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- PDB-7opo: RSK2 N-terminal kinase domain in complex with ORF45 -

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基本情報

登録情報
データベース: PDB / ID: 7opo
タイトルRSK2 N-terminal kinase domain in complex with ORF45
要素
  • Protein ORF45
  • Ribosomal protein S6 kinase alpha-3
キーワードVIRAL PROTEIN / ORF45 / RSK2 / RSK / RSK2 NTK / Viral modulation / MAPKAPK / Kaposi's sarcoma-associated herpesvirus / VF-motif
機能・相同性
機能・相同性情報


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / symbiont-mediated perturbation of host innate immune response / ribosomal protein S6 kinase activity / CREB phosphorylation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / viral tegument / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / symbiont-mediated perturbation of host innate immune response / ribosomal protein S6 kinase activity / CREB phosphorylation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / viral tegument / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / ERK/MAPK targets / Recycling pathway of L1 / central nervous system development / skeletal system development / positive regulation of cell differentiation / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / response to lipopolysaccharide / host cell Golgi apparatus / chemical synaptic transmission / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / synapse / protein kinase binding / negative regulation of apoptotic process / nucleolus / host cell nucleus / magnesium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytosol / cytoplasm
類似検索 - 分子機能
Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein ORF45 / Ribosomal protein S6 kinase alpha-3
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Human herpesvirus 8 (ヘルペスウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.75 Å
データ登録者Sok, P. / Remenyi, A. / Alexa, A. / Poti, A.
資金援助 ハンガリー, European Union, 2件
組織認可番号国
National Research Development and Innovation Office (NKFIH)KKP 126963 ハンガリー
European Union (EU)iNEXT Project 4788European Union
引用ジャーナル: Nat Commun / 年: 2022
タイトル: A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host.
著者: Alexa, A. / Sok, P. / Gross, F. / Albert, K. / Kobori, E. / Poti, A.L. / Gogl, G. / Bento, I. / Kuang, E. / Taylor, S.S. / Zhu, F. / Ciliberto, A. / Remenyi, A.
履歴
登録2021年6月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年2月2日Provider: repository / タイプ: Initial release
改定 1.12022年2月9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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22022年10月12日Group: Data collection / カテゴリ: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
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

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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: Ribosomal protein S6 kinase alpha-3
B: Protein ORF45
C: Ribosomal protein S6 kinase alpha-3
D: Protein ORF45
E: Ribosomal protein S6 kinase alpha-3
F: Protein ORF45
G: Ribosomal protein S6 kinase alpha-3
H: Protein ORF45
I: Ribosomal protein S6 kinase alpha-3
J: Protein ORF45
K: Ribosomal protein S6 kinase alpha-3
L: Protein ORF45
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)261,22218
ポリマ－258,18412
非ポリマー3,0376
水84747
1
A: Ribosomal protein S6 kinase alpha-3
B: Protein ORF45
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,5373
ポリマ－43,0312
非ポリマー5061
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-26 kcal/mol
Surface area16830 Å2
手法PISA
2
C: Ribosomal protein S6 kinase alpha-3
D: Protein ORF45
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,5373
ポリマ－43,0312
非ポリマー5061
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-21 kcal/mol
Surface area15720 Å2
手法PISA
3
E: Ribosomal protein S6 kinase alpha-3
F: Protein ORF45
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,5373
ポリマ－43,0312
非ポリマー5061
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-24 kcal/mol
Surface area16120 Å2
手法PISA
4
G: Ribosomal protein S6 kinase alpha-3
H: Protein ORF45
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,5373
ポリマ－43,0312
非ポリマー5061
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-23 kcal/mol
Surface area16050 Å2
手法PISA
5
I: Ribosomal protein S6 kinase alpha-3
J: Protein ORF45
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,5373
ポリマ－43,0312
非ポリマー5061
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-23 kcal/mol
Surface area16270 Å2
手法PISA
6
K: Ribosomal protein S6 kinase alpha-3
L: Protein ORF45
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,5373
ポリマ－43,0312
非ポリマー5061
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-25 kcal/mol
Surface area15750 Å2
手法PISA
単位格子
Length a, b, c (Å)170.290, 88.621, 160.346
Angle α, β, γ (deg.)90.000, 95.423, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 46 through 53 or (resid 54...A46 - 110
121(chain 'A' and (resid 46 through 53 or (resid 54...A120 - 227
131(chain 'A' and (resid 46 through 53 or (resid 54...A231 - 346
141(chain 'A' and (resid 46 through 53 or (resid 54...A480
211(chain 'C' and (resid 46 through 53 or (resid 54...C46 - 110
221(chain 'C' and (resid 46 through 53 or (resid 54...C120 - 227
231(chain 'C' and (resid 46 through 53 or (resid 54...C231 - 346
241(chain 'C' and (resid 46 through 53 or (resid 54...C480
311(chain 'E' and (resid 46 through 53 or (resid 54...E46 - 110
321(chain 'E' and (resid 46 through 53 or (resid 54...E120 - 227
331(chain 'E' and (resid 46 through 53 or (resid 54...E231 - 346
341(chain 'E' and (resid 46 through 53 or (resid 54...E480
411(chain 'G' and (resid 46 through 53 or (resid 54...G46 - 110
421(chain 'G' and (resid 46 through 53 or (resid 54...G120 - 227
431(chain 'G' and (resid 46 through 53 or (resid 54...G231 - 346
441(chain 'G' and (resid 46 through 53 or (resid 54...G480
511(chain 'I' and (resid 46 through 56 or (resid 57...I46 - 110
521(chain 'I' and (resid 46 through 56 or (resid 57...I120 - 227
531(chain 'I' and (resid 46 through 56 or (resid 57...I231 - 346
541(chain 'I' and (resid 46 through 56 or (resid 57...I480
611(chain 'K' and (resid 46 through 53 or (resid 54...K46 - 110
621(chain 'K' and (resid 46 through 53 or (resid 54...K120 - 227
631(chain 'K' and (resid 46 through 53 or (resid 54...K231 - 346
641(chain 'K' and (resid 46 through 53 or (resid 54...K480
152(chain 'B' and ((resid 26 and (name N or name...B26 - 69
252(chain 'D' and (resid 26 through 46 or (resid 47...D26 - 69
352(chain 'F' and ((resid 26 and (name N or name...F26 - 69
452(chain 'H' and ((resid 26 and (name N or name...H26 - 69
552(chain 'J' and resid 26 through 69)J26 - 69
652(chain 'L' and (resid 26 through 46 or (resid 47...L26 - 69

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Ribosomal protein S6 kinase alpha-3 / S6K-alpha-3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / p90RSK3 / Insulin-stimulated ...S6K-alpha-3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / p90RSK3 / Insulin-stimulated protein kinase 1 / ISPK-1 / MAP kinase-activated protein kinase 1b / MAPK-activated protein kinase 1b / MAPKAP kinase 1b / MAPKAPK-1b / Ribosomal S6 kinase 2 / RSK-2 / pp90RSK2


分子量: 36338.086 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: RPS6KA3, ISPK1, MAPKAPK1B, RSK2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P51812, non-specific serine/threonine protein kinase
#2: タンパク質
Protein ORF45


分子量: 6692.656 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Human herpesvirus 8 (ヘルペスウイルス)
株: isolate GK18 / 遺伝子: ORF45 / Variant: type P / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: F5HDE4
#3: 化合物
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP


分子量: 506.196 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H17N6O12P3
コメント: AMP-PNP, エネルギー貯蔵分子類似体*YM
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 47 / 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: 2.58 Å3/Da / 溶媒含有率: 52.26 % / 解説: Single cubic formed crystals
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 12 %PEG 6000, HEPES pH 7.5, 0.75M NaCl in reservoir / Temp details: room temperature

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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: PETRA III, EMBL c/o DESY / ビームライン: P14 (MX2) / 波長: 0.9762 Å
検出器タイプ: DECTRIS EIGER X 16M / 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: 0.9762 Å / 相対比: 1
反射解像度: 2.75→47.65 Å / Num. obs: 61675 / % possible obs: 99.5 % / 冗長度: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.048 / Rrim(I) all: 0.13 / Net I/σ(I): 11.5 / Num. measured all: 437614 / Scaling rejects: 1
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
2.75-2.827.11.5983243745480.50.6421.7241.399.2
12.3-47.656.50.02847197260.9990.0120.0349.997.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3G51

3g51


解像度: 2.75→47.65 Å / SU ML: 0.3619 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.7032
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2322 1999 3.24 %Random selection
Rwork0.2087 59651 --
obs0.2094 61650 99.36 %-
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: 86.04 Å2
精密化ステップサイクル: LAST / 解像度: 2.75→47.65 Å
タンパク質核酸リガンド溶媒全体
原子数16225 0 186 47 16458
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004716829
X-RAY DIFFRACTIONf_angle_d0.899422768
X-RAY DIFFRACTIONf_chiral_restr0.05582490
X-RAY DIFFRACTIONf_plane_restr0.00832881
X-RAY DIFFRACTIONf_dihedral_angle_d20.58466281
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.331440.31764266X-RAY DIFFRACTION99.12
2.82-2.890.31471390.31594172X-RAY DIFFRACTION99.33
2.89-2.980.3781410.3344214X-RAY DIFFRACTION99.09
2.98-3.080.38491420.31334234X-RAY DIFFRACTION99
3.08-3.190.30421420.28454243X-RAY DIFFRACTION99.8
3.19-3.310.29041430.26884264X-RAY DIFFRACTION99.59
3.31-3.460.26221420.23974237X-RAY DIFFRACTION99.64
3.46-3.650.2421440.23414277X-RAY DIFFRACTION99.68
3.65-3.880.24281430.20534255X-RAY DIFFRACTION99.57
3.88-4.170.23881420.1834278X-RAY DIFFRACTION99.46
4.17-4.590.18921430.16424245X-RAY DIFFRACTION99.07
4.59-5.260.16011430.16644279X-RAY DIFFRACTION99.48
5.26-6.620.20711440.19224299X-RAY DIFFRACTION99.2
6.62-47.650.20811470.18184388X-RAY DIFFRACTION99.06
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)
18.11161854651.86003548631.099295016046.030328787442.808695664344.45310016812-0.1668877279231.11809734603-0.0139471681706-1.123532822880.275409061333-0.258183864053-0.1906384413120.588270494306-0.1634279547030.5947083875410.04300809919630.07212129878350.5640047880120.02815074907350.363762292874-22.597524295324.036124864125.5608969678
27.372856122341.14004132293-2.954264720081.970401706660.8217360322143.483212480440.137637639664-0.00547249032551-0.159101217996-0.182150097679-0.0992379351443-0.106695400977-0.003046185083040.232587936173-0.05510643159110.5444959760780.0800082734921-0.06686706637170.3809696106860.03068193268210.395840261662-32.277551669118.324475901532.1680662013
38.104345727762.062962529232.222803366550.4199466411480.485858237610.6583841609880.4081272567430.834793746143-1.92265531051-0.5563685957610.324326393165-0.4812611455280.2759105222770.911623836086-0.9085556572091.090246068540.223498166888-0.02700718152230.689301240573-0.2329413230021.03549418806-28.851223577-0.39794078984229.4652685147
44.51704339090.5999735637020.4473611320137.675573380030.09238539416335.798259701580.3400973337490.372473127748-0.499712702711-0.301953944939-0.2321474685990.2114886375360.494131579216-0.232224598084-0.08892555159090.4343518177170.0460160983268-0.1109267204170.458304499148-0.09271753089520.493694347772-45.49533106677.6798099720132.3652078235
54.109662511420.800005388348-5.013367880819.943995968763.968059691162.000795586850.213250382535-0.3680528029190.1678087093510.599637156353-2.410552005063.58927231541-1.16451521296-3.584813297572.295029863651.068332528490.07515234286130.2743634545621.48625786784-0.3737733869921.37946957616-56.091119529711.227966204347.1011987339
62.03806740946-2.20264865313-7.532559158567.000177831672.944782730457.643638365550.1041187348871.410514569030.8249919616860.648648133891-0.0195100180567-0.8182785671610.8071262358360.167166003211-0.113803089990.7263714221320.0659885818351-0.2298396792480.6977960234580.1215392181090.56641552236-36.501159009710.651736890347.2025409062
79.289820895025.22409202157-4.418252558462.00444774554-8.530419936217.04263352516-0.1020301954171.64472531545-2.23865674016-0.747487798111-0.268726801077-1.0463344041.67740597981-1.148323714230.3347047628551.30493711123-0.09745661786150.09168251139970.811911573382-0.2888902786891.24535828571-28.605894174-0.016162684539849.1991595528
87.91996470494-4.54402952424-4.711737291636.580065302423.972035389638.664932872130.0129950484643-0.272638318644-1.768105216580.7230429554880.4383609897260.7046913613461.87002598077-0.988139515729-0.1468644682720.948812275129-0.0884858373638-0.1752683732110.4214926835040.1099444188731.17603210485-46.8720961301-5.112342102340.1092974975
99.209606265870.9457858332810.6121485203024.08228765630.8862984878364.874855946490.0126923281743-1.23702348973-1.564405370510.724452310724-0.130454485291-0.7634645034061.28202377416-0.0200850017070.08456880118860.86558569511-0.0125849039184-0.08247719755110.5344652630450.1289341332180.828604128859-17.95848484981.190883241658.8263306913
105.853567533332.69172416990.5818673799984.208219148380.4109928837662.545106129440.115075145699-0.562053041593-0.9485024254320.436942819241-0.0538344400211-0.4308836647670.5770913114350.153080705006-0.04152684577940.4986926062860.1136027754560.01663423352320.471236921320.03783933405880.447777595355-13.563910360811.850566178660.2438037003
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593.90981973863-4.02744001355-4.77818200288.203782930966.785709668956.74911148770.6267522153870.242118039135-0.221394100216-0.8764415145290.444669680182-0.4806450007330.720846036325-0.887506254562-0.9559098781561.83771289535-0.583599311978-0.1001816707351.23835670972-0.01755159472020.785895122553-67.826432967346.04628688863.35450942992
604.062986862641.027128577662.638761257336.79842574123.742769189518.574199361840.637426100874-0.5829315655281.284906621341.19507007321-0.214030138208-0.99778859165-0.4868743187080.255346501646-0.1986262791681.13622219741-0.334608170923-0.2196518281030.869736886909-0.007368417270710.970770072066-67.351500044860.613594944518.1120610846
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 246 )
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 348 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 27 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 37 )
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 47 )
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 69 )
9X-RAY DIFFRACTION9chain 'C' and (resid 46 through 81 )
10X-RAY DIFFRACTION10chain 'C' and (resid 82 through 186 )
11X-RAY DIFFRACTION11chain 'C' and (resid 187 through 206 )
12X-RAY DIFFRACTION12chain 'C' and (resid 207 through 231 )
13X-RAY DIFFRACTION13chain 'C' and (resid 232 through 246 )
14X-RAY DIFFRACTION14chain 'C' and (resid 247 through 329 )
15X-RAY DIFFRACTION15chain 'C' and (resid 330 through 347 )
16X-RAY DIFFRACTION16chain 'D' and (resid 23 through 27 )
17X-RAY DIFFRACTION17chain 'D' and (resid 28 through 37 )
18X-RAY DIFFRACTION18chain 'D' and (resid 38 through 47 )
19X-RAY DIFFRACTION19chain 'D' and (resid 48 through 69 )
20X-RAY DIFFRACTION20chain 'E' and (resid 46 through 64 )
21X-RAY DIFFRACTION21chain 'E' and (resid 65 through 138 )
22X-RAY DIFFRACTION22chain 'E' and (resid 139 through 206 )
23X-RAY DIFFRACTION23chain 'E' and (resid 207 through 231 )
24X-RAY DIFFRACTION24chain 'E' and (resid 232 through 348 )
25X-RAY DIFFRACTION25chain 'F' and (resid 25 through 34 )
26X-RAY DIFFRACTION26chain 'F' and (resid 35 through 49 )
27X-RAY DIFFRACTION27chain 'F' and (resid 50 through 69 )
28X-RAY DIFFRACTION28chain 'G' and (resid 46 through 110 )
29X-RAY DIFFRACTION29chain 'G' and (resid 111 through 139 )
30X-RAY DIFFRACTION30chain 'G' and (resid 140 through 186 )
31X-RAY DIFFRACTION31chain 'G' and (resid 187 through 206 )
32X-RAY DIFFRACTION32chain 'G' and (resid 207 through 231 )
33X-RAY DIFFRACTION33chain 'G' and (resid 232 through 246 )
34X-RAY DIFFRACTION34chain 'G' and (resid 247 through 348 )
35X-RAY DIFFRACTION35chain 'H' and (resid 23 through 27 )
36X-RAY DIFFRACTION36chain 'H' and (resid 28 through 37 )
37X-RAY DIFFRACTION37chain 'H' and (resid 38 through 47 )
38X-RAY DIFFRACTION38chain 'H' and (resid 48 through 67 )
39X-RAY DIFFRACTION39chain 'H' and (resid 68 through 70 )
40X-RAY DIFFRACTION40chain 'I' and (resid 46 through 95 )
41X-RAY DIFFRACTION41chain 'I' and (resid 96 through 139 )
42X-RAY DIFFRACTION42chain 'I' and (resid 140 through 187 )
43X-RAY DIFFRACTION43chain 'I' and (resid 188 through 222 )
44X-RAY DIFFRACTION44chain 'I' and (resid 223 through 281 )
45X-RAY DIFFRACTION45chain 'I' and (resid 282 through 316 )
46X-RAY DIFFRACTION46chain 'I' and (resid 317 through 348 )
47X-RAY DIFFRACTION47chain 'J' and (resid 26 through 38 )
48X-RAY DIFFRACTION48chain 'J' and (resid 39 through 61 )
49X-RAY DIFFRACTION49chain 'J' and (resid 62 through 70 )
50X-RAY DIFFRACTION50chain 'K' and (resid 46 through 73 )
51X-RAY DIFFRACTION51chain 'K' and (resid 74 through 132 )
52X-RAY DIFFRACTION52chain 'K' and (resid 133 through 186 )
53X-RAY DIFFRACTION53chain 'K' and (resid 187 through 223 )
54X-RAY DIFFRACTION54chain 'K' and (resid 224 through 246 )
55X-RAY DIFFRACTION55chain 'K' and (resid 247 through 316 )
56X-RAY DIFFRACTION56chain 'K' and (resid 317 through 348 )
57X-RAY DIFFRACTION57chain 'L' and (resid 25 through 29 )
58X-RAY DIFFRACTION58chain 'L' and (resid 30 through 39 )
59X-RAY DIFFRACTION59chain 'L' and (resid 40 through 54 )
60X-RAY DIFFRACTION60chain 'L' and (resid 55 through 69 )

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る