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- PDB-6k9f: Structure of unknow protein 4 -

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基本情報

登録情報
データベース: PDB / ID: 6k9f
タイトルStructure of unknow protein 4
要素Caspase recruitment domain-containing protein 8
キーワードSIGNALING PROTEIN / filament
機能・相同性
機能・相同性情報


CARD8 inflammasome complex assembly / CARD8 inflammasome complex / NACHT domain binding / Formation of apoptosome / CARD domain binding / self proteolysis / NLRP3 inflammasome complex / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of NLRP3 inflammasome complex assembly / cysteine-type endopeptidase activator activity ...CARD8 inflammasome complex assembly / CARD8 inflammasome complex / NACHT domain binding / Formation of apoptosome / CARD domain binding / self proteolysis / NLRP3 inflammasome complex / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of NLRP3 inflammasome complex assembly / cysteine-type endopeptidase activator activity / Regulation of the apoptosome activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / negative regulation of interleukin-1 beta production / pattern recognition receptor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / activation of innate immune response / intrinsic apoptotic signaling pathway / antiviral innate immune response / positive regulation of interleukin-1 beta production / negative regulation of canonical NF-kappaB signal transduction / molecular condensate scaffold activity / protein destabilization / positive regulation of inflammatory response / peptidase activity / regulation of apoptotic process / defense response to virus / inflammatory response / protein homodimerization activity / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol
類似検索 - 分子機能
FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / : / 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
Caspase recruitment domain-containing protein 8
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: 3.7 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, 2件
組織認可番号国
Ministry of Education (Singapore)tier2 シンガポール
Ministry of Education (Singapore)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15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-9948
  • 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-9948
  • 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
A: Caspase recruitment domain-containing protein 8
B: Caspase recruitment domain-containing protein 8
C: Caspase recruitment domain-containing protein 8
D: Caspase recruitment domain-containing protein 8
E: Caspase recruitment domain-containing protein 8
F: Caspase recruitment domain-containing protein 8
G: Caspase recruitment domain-containing protein 8
H: Caspase recruitment domain-containing protein 8
I: Caspase recruitment domain-containing protein 8
J: Caspase recruitment domain-containing protein 8
K: Caspase recruitment domain-containing protein 8
L: Caspase recruitment domain-containing protein 8


分子量 (理論値)分子数
合計 (水以外)125,34912
ポリマ－125,34912
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
Caspase recruitment domain-containing protein 8 / Apoptotic protein NDPP1 / CARD-inhibitor of NF-kappa-B-activating ligand / CARDINAL / DACAR / Tumor ...Apoptotic protein NDPP1 / CARD-inhibitor of NF-kappa-B-activating ligand / CARDINAL / DACAR / Tumor up-regulated CARD-containing antagonist of CASP9 / TUCAN


分子量: 10445.787 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: CARD8, KIAA0955, NDPP1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q9Y2G2

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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: caspase recruitment domain containing=protein 8 / 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 K-12 (大腸菌) / 株: K-12
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 R1.2/1.3
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 / 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: 80 e/Å2 / 検出モード: COUNTING
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
実像数: 1424
画像スキャン動画フレーム数/画像: 40

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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
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: -99.16 ° / 軸方向距離/サブユニット: 5.409 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: 1201108
3次元再構成解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 98280 / 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: 3.7→92.4 Å / SU ML: 1.19 / σ(F): 0.04 / 位相誤差: 51.8 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3017 967 3.36 %
Rwork0.253 --
obs0.2547 28800 99.84 %
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_d0.0028544
ELECTRON MICROSCOPYf_angle_d0.42311448
ELECTRON MICROSCOPYf_dihedral_angle_d22.4775424
ELECTRON MICROSCOPYf_chiral_restr0.031296
ELECTRON MICROSCOPYf_plane_restr0.0031524
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.89520.54811280.5483969ELECTRON MICROSCOPY100
3.8952-4.13930.47841520.51744011ELECTRON MICROSCOPY100
4.1393-4.45880.4581440.46623926ELECTRON MICROSCOPY100
4.4588-4.90750.41891320.37714008ELECTRON MICROSCOPY100
4.9075-5.61760.40321240.30623977ELECTRON MICROSCOPY100
5.6176-7.07720.40591460.30593990ELECTRON MICROSCOPY100
7.0772-92.42880.19321410.15293952ELECTRON 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)
13.4386-4.0187-1.26647.095-1.53745.7363-1.1303-1.7546-0.7146-0.46350.37542.65121.5732-2.48640.51041.6053-0.2365-0.09262.2289-0.12182.1878120.545105.4263126.102
23.6930.2777-3.5533.24692.73618.4773-1.6803-4.8845-2.2294-0.22830.614-0.2903-0.92711.1171.10532.55150.69390.16072.28920.5532.2829137.6324107.6605129.0704
36.6718-6.7461-4.61429.7882.70054.4702-2.3934.3596.36250.88961.4957-5.6264-1.8154-1.8921.362.4245-0.3239-0.05142.7590.05123.3864133.5162118.2451125.1177
46.4122-7.94495.59937.5761-1.86677.684-0.7886-0.73911.03360.3633-0.4379-1.14543.412-0.22960.83692.4317-0.16560.50832.2619-0.062.0515128.5411105.6298125.4959
52.96313.62393.05293.33.28562.9287-2.16261.9619-3.3034-2.08382.46930.62311.5108-2.0924-0.50172.3596-0.360.0482.2669-0.10512.5343116.659799.0499133.8835
66.46156.1529-3.01038.25421.29076.1163-1.3481.29240.7860.52931.47112.0018-0.54112.45260.64542.38830.3221-0.1132.11440.12721.8566107.714115.9981147.7366
74.41111.32690.73884.05664.90255.2637-3.7171-0.5472-0.25841.3765.19065.21893.18725.87690.68823.60970.38670.51232.26690.22722.4315122.6619107.7602150.7697
83.4437-0.941-5.30174.2239-0.68418.8421-2.58944.4207-1.60972.7352-0.4017-6.7505-4.5774-0.00730.3352.18780.73120.2762.7039-0.24933.6075125.5478118.6737146.864
9-0.60031.8658-1.01267.76051.76485.9637-0.94-0.5810.4074-0.28941.0368-0.69110.71360.11420.71042.4557-0.07250.33912.7856-0.14982.2745114.137111.4254147.2473
101.96162.05431.7331.5521.92923.89641.26260.113-1.89330.13080.18691.3451-2.6788-0.2222-1.28182.6667-0.33730.34883.18990.11942.3285100.6397113.1403155.4652
113.72972.4014-10.5369.79452.87789.4812-0.1252-0.2748-0.26010.7626-1.25460.6069-0.24040.46710.84252.37120.28710.07071.79990.10531.7619107.9656121.3182111.0512
126.4816-0.9153-4.8789.96954.92152.0095-4.1761.3488-0.30912.1495-1.257-7.5087-7.71988.17890.66932.94260.6962-0.14012.09630.65363.107121.0412121.7826108.9486
136.48213.5455-7.2475.0745-0.88846.474-0.8613-0.2521-2.85391.7938-0.0559-2.00090.2917-0.58381.00432.44590.15460.12072.8454-0.07472.0196107.531120.2976109.2839
143.57454.57774.66226.51615.27065.6173-1.62782.5636-0.91110.85530.12892.5879-0.2109-0.19780.58792.7391-0.0158-0.1812.1223-0.10482.439396.3335127.7583117.6812
152.8647-7.1402-5.81966.0797-1.03989.3453-1.12981.1471-2.2397-2.3836-1.17491.80441.7984-1.98240.38862.2816-0.51850.08211.9808-0.28422.3676132.3963103.7918164.0336
165.2653-3.4598-4.45764.37042.6164.13943.6206-4.27221.9908-1.9976-2.6136-0.6350.29092.23230.64212.64450.5295-0.1924.1818-0.33152.1246146.574113.173166.81
175.2659-0.8958-6.93093.9295-0.44159.6621-0.5902-1.63834.233-1.3543-0.3258-0.9001-10.5227-1.6172-1.11732.26081.1204-0.19062.423-0.39163.1569138.16120.8906163.0627
182.57950.99440.93311.9384-0.06552.7615-2.3373-2.0170.1963-1.47621.1836-1.7036-0.02052.53680.33872.55520.38930.54952.111-0.16382.5335135.5761111.5707160.7296
194.43421.9735-2.52693.9242-6.27586.97140.1643-1.2878-0.5640.4217-1.9990.59740.1274-0.05731.62643.4205-0.17460.57722.1242-0.42792.2847137.769299.8298169.0009
205.2953-2.80713.53974.65063.06066.6304-1.4357-1.12131.81060.8716-0.72260.2307-0.41830.03851.46522.8386-0.0585-0.12352.47850.68382.0803119.733154.6379153.1781
212.28260.91981.23712.82772.30771.93461.11910.9512-2.0785-3.0976-1.6998-1.78233.4097-0.15461.26952.4023-0.15730.4673.21590.41712.0786109.1367141.1516156.0735
222.74121.09871.49711.86143.19638.67870.1089-1.5578-9.2341-0.5355-1.4275-0.65072.26091.40111.17022.3846-0.00160.56722.54110.57883.8067119.4781136.4814152.2723
234.63580.3082-1.37681.034.33132.66011.0692-0.2954-0.12820.6995-1.3357-0.5512-0.3754-0.16121.46512.58290.3027-0.31751.58990.13771.9364114.1291148.9243152.6999
245.3834-0.49165.04171.73-3.17248.52990.85690.46124.02373.5122-2.0121-1.8189-3.12421.34290.49393.14290.7172-0.02241.47870.12152.9935117.9515161.9322160.9161
256.9324-5.05931.49396.4409-5.04725.717-0.396-0.0038-3.07-5.43450.5081-0.1744-1.05350.2207-0.15542.3848-0.67330.57972.1214-0.01592.3133137.2876104.7299104.4437
264.77320.1753-2.2043.2575-3.61424.73632.5127-1.9022-3.13911.2879-3.6025-1.5655-4.81533.43581.06461.8425-0.59140.01482.6560.3732.1349149.4924116.556107.4515
278.68432.4298-1.37929.0455-8.69212.0784-2.0381-2.86046.72060.9353-1.95031.1985-6.4128-8.9166-0.36132.6547-0.02580.15822.6996-0.39982.544139.8707122.6401103.6018
288.60953.0273-1.30074.0897-5.12086.4347-0.072-2.06252.97210.4167-0.6222-3.0726-0.42130.71320.53732.76450.18770.10852.12820.10462.084143.5919109.5713103.9776
292.58372.8946-0.35149.15445.83045.9198-2.8781-3.2131-4.6249-3.7971.5405-2.0104-0.093-1.36931.72012.17480.42590.55362.16610.45182.9323137.975497.1486112.255
307.93677.14412.40636.86790.21233.30150.903-0.8848-4.34861.5722-2.1253-1.78162.54561.6883-0.16132.71020.62840.15282.3336-0.18072.4273156.1315124.7454120.6607
312.43252.774-2.14155.5731-4.82124.86421.7301-0.53871.24031.73780.6349-0.1976-3.7096-2.73970.1952.7616-0.38780.01542.19080.20582.3351151.1806141.1207123.5814
328.83562.13928.45371.92896.26762.04465.5283-0.55953.25040.81-7.17753.74840.8671-4.5291-0.84453.21020.79840.53151.49680.27113.2233141.443135.4586119.7267
335.95237.57963.94177.32154.61414.1905-0.131-0.8007-0.04041.2808-0.59240.06841.32461.61230.09992.79780.82860.07982.78830.31082.3517154.7011132.6199120.1312
34-0.1299-0.0688-0.26675.8774-0.66192.84363.29986.57012.05093.6669-2.4391-3.83980.52872.3856-0.77621.61640.42330.08783.3390.31132.1244163.1242121.8566128.5057
352.4881-3.67552.93217.79513.31673.4307-1.4763-1.61252.3377-1.35260.2865-1.77180.89481.73330.28771.8237-0.4382-0.06232.61410.30321.9739131.4918156.6851115.2268
366.6494-1.66595.53843.8219-0.29535.1129-0.3635-3.34750.80382.41892.37711.04282.5391-6.65171.20752.11580.66670.26413.1522-0.10011.9805116.0096149.1811118.1784
375.69512.04725.46425.05163.9577.2515-4.19080.3593-10.0034-0.5032.67761.33997.38625.96760.71243.13720.36160.49493.37930.70953.0982123.2474140.4982114.4393
383.1749-7.6213-0.15576.29864.8388.889-0.623-1.1817-2.69481.2622-0.37922.80531.0817-0.61560.9692.9079-0.71-0.09642.71250.0442.5116123.8545154.0257114.7746
392.5938-0.39862.33554.4467-5.64597.2193-0.15371.48453.3667-4.26930.86751.0228-0.4031-4.31880.5812.42530.1430.23732.51960.19652.1586133.162163.9651123.1617
407.34662.80790.09236.66086.39276.80.17360.21722.50961.7707-1.42142.6582-3.18222.1990.45992.1212-0.2142-0.17122.05850.10292.23107.1191143.5033131.4081
412.89512.02554.02243.47950.66847.71955.80811.04954.42012.6471-3.352.73135.32751.43470.4772.6378-0.53670.81892.899-0.11852.3228106.7796126.353134.4802
425.29931.82635.18082.17041.27414.88741.5751.3204-5.3117-0.8462-0.4041-2.5698-0.0426-1.80280.1683.20970.7550.29462.6918-0.09583.3971117.8022128.8524130.5452
436.93647.0871-1.73325.8293-0.0655.4951.2538-1.5296-1.57320.9397-1.463-0.4642-0.4271-2.27040.4942.78180.44960.0792.82360.01962.2413106.098135.6472130.9472
441.2137-1.49780.82432.7046-3.35394.48790.52454.0218-0.3663-1.2504-2.2487-0.5142-2.1303-2.28691.52392.95340.60880.12772.93270.06542.1888101.4207148.3726139.381
458.84022.0512-0.00466.0393-0.99694.4346-3.23173.01980.8384-2.09793.135-2.38633.849-0.3303-0.01462.58320.21630.07693.07310.20962.6283146.9108150.7745136.8871
468.3026-1.96172.93222.2282-1.47571.9517-0.3074-3.88092.1644-1.35721.9657-0.9244-1.6578-4.7910.29022.89970.7757-0.16253.370.06781.9729130.1584153.828139.9109
479.5475-6.93425.64185.5907-6.08568.6214-0.02512.2667-2.24772.4520.59745.27443.9430.20120.29213.197-0.22930.27462.26790.20713.227130.8082142.5753135.938
482.6356-3.3181-0.60544.52443.57578.5495-0.9352-0.6992-0.13151.23151.50980.5889-0.92470.13180.1882.8563-0.4184-0.0233.550.07492.2051139.3918153.0701136.3776
496.352.7247-5.8422.7681-0.69146.3508-5.49450.15152.7881-3.57841.993-1.6274.82613.24942.39363.2124-0.1316-0.20572.59010.45382.5441152.5531155.6375144.8488
506.8138-5.8233-2.57936.38442.62174.4065-0.57-0.636-1.59131.9909-0.63990.11522.1914-0.53090.99023.0525-0.28610.47141.6091-0.02792.0423147.704110.4166142.3658
512.74752.4435-2.18997.8690.32652.31521.46642.7201-1.78313.6168-0.9626-2.2249-5.01581.83230.75152.2036-0.3297-0.22012.82540.19622.077153.5174126.5268145.2309
526.75363.2397-1.39951.6411-1.06456.44543.4811-3.70877.39340.7759-4.48651.31-0.5911-4.21911.35212.0925-0.00880.2132.1117-0.59554.2249142.2639127.6702141.3673
537.24944.30450.37681.17010.4647.76680.0625-0.55230.9921.3555-0.38920.58170.39030.35890.95142.36310.03240.34952.32210.23832.4166151.2062117.5108141.8235
545.3879-5.5109-0.07456.10542.19124.62683.2657-0.4602-2.0992-3.0109-2.9036-3.24940.0036-1.53531.35422.57220.67970.1823.19450.51382.3954151.6587104.0101150.288
556.998.37092.58442.9907-1.67727.1368-0.6067-0.0748-1.461-0.6151-1.077-2.4775-0.5964-0.63790.55742.33720.73710.43671.79290.04472.2679155.9214136.629158.6252
564.23192.59711.98124.43421.58442.0919-0.53763.88760.14335.50731.07250.5224-3.4798-1.56461.4763.01650.53530.64642.6857-0.03162.3513144.2735149.1664161.4256
572.77960.96740.90076.1313-4.53053.22952.84233.00670.71184.0691-4.66965.7852.7752-5.31080.64392.665-0.68970.78662.28040.02183.3674138.0607139.6334157.7827
587.97772.72374.06335.3887-0.71254.034-1.12780.89381.14961.14160.36361.8248-1.60081.8671.08122.08380.02590.19622.89430.61572.0444151.1977143.0237158.1223
591.73742.7117-3.59095.1831-5.66816.7155-3.2489-0.16193.8777-5.44153.2347-3.63120.73241.58850.30472.803-0.57340.04122.86760.20122.0724163.4355137.3576166.4111
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON MICROSCOPY1chain 'A' and (resid 451 through 468 )
2ELECTRON MICROSCOPY2chain 'A' and (resid 469 through 482 )
3ELECTRON MICROSCOPY3chain 'A' and (resid 483 through 494 )
4ELECTRON MICROSCOPY4chain 'A' and (resid 495 through 524 )
5ELECTRON MICROSCOPY5chain 'A' and (resid 525 through 537 )
6ELECTRON MICROSCOPY6chain 'B' and (resid 451 through 468 )
7ELECTRON MICROSCOPY7chain 'B' and (resid 469 through 482 )
8ELECTRON MICROSCOPY8chain 'B' and (resid 483 through 494 )
9ELECTRON MICROSCOPY9chain 'B' and (resid 495 through 524 )
10ELECTRON MICROSCOPY10chain 'B' and (resid 525 through 537 )
11ELECTRON MICROSCOPY11chain 'C' and (resid 451 through 482 )
12ELECTRON MICROSCOPY12chain 'C' and (resid 483 through 494 )
13ELECTRON MICROSCOPY13chain 'C' and (resid 495 through 524 )
14ELECTRON MICROSCOPY14chain 'C' and (resid 525 through 537 )
15ELECTRON MICROSCOPY15chain 'D' and (resid 451 through 468 )
16ELECTRON MICROSCOPY16chain 'D' and (resid 469 through 482 )
17ELECTRON MICROSCOPY17chain 'D' and (resid 483 through 494 )
18ELECTRON MICROSCOPY18chain 'D' and (resid 495 through 509 )
19ELECTRON MICROSCOPY19chain 'D' and (resid 510 through 537 )
20ELECTRON MICROSCOPY20chain 'E' and (resid 451 through 468 )
21ELECTRON MICROSCOPY21chain 'E' and (resid 469 through 482 )
22ELECTRON MICROSCOPY22chain 'E' and (resid 483 through 494 )
23ELECTRON MICROSCOPY23chain 'E' and (resid 495 through 524 )
24ELECTRON MICROSCOPY24chain 'E' and (resid 525 through 537 )
25ELECTRON MICROSCOPY25chain 'F' and (resid 451 through 468 )
26ELECTRON MICROSCOPY26chain 'F' and (resid 469 through 482 )
27ELECTRON MICROSCOPY27chain 'F' and (resid 483 through 494 )
28ELECTRON MICROSCOPY28chain 'F' and (resid 495 through 524 )
29ELECTRON MICROSCOPY29chain 'F' and (resid 525 through 537 )
30ELECTRON MICROSCOPY30chain 'G' and (resid 451 through 468 )
31ELECTRON MICROSCOPY31chain 'G' and (resid 469 through 482 )
32ELECTRON MICROSCOPY32chain 'G' and (resid 483 through 494 )
33ELECTRON MICROSCOPY33chain 'G' and (resid 495 through 524 )
34ELECTRON MICROSCOPY34chain 'G' and (resid 525 through 537 )
35ELECTRON MICROSCOPY35chain 'H' and (resid 451 through 468 )
36ELECTRON MICROSCOPY36chain 'H' and (resid 469 through 482 )
37ELECTRON MICROSCOPY37chain 'H' and (resid 483 through 494 )
38ELECTRON MICROSCOPY38chain 'H' and (resid 495 through 524 )
39ELECTRON MICROSCOPY39chain 'H' and (resid 525 through 537 )
40ELECTRON MICROSCOPY40chain 'I' and (resid 451 through 468 )
41ELECTRON MICROSCOPY41chain 'I' and (resid 469 through 482 )
42ELECTRON MICROSCOPY42chain 'I' and (resid 483 through 494 )
43ELECTRON MICROSCOPY43chain 'I' and (resid 495 through 524 )
44ELECTRON MICROSCOPY44chain 'I' and (resid 525 through 537 )
45ELECTRON MICROSCOPY45chain 'J' and (resid 451 through 468 )
46ELECTRON MICROSCOPY46chain 'J' and (resid 469 through 482 )
47ELECTRON MICROSCOPY47chain 'J' and (resid 483 through 494 )
48ELECTRON MICROSCOPY48chain 'J' and (resid 495 through 524 )
49ELECTRON MICROSCOPY49chain 'J' and (resid 525 through 537 )
50ELECTRON MICROSCOPY50chain 'K' and (resid 451 through 468 )
51ELECTRON MICROSCOPY51chain 'K' and (resid 469 through 482 )
52ELECTRON MICROSCOPY52chain 'K' and (resid 483 through 494 )
53ELECTRON MICROSCOPY53chain 'K' and (resid 495 through 524 )
54ELECTRON MICROSCOPY54chain 'K' and (resid 525 through 537 )
55ELECTRON MICROSCOPY55chain 'L' and (resid 451 through 468 )
56ELECTRON MICROSCOPY56chain 'L' and (resid 469 through 482 )
57ELECTRON MICROSCOPY57chain 'L' and (resid 483 through 494 )
58ELECTRON MICROSCOPY58chain 'L' and (resid 495 through 524 )
59ELECTRON MICROSCOPY59chain 'L' and (resid 525 through 537 )

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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