
33.521001398551.059735973173.660556681654.845469850810.4172876677234.311177810280.05540621396780.16095470028-0.258549489780.0686907443015-0.170765652134-0.189600049241-0.07149580395790.7651715403070.1053134930660.281216168591-0.1029940454720.0784067482460.5632128848420.0181234941710.344424427544-6.8806237275510.8609659941-10.0832994413
46.815102481210.9196703091624.94669723897.035262676445.354157706468.00099588430.480714260443-0.277541271571-0.7987762688860.827868460693-0.05620878406770.09360094964310.7990923007590.361021197607-0.4279704787740.23918640699-0.01152628858760.03572789042420.3749510588810.007145617645040.408843247131-15.08674309273.94187487645-9.7477661755
53.565942494660.4626683813732.886540060763.093626203111.323152924783.03062774294-0.0657140870057-0.05364414146050.03393973577120.08651978725370.0482250351824-0.0905988395732-0.4390360458380.4395591094870.1041755827010.26930677186-0.1110860038880.07178998586850.404183170277-0.04048327199250.314033607825-14.724710635513.0054908005-11.1762672088
62.584973250473.434804366072.414827249389.413271869524.233288103212.80648890987-0.01914401191110.983066126155-0.149623430426-0.8768239785090.0133102257832-0.48414159446-0.1629387738160.434298475574-0.1278711046370.5014092829260.0107062300014-0.03349563280760.455783875932-0.08415571168070.39787265352-24.7880536625.5754082496-34.0612014358
73.8471629195-5.53236396927-1.276438295357.968573500621.806120243371.461023297750.467538139150.9416967505510.221048534636-2.15420791422-0.1109074459751.05215873696-1.74679932337-0.690327338529-0.411152553561.063694206330.0544822451677-0.1979940235950.5011670390720.08520094583590.595942721434-29.137886412316.2533603466-33.1914699425
87.09016862676-1.655931293775.248010074746.52752766951-4.268107070475.48643868717-0.224494193716-0.225351697320.3063550262830.235862102119-0.06391396035990.537490387984-0.956201675143-0.9248349123110.1806088455320.3604747947940.0352444269437-0.04373630118190.292754805889-0.06834175210230.31844518215-28.418963150314.8841938288-18.865653822
94.03776852019-1.325741075561.109006870386.29123592063.487363838382.838086252470.2657611795420.4802981108310.829440904513-1.188816635590.103042025556-0.0535986229544-1.457128823240.425039707493-0.2388983445910.594831143962-0.1087788607460.07118840530050.2946296313710.01290637916770.455437634651-20.991397534819.9351361534-22.1028099355
106.00753047067-0.2483337810313.894368673244.119676951464.313784734318.396714117110.110463670302-0.458139119960.3654041945-0.0703775366393-0.1113237485950.122844925871-1.077263851930.3418936452290.05281883660650.274710584985-0.1192943988990.07629232402660.328609648758-0.04891986654580.317652042961-18.820597001115.8501668211-12.1055017526
114.149677420994.366311902024.276622904696.747363614712.74992810685.84486848410.5903776800940.138291238993-1.405362684960.281814713102-0.0579160467784-0.3137497067031.03088949244-0.117542847027-0.734748629260.632505685527-0.0748048537257-0.06096631801160.562826984072-0.04097721229150.49356434391-33.5388618167-8.85522776888-23.084006386
128.267989267550.6963501770686.930282844444.651615471570.3789282345817.055439148360.3305023163580.216698098805-0.767128493831-0.5036566397330.03117587504521.233563384330.568962075332-0.893930572162-0.2200414947010.73532131075-0.295581662824-0.2332982320041.32080529373-0.1617623315920.900841344352-55.271962641-9.30651802189-35.2128835013
136.999206963682.35639238354.396003688634.483540481561.571740054544.23045252350.276038993406-0.23525786725-0.3983165111680.0210105853888-0.1610836570870.3205225972310.580649995601-0.724343649043-0.08936352037120.278356619373-0.0680540649253-0.005690006759540.466849276987-0.103060186760.339243777931-37.027105075-2.25356658896-21.3167901932
142.29563669061.342440526410.08896060536697.056261142786.392058443327.92538335148-0.1248510428210.616679268519-0.0316965750039-0.4310232832960.574283847503-0.1182312415830.3872319705150.774431540544-0.5159068625050.483424645275-0.100525585717-0.07602835744670.678790812037-0.168805868760.460596405363-39.4659363403-2.72703952025-38.6196010296
156.807053030791.071436147583.490296468034.141536580260.8147839617965.4854393515-0.2780903341190.5159590790320.405690090705-0.7875873270590.09232820937730.577060576287-0.605001082416-0.7451088825350.3915069642220.4153530394260.0876660795301-0.1213378397240.620045565085-0.1194053706430.43824096261-40.86127725237.85947145559-30.1685038216
165.209430468771.450529297663.81140953632.355536357070.7981283855013.572489572320.004534164872830.2443899860010.16817452315-0.631888152930.0452103806210.956714287483-0.246141980381-1.159899388610.1924323556830.3956382655950.0393901943255-0.211008886091.00615790265-0.1830371634950.629471247689-48.13984401534.33050186502-31.3256445968
175.332675794021.67208824982.517172466863.980744391380.3887434759541.233918507690.140029223304-0.589307787256-0.6802684081930.0176439857592-0.2332181950220.5086122602030.240168239089-1.42386338919-0.2962417878280.329818559595-0.134798393706-0.00417584032890.834167377099-0.1917258798830.571699971221-44.3891603687-1.43688799209-22.0820662729
187.521398978171.274379981433.269316756763.34233967186-0.3805289248181.876606967720.1610844633130.165416440492-0.312346513381-0.604905519193-0.2129047696380.6335403854460.330977889065-1.17555838220.0224936388710.508587093254-0.0718395197593-0.1100339741560.741354808202-0.1838960456140.477185728994-43.6604443327-2.8143000366-34.2384955099
198.59506809997-0.2789377190965.590846058327.19343331666-0.8395554898613.692929852060.3402254543960.0647793209651-0.329917532094-0.296062081026-0.122547328969-0.04753016458210.2700197106150.2835131707650.0146909107620.238846738406-0.03992393700810.03785903409710.273604276145-0.04171719835830.297681139159-22.74769528514.90195888968-17.3815959422
205.569267066995.282673240031.307094075728.796257683557.063485207429.37002614105-0.2751993190350.0104436414839-1.11080646757-0.5506317898310.245819274375-0.2171271006180.805580451241-0.258661446347-0.1850517725460.5851660115580.0490065311926-0.009516891903050.358720304947-0.09956319272620.512667837389-30.1872809027-3.66499146723-28.478926273
217.500647050830.3214824233690.8206561053938.215469072320.22059836185.860879350940.5085633238670.795445664026-1.1213917857-1.14388297325-0.08865722995220.9814599857320.590865515297-0.768197270795-0.4799364375880.854756936881-0.399734707317-0.2290254205720.982049912427-0.2959187134120.790735339403-49.8678547864-11.1670011972-38.7608061492
225.45987425326-2.11558277455-2.962669397746.663260369591.078534145011.749548507810.2313205972010.647400689238-0.00120973604229-0.167259478550.0538058597452-1.029577395460.5575327961810.887545082986-0.3727239107740.64619297840.630499870037-0.1358951598021.59265409127-0.1321520264060.608480809347-1.1570126292-14.4006985969-14.3826744706
233.830739903330.280135179741-1.637823561721.774640908821.170557754443.36559360584-0.1404699067880.250120558648-0.6346574100980.02058808428130.308551929302-0.9614973299850.3162191267370.627969147152-0.06519292282561.263593397130.8402410093980.04794329670611.33463896715-0.1614206467920.747427357108-3.55551290667-22.6872469375-12.127108771
241.21118725323-0.384688688034-0.9474260645692.89989664681.632150546852.93484443435-0.06171866830980.540202618131-0.559217849436-0.207053957631-0.0619191143515-0.2105920833470.9707436688460.7654356361190.1364808934041.351228410061.009767989680.1721655749030.883329971197-0.394464694920.34198714854-9.10256162228-21.2798388079-17.9283665035
253.83616738641-0.05646098096621.971622242984.39617806576-0.09268674669882.34720520721-0.2936560685740.2468379586370.110737201460.2232410276110.0491918936941-0.297935161780.7791948654711.592058648940.2660960022160.5166912163660.279082262750.01468143789690.629265897470.004186911326820.447509748877-14.3389343349-9.0312522864-10.701233717
266.457755009093.244920504744.835420307436.880223983437.055461113997.75502020089-0.3343184387141.315977678220.435792716938-1.866562616650.3006888371890.249319067258-0.6674264089920.216348032428-0.0007104857322410.9913175474620.223707825574-0.07613885658281.084998240920.02331620729810.448123896917-16.8120385732-7.2240689513-24.5546603074
272.55219489493-1.30777096565-1.766530144872.327082299962.619462005883.43768689856-0.1525129738970.289473004295-0.3453499407140.1113365620220.1613545468170.03319123840461.194037374690.720613716204-0.009747218705910.7655481010330.2150769978770.02733629466570.457390171178-0.06121496740510.395426781951-21.6924592694-12.5668503818-6.16067535958
283.555931508614.60045164811.548823103726.344559236970.2979503668238.522595142070.188368965468-0.736659478095-0.1572629724850.68349283287-0.4385593431980.8158521434381.89556034437-0.4465822505470.1684113811590.859639131988-0.03245732395220.1496727012940.4326956760970.003689541403950.638296553446-30.1460394948-10.524368618.82123237875
294.58453896589-0.37939780033-4.888914096617.449654421351.676692833796.32521692186-0.325215479040.519176432569-0.8267695608880.42840521589-0.6042002113150.7747097973360.162923414932-0.9002915787370.661115474790.630746458858-0.0680103812510.02207466093230.33343304054-0.1280087017580.5498476476-33.110464591-11.9843969935-5.73235733056
301.868294621480.2717104384860.941866041872.905434893261.748805221591.49672972138-0.247161709116-0.193760867384-0.4599656816330.9821335102540.2399972449050.3219637866750.4188479123750.0067487319772-0.02926342615851.16596097282-0.007429239936880.03686144187620.312070713815-0.02370555643510.621039559824-27.6383339702-19.1815457955-2.66239798464
315.15040651115-0.224211837782-0.8543155911774.03892629429-2.119665514916.020599958230.2139115554110.736413167056-0.432912224873-0.01144816717640.04866530086090.006775152531041.764226882890.0230020352211-0.1981129603520.8717164734960.178834763018-0.01641755820.400749515796-0.07181825234710.454475962137-24.5647084965-16.3473493655-12.6157508838
321.91269546615-2.92832907721-1.398252801597.682684851513.326237417675.344505348590.09346745396720.04725740834680.625749155122-0.006036222448480.243641102716-0.114183200309-0.537694893566-0.447669871675-0.3400839259670.2539661634550.0579245968057-0.01008851777650.3056962548840.02178920360520.238941461559-39.103862381716.27834591664.24185905546
330.492197169091-1.47540503223-1.395554169356.517338972033.231822665166.123942321330.1229609439190.223958801258-0.211891421191-0.290066200961-0.1088776791930.191090930923-0.251979612547-0.579815287599-0.01609199574810.1893673925030.0121056287673-0.0200144398540.308310855902-0.009899961995570.256174561483-35.14702466446.96529220031-3.42868916889
345.370359279771.199795291971.507319369453.936231654464.66423607196.239836323340.05700789853-0.698200163904-0.1290860276251.352135828080.28836179427-0.6387385134520.5380167082630.0721021259938-0.3641122756470.5664241624010.138021582287-0.01724094726510.383859781456-0.02419607898460.386715398819-36.86868801518.8767860222713.7930802907
359.41854964577-1.9317012943-1.702318993524.891122332462.767310779048.50441084906-0.33776508310.156331281999-0.8668308634940.747775854642-0.0895638883490.6609519852211.38904800074-1.225258039110.4600215586160.365848982829-0.1089207120470.1058643998310.3687286652180.007582126502580.385822894011-41.9625522854-0.8414684339075.80784342474
363.42653921121-1.71991136446-3.368222311024.997203573842.231164632933.45342166386-0.1013584476070.0571880840361-0.1553481488570.34545188322-0.07202478580930.8805948993450.283194012237-1.172674399170.09496936018390.248242922259-0.01794799846250.03535476036270.560538610284-0.03252056721210.473454119771-45.22036753126.714761831762.72471321551
372.61242289096-2.49509103662-0.7968383549874.331917987831.688057423882.99663720475-0.189733646422-0.233314598545-0.01801248255290.3783491196880.1734253794420.2157523366350.0481740052527-0.442551375430.03105862708970.2152797503460.02732275806140.01785132191090.2804087637050.003443953386580.296702467412-35.96459203825.939423352174.4342973372
387.29934261007-4.42743034618-5.700634083573.873984200675.810730410869.18532972764-0.178478815907-0.4482087977860.3736401441360.3229346800170.3183477211990.0220552871038-0.570049092128-0.12364542148-0.3227041778840.407582948720.0910917273078-0.01822940461160.320261305450.03700265281150.356953338298-34.763278036312.30316160368.05350114033
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 715 through 726 )
2X-RAY DIFFRACTION2chain 'A' and (resid 727 through 755 )
3X-RAY DIFFRACTION3chain 'A' and (resid 756 through 781 )
4X-RAY DIFFRACTION4chain 'A' and (resid 782 through 793 )
5X-RAY DIFFRACTION5chain 'A' and (resid 794 through 814 )
6X-RAY DIFFRACTION6chain 'A' and (resid 815 through 825 )
7X-RAY DIFFRACTION7chain 'A' and (resid 826 through 833 )
8X-RAY DIFFRACTION8chain 'A' and (resid 834 through 845 )
9X-RAY DIFFRACTION9chain 'A' and (resid 846 through 857 )
10X-RAY DIFFRACTION10chain 'A' and (resid 858 through 866 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 8 )
12X-RAY DIFFRACTION12chain 'D' and (resid 9 through 18 )
13X-RAY DIFFRACTION13chain 'D' and (resid 19 through 34 )
14X-RAY DIFFRACTION14chain 'D' and (resid 35 through 46 )
15X-RAY DIFFRACTION15chain 'D' and (resid 47 through 60 )
16X-RAY DIFFRACTION16chain 'D' and (resid 61 through 73 )
17X-RAY DIFFRACTION17chain 'D' and (resid 74 through 83 )
18X-RAY DIFFRACTION18chain 'D' and (resid 84 through 101 )
19X-RAY DIFFRACTION19chain 'D' and (resid 102 through 109 )
20X-RAY DIFFRACTION20chain 'D' and (resid 110 through 117 )
21X-RAY DIFFRACTION21chain 'D' and (resid 118 through 124 )
22X-RAY DIFFRACTION22chain 'B' and (resid 715 through 726 )
23X-RAY DIFFRACTION23chain 'B' and (resid 727 through 738 )
24X-RAY DIFFRACTION24chain 'B' and (resid 739 through 773 )
25X-RAY DIFFRACTION25chain 'B' and (resid 774 through 787 )
26X-RAY DIFFRACTION26chain 'B' and (resid 788 through 797 )
27X-RAY DIFFRACTION27chain 'B' and (resid 798 through 819 )
28X-RAY DIFFRACTION28chain 'B' and (resid 820 through 833 )
29X-RAY DIFFRACTION29chain 'B' and (resid 834 through 845 )
30X-RAY DIFFRACTION30chain 'B' and (resid 846 through 857 )
31X-RAY DIFFRACTION31chain 'B' and (resid 858 through 866 )
32X-RAY DIFFRACTION32chain 'C' and (resid 1 through 18 )
33X-RAY DIFFRACTION33chain 'C' and (resid 19 through 34 )
34X-RAY DIFFRACTION34chain 'C' and (resid 35 through 46 )
35X-RAY DIFFRACTION35chain 'C' and (resid 47 through 60 )
36X-RAY DIFFRACTION36chain 'C' and (resid 61 through 83 )
37X-RAY DIFFRACTION37chain 'C' and (resid 84 through 109 )
38X-RAY DIFFRACTION38chain 'C' and (resid 110 through 124 )

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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://pdbjlc1.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