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- PDB-6k99: Structure of ASC CARD filament -

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基本情報

登録情報
データベース: PDB / ID: 6k99
タイトルStructure of ASC CARD filament
要素Apoptosis-associated speck-like protein containing a CARD
キーワードSIGNALING PROTEIN / filament
機能・相同性
機能・相同性情報


Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / The AIM2 inflammasome / AIM2 inflammasome complex / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / icosanoid biosynthetic process ...Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / The AIM2 inflammasome / AIM2 inflammasome complex / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / icosanoid biosynthetic process / IkappaB kinase complex / NLRP1 inflammasome complex / canonical inflammasome complex / macropinocytosis / interleukin-6 receptor binding / NLRP3 inflammasome complex / NLRP3 inflammasome complex assembly / BMP receptor binding / positive regulation of adaptive immune response / osmosensory signaling pathway / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / negative regulation of protein serine/threonine kinase activity / negative regulation of interferon-beta production / CLEC7A/inflammasome pathway / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage cytokine production / positive regulation of actin filament polymerization / negative regulation of NF-kappaB transcription factor activity / tropomyosin binding / positive regulation of release of cytochrome c from mitochondria / pyroptotic inflammatory response / : / positive regulation of activated T cell proliferation / cysteine-type endopeptidase activator activity involved in apoptotic process / The NLRP3 inflammasome / positive regulation of interleukin-10 production / intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to interleukin-1 / negative regulation of cytokine production involved in inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of defense response to virus by host / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / activation of innate immune response / positive regulation of chemokine production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of DNA-binding transcription factor activity / regulation of protein stability / protein homooligomerization / : / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / SARS-CoV-1 activates/modulates innate immune responses / azurophil granule lumen / positive regulation of tumor necrosis factor production / positive regulation of T cell activation / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / protease binding / defense response to virus / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / transmembrane transporter binding / microtubule / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / defense response to Gram-positive bacterium / positive regulation of apoptotic process / Golgi membrane / innate immune response / neuronal cell body / Neutrophil degranulation / nucleolus / apoptotic process / enzyme binding / endoplasmic reticulum / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
CARD8/ASC/NALP1, CARD domain / : / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily
類似検索 - ドメイン・相同性
Apoptosis-associated speck-like protein containing a CARD
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 4.1 Å
データ登録者Gong, Q. / Xu, C. / Zhang, J. / Boo, Z.Z. / Wu, B.
資金援助 シンガポール, 1件
組織認可番号国
Ministry of Education (Singapore)tier2 and tier1 シンガポール
引用ジャーナル: Nat Commun / 年: 2021
タイトル: Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8.
著者: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / John ...著者: Qin Gong / Kim Robinson / Chenrui Xu / Phuong Thao Huynh / Kelvin Han Chung Chong / Eddie Yong Jun Tan / Jiawen Zhang / Zhao Zhi Boo / Daniel Eng Thiam Teo / Kenneth Lay / Yaming Zhang / John Soon Yew Lim / Wah Ing Goh / Graham Wright / Franklin L Zhong / Bruno Reversade / Bin Wu /
要旨: Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 ...Nod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIIND-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIIND-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIIND. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells-a process that is greatly enhanced by NLRP1-FIIND which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes.
履歴
登録2019年6月14日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年9月16日Provider: repository / タイプ: Initial release
改定 1.12021年3月24日Group: Database references / Structure summary / カテゴリ: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 1.22024年3月27日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • 単純化した表面モデル + あてはめた原子モデル
  • マップデータ: EMDB-9947
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-9947
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
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
G: Apoptosis-associated speck-like protein containing a CARD
A: Apoptosis-associated speck-like protein containing a CARD
B: Apoptosis-associated speck-like protein containing a CARD
C: Apoptosis-associated speck-like protein containing a CARD
D: Apoptosis-associated speck-like protein containing a CARD
E: Apoptosis-associated speck-like protein containing a CARD
F: Apoptosis-associated speck-like protein containing a CARD
H: Apoptosis-associated speck-like protein containing a CARD
I: Apoptosis-associated speck-like protein containing a CARD
J: Apoptosis-associated speck-like protein containing a CARD
K: Apoptosis-associated speck-like protein containing a CARD
L: Apoptosis-associated speck-like protein containing a CARD


分子量 (理論値)分子数
合計 (水以外)117,30212
ポリマ－117,30212
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: assay for oligomerization
タイプ名称対称操作数
identity operation1_5551

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要素

#1: タンパク質
Apoptosis-associated speck-like protein containing a CARD / hASC / Caspase recruitment domain-containing protein 5 / PYD and CARD domain-containing protein / ...hASC / Caspase recruitment domain-containing protein 5 / PYD and CARD domain-containing protein / Target of methylation-induced silencing 1


分子量: 9775.143 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PYCARD, ASC, CARD5, TMS1 / 発現宿主: Escherichia coli K-12 (大腸菌) / 株 (発現宿主): K-12 / 参照: UniProt: Q9ULZ3

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: FILAMENT / ３次元再構成法: らせん対称体再構成法

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試料調製

構成要素名称: ASC CARD filament / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
由来(天然)生物種: Homo sapiens (ヒト)
由来(組換発現)生物種: Escherichia coli (大腸菌) / 株: Bl21(DE3)
緩衝液pH: 8
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/2
急速凍結装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: DARK FIELD / 倍率（公称値）: 115000 X / Calibrated defocus min: 1500 nm / 最大 デフォーカス（補正後）: 2500 nm / Cs: 2.7 mm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 40 e/Å2
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
実像数: 3183

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解析

ソフトウェア名称: PHENIX / バージョン: (dev_2405: ???) / 分類: 精密化
EMソフトウェア
ID名称バージョンカテゴリ
1RELION2粒子像選択
2EPU2.3画像取得
4RELION2CTF補正
7Coot0.8.9.1 ELモデルフィッティング
9RELION2初期オイラー角割当
10RELION2最終オイラー角割当
11RELION2分類
12RELION2３次元再構成
13PHENIXdev 2405モデル精密化
CTF補正タイプ: NONE
らせん対称回転角度/サブユニット: -100.614 ° / 軸方向距離/サブユニット: 5.27 Å / らせん対称軸の対称性: C1
粒子像の選択選択した粒子像数: 877408
3次元再構成解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 59566 / 対称性のタイプ: HELICAL
原子モデル構築プロトコル: RIGID BODY FIT / 空間: REAL
精密化解像度: 4.1→62.582 Å / SU ML: 0.7 / σ(F): 0.09 / 位相誤差: 35.06 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射
Rfree0.2255 762 3.7 %
Rwork0.1871 --
obs0.1886 20584 99.55 %
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
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.0038436
ELECTRON MICROSCOPYf_angle_d0.69311448
ELECTRON MICROSCOPYf_dihedral_angle_d15.8335076
ELECTRON MICROSCOPYf_chiral_restr0.0431260
ELECTRON MICROSCOPYf_plane_restr0.0041452
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.41650.45461670.40633891ELECTRON MICROSCOPY100
4.4165-4.86080.3781150.3144026ELECTRON MICROSCOPY99
4.8608-5.56380.33421960.25173952ELECTRON MICROSCOPY100
5.5638-7.00830.3151320.24893965ELECTRON MICROSCOPY100
7.0083-62.5890.12271520.09953988ELECTRON MICROSCOPY100
精密化 TLS

手法: refined / Refine-ID: ELECTRON MICROSCOPY

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)
15.20742.66145.64153.43051.95536.3224-3.5806-1.4117-0.168-1.00370.73760.70220.1648-3.411-0.10954.8119-0.85050.46372.5658-0.06511.3898139.9298158.2209-119.5417
24.83095.035-3.05315.9159-3.23172.4152.18233.4444.5297-0.9404-1.79543.174-1.2682.6829-0.43492.33930.17370.0472.38250.0551.1772132.9456151.7167-126.212
35.66842.28315.26872.0034-1.4686.2886.44452.3004-1.5078-2.5792-3.8573-1.26167.8969-2.0664-1.99622.49450.3756-0.29353.0334-0.00591.4256143.8744144.2576-131.7535
45.71972.9321-4.04622.01914.48296.18220.2655-2.41234.69413.5553-1.2258-2.49965.58532.5579-1.48711.9982-1.3601-0.59510.99310.39081.6695150.831141.4915-124.8927
51.79741.26330.84964.63332.07733.30163.43022.05982.752.0464-3.7651-1.39063.5778-1.39130.53231.698-0.6797-0.33622.1747-0.35522.3577140.4141135.3606-125.5012
63.4118-0.8697-0.04864.20314.31324.446-1.20240.21582.30431.85781.4588-0.5348-1.9431-0.64880.21711.3724-0.179-0.01871.16-0.34081.2594137.2802144.0071-121.0068
77.1052-4.9074-3.92253.83792.42152.08861.28350.35912.0083-4.1729-1.37-3.6134-6.05042.7093-0.82863.3058-0.85010.24812.51580.22261.3817147.0819153.9942-125.066
81.96180.3419-1.88580.13611.01145.2153-1.3107-4.44066.8305-5.10684.49430.9729-7.8456-9.3758-3.9193.97161.34950.26713.16260.45112.7019135.8892160.2837-132.3286
95.65261.74546.79872.62512.378.1773-0.72871.08571.26520.66363.0731-0.77454.39320.8744-2.5012.03550.6011-0.23733.88680.21711.621699.6464132.7235-124.8042
101.9696-2.7529-0.46514.636-3.77344.9973-1.74893.8308-8.1631-3.9167-0.51121.3107-1.6712-1.5299-1.3022.26030.2443-0.11991.86380.14891.4406107.262127.2123-131.5372
114.09443.2390.12574.1551-2.35963.8987-0.88391.48383.5797-2.61742.0522-0.3509-1.1142-0.53650.38382.77680.20090.1051.7519-0.10231.6995112.6576139.2951-137.0962
124.8412-5.4207-0.93436.5886-0.93375.0963-0.69370.0037-0.2103-1.4450.5088-0.0907-1.36850.7323-0.1762.8640.23-0.26351.4215-0.41651.9471119.4711140.3503-130.5681
136.96644.0683-6.26283.0377-3.05575.16412.2791-2.53832.2741-0.08310.43140.1512-0.94911.6095-1.53381.74370.14990.00411.2848-0.24061.1577114.1663132.7523-126.2808
142.97961.63473.60294.28773.30624.2492-0.37071.44790.34-2.96140.49812.6169-3.6567-1.4812-0.77842.20240.72090.04522.86170.29911.3143102.4206140.5847-130.3524
151.57241.5431.52914.12644.41886.04791.58485.207-0.30282.9847-3.73842.9470.5012-5.88440.73242.41480.18670.10162.2879-0.20172.530398.3446128.4175-137.5329
162.46462.46781.95682.3431.64562.0065-1.55542.6302-2.0733-1.46360.757-0.45872.5272-3.03252.5133.1334-0.40370.20743.8575-0.08051.711157.2602144.2636-98.5765
178.9752-1.9655-5.5392.12393.7648.8539-0.71710.76530.885-2.79661.63080.3224-0.19560.26330.09192.29790.3991-0.31662.1711-0.16461.1984149.1947138.3712-107.6056
183.79263.90421.94024.15592.43225.88580.98641.7777-1.0859-1.5937-1.87171.27362.5861-1.78541.78682.43850.20470.01241.829-0.14491.6062145.9572126.1548-104.3131
196.9023-0.82755.97868.8323-3.34695.7438-0.00611.07610.5191-1.4473-0.2532-0.55160.12642.95630.32881.26960.0145-0.03371.7461-0.09711.1324153.3751135.7422-102.117
202.05771.93492.14847.6371-9.17871.8903-2.5982.63796.17760.0361.7059-3.4102-13.5882-4.5961-0.75543.82750.44920.6142.53180.42552.7267155.7572148.4644-111.0649
216.54650.6649-2.97758.36354.9354.53341.3237-0.22032.46731.8125-0.04511.3926-1.03831.94024.53214.6881-1.5996-0.12753.01910.10751.9578110.87104.8055-109.1284
227.5929-0.37884.15963.3511-0.70775.0882.05590.9772-1.0907-2.1771-1.22520.22030.8855-1.8184-0.3542.20460.09950.01272.30340.22791.1686116.2811113.1071-118.1377
235.09584.6065-0.57396.73252.05995.9021-1.4271-1.30542.9626-1.4249-0.2561-0.8071-0.06930.58931.28332.0144-0.1021-0.09432.02810.16781.4827114.7409125.6383-114.7609
244.6968-5.665-0.64817.51610.49198.3391.71880.0003-0.1514-0.9157-0.89750.3710.6925-1.8732-0.56421.8744-0.2946-0.15832.2943-0.02081.3058111.2965113.9101-112.7094
259.03211.20683.99854.71384.42445.0647-1.52820.0545-9.4323-2.2756-0.04840.30444.17478.6436-0.02233.18930.57380.22922.96610.28812.7489113.6816101.3686-121.8364
263.4897-0.49711.95288.2618-4.94055.2505-0.68472.1424-0.54151.07284.5865-1.92420.61744.6088-0.64832.5949-0.37010.08191.8772-0.32841.6186147.4211154.6607-156.6724
272.53582.4117-7.44952.80522.6056.08353.194.53882.1481-4.4451-3.780.0417-0.4551-0.12270.86731.42240.0992-0.34741.3572-0.02441.5026142.7219145.7661-165.6324
285.45441.91054.16865.1041-2.936.5739-4.29583.42350.6319-0.7851.54860.4793.00730.43491.70071.5740.68120.07181.3913-0.2491.5038145.5614133.3984-162.284
297.74793.37336.47229.2214-0.37596.0086-0.51111.9709-0.0799-0.32431.076-0.42370.24462.3287-0.44331.4755-0.28140.01071.7471-0.13551.1742147.7667145.3969-160.2143
308.36183.0647-6.11291.3313-2.69739.2370.3254-0.10651.634-2.60333.38780.447-0.1793-5.47-2.40843.2825-0.3238-0.42531.3606-0.24742.0047143.9664157.7117-169.1288
316.40731.1275-5.36533.78041.49577.2420.60462.40462.8134-2.48340.1844-1.4397-4.7303-5.0966-1.51843.52560.4510.28292.75970.22691.4915117.3892156.88-140.6502
326.57224.8709-3.81459.3404-7.72415.9296-0.03931.86290.34830.94641.54160.03060.1331-0.7266-1.02932.2326-0.1351-0.01131.8863-0.43691.2487122.4953148.3053-149.8345
332.8936-2.55711.87553.91151.61337.1949-1.18960.7451-0.60450.58590.84570.91051.11322.3372-0.13672.0384-0.04550.21051.737-0.31781.5987134.3756144.1064-146.4504
348.31731.5166-5.88199.41677.84998.91310.32640.29611.0861-2.87290.73610.2678-4.81130.8623-0.5322.2247-0.0163-0.10811.03110.04870.9272125.4275152.347-144.3719
355.80191.73534.8160.70231.16085.62052.64742.90874.2018-7.7311-0.23367.1587-1.5379-6.3827-2.39363.18081.1101-0.46142.98460.45393.3664113.0476155.7356-153.3183
361.61020.97371.74724.03442.40712.3051-0.5829-1.28521.7746-2.1654-1.7892-2.93392.799-0.6562.48982.56730.96720.28762.49110.5241.7288110.2129152.3369-103.8849
374.50770.33350.71238.6263-1.20811.42161.65893.2677-0.6245-1.6733-0.2991.169-2.98510.1807-0.72572.298-0.30850.31561.8901-0.20160.8901117.3929145.559-112.947
384.7914-3.8796-4.13724.25731.28386.7545-0.7038-0.9182-1.31911.1431-0.8526-2.23230.64740.1351.81622.4124-0.5287-0.00741.73340.06731.619129.9803144.6176-109.5331
395.41032.34190.58518.61457.00055.66020.38340.6370.393-1.11470.3736-0.0467-2.2958-0.7637-0.21622.0290.05920.05051.4935-0.03681.234119.0875150.2243-107.4416
406.13922.38295.42972.69292.52065.0931-0.0058-0.80891.84190.1651-0.83513.8879-0.4506-5.443-1.40552.8362-0.00010.49452.9967-0.05612.4402106.2946150.0956-116.5462
411.59991.74021.31872.4674-0.14448.6401-0.87951.4262-1.25711.8381.2896-2.0596-4.86732.5981-1.5313.04670.851-0.32.764-0.51981.6943157.5407113.9309-114.3853
425.0908-3.75133.03214.37131.21258.3323-1.08841.17950.82260.88410.5190.0230.8873-0.37720.72442.2047-0.069-0.37232.2536-0.15941.4112148.2095117.7619-123.3806
435.7519-3.201-1.16633.61283.93124.9562-0.63310.41471.08271.2292-0.39360.9011-0.9631-0.4310.78672.21090.227-0.19051.33640.08871.7565136.1812113.9451-120.0428
443.5124-0.68662.82074.1767-3.00322.82340.0606-0.8273-1.26143.90230.61381.4921-2.0987-0.7483-0.51341.74840.32340.16171.42750.3131.2815143.9384119.0775-115.746
458.87645.1066-3.21074.6264-0.41561.8803-1.71321.0646-1.0965-3.06030.4828-0.33850.49060.80130.7922.95680.7668-0.04661.8276-0.05921.3502152.0413107.5926-119.9178
465.07294.9459-6.11016.6287-6.16037.4447-3.3795-3.3124-2.62081.5615-2.5761-8.2989-1.56996.57151.27472.40790.3061-0.1642.94920.3683.0527160.2381117.5254-127.0998
473.0911.96840.85232.04877.67355.4233-2.63228.20591.95934.39160.95062.56096.7047-2.57890.04922.2102-0.695-0.61122.6480.60871.9578105.0597110.9993-145.9543
487.6939-5.03171.62745.0254-2.50017.45161.45121.6468-1.5265-2.4638-0.8447-0.10991.1269-2.6039-0.44451.8601-0.01110.08531.90780.11011.3979112.5083117.5914-155.1411
492.66160.65570.79097.42746.20995.4121-0.70732.52530.43961.0421-0.866-1.8534-0.42451.57981.26431.21190.19770.14261.71390.33681.4317114.2976130.1286-151.7318
509.3924-1.3518-6.87787.1648-4.54026.4455-0.20492.3417-0.5671-0.28730.86570.06910.8153-2.3764-0.18471.3053-0.2443-0.13051.9032-0.21010.8864107.9962119.6429-149.6957
512.02893.09441.91473.94052.39736.7091-1.94826.2637-5.0347-6.21156.88570.50812.43686.7001-4.72973.0064-0.5474-0.01822.2098-0.02892.435107.0965106.8634-158.6611
520.1061-0.3794-0.39841.66011.54351.69541.0867-2.56930.77631.099-0.03440.3936-1.61583.7414-0.46524.8625-0.4209-0.1652.246-0.25071.4435132.21297.9424-130.1201
536.37865.27182.69559.19784.70731.90421.2562.71370.6359-0.8545-0.0142-0.62041.10670.0068-0.85262.6109-0.0805-0.04182.12310.09931.2678130.5424107.68-139.2516
546.90135.5958-1.01713.305-1.20775.24490.98984.83671.32262.5080.07920.5994-2.1603-2.5907-1.28352.1886-0.40670.23181.9666-0.08711.4377120.9227115.9473-135.814
555.9961-1.4457-0.15477.7712-6.07855.073-1.43911.8054-1.3154-1.86782.43330.99332.9858-1.225-1.01721.9399-0.4767-0.00811.3986-0.00780.967126.3505104.9799-133.7899
562.02062.03212.26338.4035-1.96361.9557-6.5914-6.5944-7.4515-2.9346-0.8641-1.2937-0.194310.9037-4.35051.45480.4688-0.17253.5905-0.31862.7023136.689297.3696-142.8743
572.27332.2278-0.87989.312-1.23451.503-0.3296-3.9645-1.3512-1.89630.14683.95554.00251.6908-1.51653.03011.2866-0.28282.5962-0.681.5058152.5231107.1625-151.3567
584.2559-1.44332.1725.54463.54193.5647-0.16850.29011.1039-1.07210.65920.00590.1030.0039-0.24721.79750.23560.10421.64310.22811.5253144.6587113.4047-160.437
597.1051-0.4153-7.65042.99820.10397.4934-0.6163-0.04440.3972-1.6391-0.7840.6695-0.7447-1.20360.55851.4932-0.0762-0.34991.6784-0.13271.4444131.9591112.9863-157.0708
607.1312.8278-0.37726.3668-6.11476.08370.87740.7450.0229-2.66060.28840.03542.12131.2199-1.1462.00340.0934-0.16621.24330.0051.2183143.3917108.5707-155.082
617.07425.7875-4.8924.7191-3.66354.43975.99992.4599-2.1714-5.7577-1.2859-3.43592.61271.046-4.01781.86490.93750.36893.0411-0.00232.3852156.1105110.0285-164.0021
628.48265.5891.47059.00332.98421.0730.17835.1705-5.0289-4.28776.2091-2.7261-4.15014.6999-1.83592.89920.2420.34873.2251-0.30861.7452160.3498136.1867-135.4165
6310.5787-5.8382-3.17597.5786-0.01078.07050.32840.2077-0.0317-4.61511.51130.13011.0651-0.2913-0.89852.4284-0.0279-0.03731.7967-0.01291.0144151.0037132.7926-144.5172
644.64-5.48653.50686.1414-5.37435.3122.434-0.33622.2329-3.359-2.3719-1.24841.4831-2.1518-0.07352.13250.3063-0.37381.8284-0.11731.6247144.6169121.9109-141.1321
655.7769-2.42646.37467.3434-1.48185.83381.64482.5876-0.8034-0.6565-1.3029-0.2783-0.7153.5181-0.14511.42470.3574-0.03992.0451-0.03741.2206154.4075129.1439-139.1144
661.9085-0.47221.80617.4781-8.92011.9816-0.80625.84027.93056.69490.2395-8.1933-6.6552-1.7511-1.20333.84060.4069-0.06832.18420.06153.6503160.1778140.6738-148.0864
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON MICROSCOPY1chain 'G' and (resid 112 through 117 )
2ELECTRON MICROSCOPY2chain 'G' and (resid 118 through 128 )
3ELECTRON MICROSCOPY3chain 'G' and (resid 129 through 136 )
4ELECTRON MICROSCOPY4chain 'G' and (resid 137 through 142 )
5ELECTRON MICROSCOPY5chain 'G' and (resid 143 through 154 )
6ELECTRON MICROSCOPY6chain 'G' and (resid 155 through 168 )
7ELECTRON MICROSCOPY7chain 'G' and (resid 169 through 184 )
8ELECTRON MICROSCOPY8chain 'G' and (resid 185 through 194 )
9ELECTRON MICROSCOPY9chain 'A' and (resid 112 through 117 )
10ELECTRON MICROSCOPY10chain 'A' and (resid 118 through 128 )
11ELECTRON MICROSCOPY11chain 'A' and (resid 129 through 136 )
12ELECTRON MICROSCOPY12chain 'A' and (resid 137 through 154 )
13ELECTRON MICROSCOPY13chain 'A' and (resid 155 through 168 )
14ELECTRON MICROSCOPY14chain 'A' and (resid 169 through 184 )
15ELECTRON MICROSCOPY15chain 'A' and (resid 185 through 194 )
16ELECTRON MICROSCOPY16chain 'B' and (resid 112 through 117 )
17ELECTRON MICROSCOPY17chain 'B' and (resid 118 through 136 )
18ELECTRON MICROSCOPY18chain 'B' and (resid 137 through 154 )
19ELECTRON MICROSCOPY19chain 'B' and (resid 155 through 184 )
20ELECTRON MICROSCOPY20chain 'B' and (resid 185 through 194 )
21ELECTRON MICROSCOPY21chain 'C' and (resid 112 through 117 )
22ELECTRON MICROSCOPY22chain 'C' and (resid 118 through 136 )
23ELECTRON MICROSCOPY23chain 'C' and (resid 137 through 154 )
24ELECTRON MICROSCOPY24chain 'C' and (resid 155 through 184 )
25ELECTRON MICROSCOPY25chain 'C' and (resid 185 through 194 )
26ELECTRON MICROSCOPY26chain 'D' and (resid 112 through 117 )
27ELECTRON MICROSCOPY27chain 'D' and (resid 118 through 136 )
28ELECTRON MICROSCOPY28chain 'D' and (resid 137 through 154 )
29ELECTRON MICROSCOPY29chain 'D' and (resid 155 through 184 )
30ELECTRON MICROSCOPY30chain 'D' and (resid 185 through 194 )
31ELECTRON MICROSCOPY31chain 'E' and (resid 112 through 117 )
32ELECTRON MICROSCOPY32chain 'E' and (resid 118 through 136 )
33ELECTRON MICROSCOPY33chain 'E' and (resid 137 through 154 )
34ELECTRON MICROSCOPY34chain 'E' and (resid 155 through 184 )
35ELECTRON MICROSCOPY35chain 'E' and (resid 185 through 194 )
36ELECTRON MICROSCOPY36chain 'F' and (resid 112 through 117 )
37ELECTRON MICROSCOPY37chain 'F' and (resid 118 through 136 )
38ELECTRON MICROSCOPY38chain 'F' and (resid 137 through 154 )
39ELECTRON MICROSCOPY39chain 'F' and (resid 155 through 184 )
40ELECTRON MICROSCOPY40chain 'F' and (resid 185 through 194 )
41ELECTRON MICROSCOPY41chain 'H' and (resid 112 through 117 )
42ELECTRON MICROSCOPY42chain 'H' and (resid 118 through 136 )
43ELECTRON MICROSCOPY43chain 'H' and (resid 137 through 154 )
44ELECTRON MICROSCOPY44chain 'H' and (resid 155 through 168 )
45ELECTRON MICROSCOPY45chain 'H' and (resid 169 through 184 )
46ELECTRON MICROSCOPY46chain 'H' and (resid 185 through 194 )
47ELECTRON MICROSCOPY47chain 'I' and (resid 112 through 117 )
48ELECTRON MICROSCOPY48chain 'I' and (resid 118 through 136 )
49ELECTRON MICROSCOPY49chain 'I' and (resid 137 through 154 )
50ELECTRON MICROSCOPY50chain 'I' and (resid 155 through 184 )
51ELECTRON MICROSCOPY51chain 'I' and (resid 185 through 194 )
52ELECTRON MICROSCOPY52chain 'J' and (resid 112 through 117 )
53ELECTRON MICROSCOPY53chain 'J' and (resid 118 through 136 )
54ELECTRON MICROSCOPY54chain 'J' and (resid 137 through 154 )
55ELECTRON MICROSCOPY55chain 'J' and (resid 155 through 184 )
56ELECTRON MICROSCOPY56chain 'J' and (resid 185 through 194 )
57ELECTRON MICROSCOPY57chain 'K' and (resid 112 through 117 )
58ELECTRON MICROSCOPY58chain 'K' and (resid 118 through 136 )
59ELECTRON MICROSCOPY59chain 'K' and (resid 137 through 154 )
60ELECTRON MICROSCOPY60chain 'K' and (resid 155 through 184 )
61ELECTRON MICROSCOPY61chain 'K' and (resid 185 through 194 )
62ELECTRON MICROSCOPY62chain 'L' and (resid 112 through 117 )
63ELECTRON MICROSCOPY63chain 'L' and (resid 118 through 136 )
64ELECTRON MICROSCOPY64chain 'L' and (resid 137 through 154 )
65ELECTRON MICROSCOPY65chain 'L' and (resid 155 through 184 )
66ELECTRON MICROSCOPY66chain 'L' and (resid 185 through 194 )

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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

他の情報も見る