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- PDB-6k8j: Structure of NLRC4 CARD filament -

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基本情報

登録情報
データベース: PDB / ID: 6k8j
タイトルStructure of NLRC4 CARD filament
要素NLR family CARD domain-containing protein 4
キーワードSIGNALING PROTEIN / filament
機能・相同性
機能・相同性情報


IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / canonical inflammasome complex / caspase binding / positive regulation of protein processing / pattern recognition receptor signaling pathway / activation of cysteine-type endopeptidase activity / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response ...IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / canonical inflammasome complex / caspase binding / positive regulation of protein processing / pattern recognition receptor signaling pathway / activation of cysteine-type endopeptidase activity / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / endopeptidase activator activity / detection of bacterium / activation of innate immune response / positive regulation of interleukin-1 beta production / protein homooligomerization / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / defense response to bacterium / inflammatory response / positive regulation of apoptotic process / intracellular membrane-bounded organelle / innate immune response / apoptotic process / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
NLR family CARD domain-containing protein 4 / NLRC4, helical domain / : / NLRC4 helical domain / Nlrc4-like, winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / CARD domain / CARD caspase recruitment domain profile. ...NLR family CARD domain-containing protein 4 / NLRC4, helical domain / : / NLRC4 helical domain / Nlrc4-like, winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
NLR family CARD domain-containing protein 4
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: 3.3 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12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-9946
  • 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-9946
  • 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: NLR family CARD domain-containing protein 4
L: NLR family CARD domain-containing protein 4
K: NLR family CARD domain-containing protein 4
J: NLR family CARD domain-containing protein 4
I: NLR family CARD domain-containing protein 4
H: NLR family CARD domain-containing protein 4
F: NLR family CARD domain-containing protein 4
E: NLR family CARD domain-containing protein 4
D: NLR family CARD domain-containing protein 4
C: NLR family CARD domain-containing protein 4
B: NLR family CARD domain-containing protein 4
A: NLR family CARD domain-containing protein 4


分子量 (理論値)分子数
合計 (水以外)139,20512
ポリマ－139,20512
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
NLR family CARD domain-containing protein 4 / CARD / LRR / and NACHT-containing protein / Clan protein / Caspase recruitment domain-containing ...CARD / LRR / and NACHT-containing protein / Clan protein / Caspase recruitment domain-containing protein 12 / Ice protease-activating factor / Ipaf


分子量: 11600.412 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: NLRC4, CARD12, CLAN, CLAN1, IPAF, UNQ6189/PRO20215
発現宿主: Escherichia coli K-12 (大腸菌) / 株 (発現宿主): K-12 / 参照: UniProt: Q9NPP4

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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: NLRC4 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
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 / 最大 デフォーカス（公称値）: 2500 nm / 最小 デフォーカス（公称値）: 1500 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: 2109
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
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
9PHENIXdev 2405モデル精密化
10RELION2初期オイラー角割当
11RELION2最終オイラー角割当
12RELION2分類
13RELION2３次元再構成
CTF補正タイプ: NONE
らせん対称回転角度/サブユニット: -100.55 ° / 軸方向距離/サブユニット: 5.17 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: 382715
3次元再構成解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 120602 / 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: 3.3→82.5 Å / SU ML: 1.15 / σ(F): 0.01 / 位相誤差: 51.13 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射
Rfree0.3057 1505 4.12 %
Rwork0.2571 --
obs0.2593 36562 99.78 %
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_d0.0028472
ELECTRON MICROSCOPYf_angle_d0.36411376
ELECTRON MICROSCOPYf_dihedral_angle_d11.7825208
ELECTRON MICROSCOPYf_chiral_restr0.0371284
ELECTRON MICROSCOPYf_plane_restr0.0031440
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.40650.58241400.59283117ELECTRON MICROSCOPY100
3.4065-3.52830.60361360.5853265ELECTRON MICROSCOPY100
3.5283-3.66950.57731480.5593153ELECTRON MICROSCOPY100
3.6695-3.83650.52391220.52123221ELECTRON MICROSCOPY100
3.8365-4.03880.59151370.49883157ELECTRON MICROSCOPY100
4.0388-4.29180.49641440.41873219ELECTRON MICROSCOPY100
4.2918-4.62320.34551440.31443188ELECTRON MICROSCOPY100
4.6232-5.08840.3321280.27393183ELECTRON MICROSCOPY100
5.0884-5.82450.35371330.25913177ELECTRON MICROSCOPY100
5.8245-7.33760.35331390.28133179ELECTRON MICROSCOPY99
7.3376-82.52580.18241340.15373198ELECTRON 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)
12.3086-0.02331.31247.6064-2.25581.8513-1.22560.6622-2.4865-2.835-0.902-0.31963.67550.73543.24962.94770.34380.70232.56130.13832.1845-19.8685-59.694145.0171
26.4784-6.6834-0.81827.07712.06061.7805-4.6301-0.031-1.5712-1.9382-0.3008-4.75645.11642.42051.8542.90550.59240.12892.6520.14641.7945-27.8419-57.880552.5911
34.39983.9656-0.87415.5185-4.32974.36572.4535-0.78791.47790.41360.02490.5246-2.3876-2.5955-0.92472.239-0.46960.3592.72570.44272.0117-20.7276-42.477253.4378
43.51342.5952.00962.91650.48043.28023.3293.25145.7456-2.39760.4301-6.14380.5008-1.9099-1.5023.0885-0.21220.57262.37820.97924.4036-27.2746-37.650247.4926
55.08272.20366.93382.29862.89859.80982.75132.0373.5469-0.7635-1.5781-5.2305-3.2058-8.6076-1.53092.5837-0.73551.22563.5917-0.27263.9471-34.9596-44.94351.0881
63.8292-3.28092.44575.4054-1.48613.70240.77383.0887-2.6033-0.70090.00823.1519-0.4139-0.5333-0.28651.9470.12120.47113.25990.57052.6063-25.0297-49.666344.3259
73.13441.3175-0.20024.5288-4.16368.22170.55840.7544-1.27031.1092-1.8-3.8301-3.0723-2.43681.38512.65730.31680.39223.24150.31962.1953-13.6516-50.394651.4788
85.3181-0.4181-3.08253.2759-2.44545.2769-1.7892-2.2938-2.94951.65771.6739-2.25861.31814.61152.04422.8427-0.23620.56962.18070.34572.2741-17.7062-58.948558.0431
97.4519-2.90133.51585.86194.22548.7329-0.0210.04-1.12880.4999-0.12321.51191.5499-0.9868-0.24152.44670.0270.31071.69560.2591.7073-59.5276-57.011519.5543
106.3951-4.53954.52758.05960.79287.1198-5.36988.55521.7274-6.06451.66120.4691-4.12534.281-1.64662.97730.3540.54442.6351-0.434.2159-45.6116-57.517916.4966
114.67123.8948-0.50634.19810.86442.3780.4179-1.2071-0.7969-4.89992.43961.3197-3.68866.7144-1.61814.40530.96560.80992.79750.173.0913-48.7355-47.344119.9532
125.38773.1133-2.66673.23841.6634.2632-0.39483.78290.636-6.59330.7732-0.1195-4.53531.4559-0.57262.7375-0.62580.57371.98670.21482.5346-57.3656-54.16413.2973
133.84380.20173.16444.29553.24665.502-0.49350.762-0.93721.6224-0.45321.6291.4659-1.46370.85512.4745-0.21710.43172.54530.18132.0959-65.9519-60.298123.5971
145.3249-2.9741-3.57844.1198-0.04213.57291.05481.0054-1.9588-3.58450.1956-0.54543.9757-1.55410.98062.92170.13790.29222.80790.22062.3631-37.6389-70.384465.6097
157.3171-2.182-4.85672.44641.28313.984-2.00342.7902-4.1002-2.2401-0.9434-0.69691.6212.8939-0.18462.9313-0.1304-0.10241.35390.07242.1294-42.3413-63.717873.2774
163.4182-1.87681.50028.67590.67552.85780.1686-1.16472.0085-0.22551.0045-0.7468-1.45042.7613-0.46611.5396-0.05940.06292.29080.1181.8873-26.7653-57.036874.0874
174.01911.1004-1.23.4026-3.94294.81181.1616-0.25961.7076-7.18421.0756-6.3914-3.91-2.9004-1.72382.2804-1.47862.4242.54040.8454.1728-28.3989-49.099268.2094
187.7522-1.2718-4.71986.1774.71595.38084.153-0.93122.4559-4.21772.3088-6.7004-4.7786-0.6461-1.77972.67670.22350.52713.93860.78454.1184-39.0306-49.382771.7923
195.8322-2.50742.00676.36094.99117.220.11322.05460.9673-4.90633.06891.79-7.2556-0.2722-1.88882.77780.7110.64622.52470.38042.7588-37.3132-58.055566.7112
205.66022.5904-0.79721.1934-0.52344.5751-1.20762.78092.322-3.2099-0.6624-0.831-2.50734.20390.38173.47660.90340.95471.80630.35992.0494-27.8292-63.312360.4737
213.7586-1.5791-1.76872.2661-0.02364.10410.6119-0.6706-1.3107-3.5428-2.2104-0.8054-0.26633.69230.65692.80390.37560.35943.11360.22271.9789-26.829-67.638972.1522
228.8979-2.1098-0.714.11053.64435.212-1.50762.2526-1.1571-0.64641.76711.98651.16363.16010.47092.5429-0.13440.48052.07380.20772.3664-35.5573-71.259578.6755
232.50273.01472.64185.54264.64594.39382.40531.70045.6296-3.598-4.1739-2.0614-0.55461.93551.03792.92170.27640.27632.740.53222.7911-49.9632-14.003619.1473
244.8993-0.02273.86145.1078-0.73733.2687-1.62783.28495.9523-3.5581-6.7748-1.0959-0.23631.94634.15943.10540.36680.63971.44910.20411.0583-44.6617-20.264226.6861
254.3463.36760.62285.38564.00233.83010.0565-1.99031.9678-0.01560.48130.72873.00821.1114-1.75581.7347-0.19080.07962.4126-0.18681.7991-57.2525-28.057529.6309
263.25910.04492.94034.7135-0.15263.0481.42863.5279-0.4698-2.9335-2.24363.0343.89930.88390.34262.41380.00980.50823.05660.18792.1801-65.2543-28.697922.7159
277.28815.16155.28844.63164.09664.2519-0.37987.23491.5634-7.1087-2.43216.04730.01282.45151.40133.35760.6763-1.32213.5953-0.15364.9024-57.3807-36.104421.6148
286.59735.49563.44575.3641.22424.16181.99213.56514.7438-0.7086-1.96955.1649-0.23872.78720.96421.77840.27-0.32813.0140.36493.4618-46.8896-34.833625.1789
295.0435-2.15834.48335.4757-5.77337.2513.81734.45920.0102-5.65-1.8286-4.7745.15051.1909-0.99862.18970.5248-0.16822.45940.32222.9237-49.1879-26.381920.1747
304.5944-0.827-3.7692.20985.5585.19331.2245-0.4253-0.58010.826-1.41972.05021.4591-0.5930.98483.27150.31160.41212.7229-0.02132.0355-60.1424-18.798122.4705
316.1491-5.73221.36196.7052-0.52833.381-0.7573-2.34050.66452.15170.5431-1.2399-3.3858-1.71470.47832.69780.02260.01622.45780.04162.1138-52.0867-13.298732.1055
322.88161.0480.99932.48121.17571.4192-1.76394.2243-2.7549-1.4097-0.9509-4.21381.01960.62632.11732.2034-0.23230.52773.1327-0.02522.7829-13.7726-39.796924.2755
334.14352.86162.26856.08610.85211.3962-4.54091.6504-1.4018-1.9423-0.5121-7.10491.20373.52790.72181.6687-0.5811-0.07923.33330.061.0116-20.8712-43.862131.826
348.4799-1.3664-6.21752.40651.69215.20110.0317-1.3509-0.15012.42451.0145-0.6233-0.8222-4.0556-1.14672.2371-0.1657-0.19691.75720.21341.8712-26.3005-30.051234.7797
355.99145.66565.6896.70815.84415.6763-0.51883.9862.7285-1.7134-0.82830.48450.0641.7909-0.25322.9339-0.22230.11182.7191-0.11931.7813-25.4647-22.062227.8794
362.2796-6.5315.52917.81510.1183.48741.2687.38631.7085-1.25890.5682-2.30190.9438-2.1316-0.36923.5426-0.03860.36212.26051.24474.0323-34.2168-28.535626.8694
372.7121-3.2904-1.00924.47971.43670.4881-3.33762.84632.26791.75264.5377-1.12964.2123-3.0344-1.26424.7855-1.2190.36182.92871.33243.6801-34.8646-39.138430.4373
383.84990.51380.66724.0625-2.13393.14710.24234.6076-2.8633-2.24222.10954.53530.8305-6.6607-2.4462.769-0.74510.25042.96850.6123.4398-26.1046-38.318325.3511
394.5689-2.07923.85016.2379-1.69733.5227-2.29862.2445-0.0025-4.06232.35252.88830.49574.3875-0.83972.1568-0.3637-0.00143.20660.00172.1039-19.9992-29.350919.1209
403.0617-3.2209-0.39973.18641.56012.7819-0.5674-0.92921.09846.46570.2831-2.676-2.80971.05540.26922.9449-0.1588-0.10963.11550.27642.0143-15.5129-28.755630.7475
413.24470.7369-2.33352.7959-1.53443.24450.6425-1.7846-0.30550.6252-0.1219-2.3568-3.21154.21730.44812.820.21190.40772.57120.19292.157-12.6746-37.817237.2925
421.88511.73891.25681.87432.17891.9648-1.54231.2017-2.1327-5.6072-0.94761.93-2.02331.00652.43583.4594-0.08740.26291.7682-0.14232.1633-45.8073-70.599229.4734
436.8351-8.1002-5.36442.00966.42144.4429-0.70380.3676-3.446-1.8816-4.2615-0.9316-2.43343.79220.62483.1922-0.48930.11951.42150.73311.7484-48.4542-62.889337.0816
444.2452-0.5481-3.37034.45252.50534.5827-0.5147-0.542-2.21651.68731.6967-0.1408-3.13811.4562-1.24171.61310.08650.352.45310.55841.769-33.9068-60.102540.0054
454.17585.64741.33428.3151.30720.4055-2.43690.0044-0.44280.0379-1.759-8.25392.7639-0.61892.12182.91770.72950.01982.75860.02242.0516-26.2213-62.4133.0667
462.04233.15512.48114.4423-0.53071.0063.66250.1077-0.5037-4.66261.6185-3.7693-3.0172-2.381-2.0062.04450.26141.5973.30150.5234.1712-30.9839-52.64332.0416
476.8149-1.0371-0.8110.3232-0.46756.90673.17712.6243-0.9824-3.27753.4356-8.0883-3.38610.7425-1.77650.13922.49981.37634.3266-0.24574.5999-41.2705-50.00835.6006
485.1479-3.4807-2.9865.63757.03048.9455-0.53972.08043.1368-4.23511.03112.5864-7.44182.3563-0.68882.90610.21570.61161.75390.30712.6569-42.0418-58.789530.5325
497.0546-0.94035.66293.1781-1.69884.8307-0.91331.93042.2446-0.6540.725-1.78795.18930.54681.52522.89710.20710.75151.97440.35232.3333-34.3895-66.457924.3301
503.1092-1.6854-4.8192.61812.66039.6231-0.4277-4.1068-2.89721.37940.6762-0.8585-0.947-0.30010.9812.8355-0.32940.2083.12510.72652.2978-34.6455-70.924435.9103
513.89471.21362.17464.4544.06215.28742.1150.8268-2.19853.4624-0.78790.88383.69131.73240.40212.9034-0.21330.17052.89410.14562.2259-44.0774-72.011442.4237
523.39294.1769-2.6155.9702-4.66053.4282-0.96251.86840.5149-1.4982.1969-2.61512.30842.1427-0.19232.8469-0.21250.48652.81520.23332.1772-15.4844-31.877460.4511
530.4128-0.13890.72261.9007-3.77282.42980.29744.01842.36840.334-1.7971-8.11792.145-2.39322.14171.8821-0.70780.27063.0415-0.06791.7968-21.2462-37.655668.0522
546.2119-1.78575.28621.90962.73886.27443.12330.73260.72414.94540.3859-0.0673-1.3579-5.4277-1.20582.02880.61120.96861.99220.21042.174-30.266-25.917270.94
554.54640.1051.53096.8815-6.97656.68420.81510.60432.0521.30441.19423.69230.798-1.1107-2.15592.65850.17350.18722.33050.45072.4245-35.3508-22.983163.3777
562.86472.17040.02614.691-3.24675.0248-0.97642.3411-1.6439-3.66772.60190.58781.4673-3.7555-1.33392.7493-0.34410.35732.56210.75142.5904-30.2014-34.723863.0092
577.4103-2.67795.45392.4931-3.29314.7101-0.91611.54461.4428-0.0112-0.36750.7909-2.439-1.51270.90683.112-0.46470.09372.79690.41081.8759-21.283-22.167663.8233
583.9512.5028-0.01194.9457-2.14413.1431.15760.1713-2.19113.4-1.6554-2.0062-1.34030.00710.84272.1131-0.01570.09072.42310.39362.5669-15.0318-29.641773.4766
597.39535.38014.95936.31786.05295.8984-1.33942.5176-2.0938-1.09482.25121.45680.719-2.1728-0.88391.868-0.3219-0.02062.87880.31412.1054-71.4952-41.542470.8309
603.51-1.8199-2.74649.24327.00415.8675-0.49693.56261.15390.1237-2.26385.89880.7435-1.90020.12531.6122-0.20330.80823.11850.25222.6526-64.0742-38.202778.4298
618.34450.9855-2.83638.05363.63583.1372.1766-1.98520.54862.4976-0.2838-0.99343.90466.2346-0.34292.29870.91670.10711.36650.59891.8603-59.8296-52.382881.3345
627.39851.15485.84013.5482.26735.94321.43231.4699-2.5466-0.44070.1053-3.5648-0.1442.1663-2.10322.7536-0.20750.54172.22420.18172.6115-56.1101-56.950273.7703
637.75622.08465.6463.9264.77547.21760.20374.2095-8.55062.07880.6964-2.2796-4.10997.3453-0.77673.8393-0.92650.73312.5759-0.49953.9399-50.5718-44.142976.9263
645.93733.21225.31615.05851.83465.8393.05914.66942.7792-2.54280.7254-0.34431.23226.5203-0.59222.1391-0.51290.44572.1533-0.15882.5795-59.3564-44.189271.8773
651.9306-1.8126-0.97383.2934-2.55122.13290.30622.1021-5.13170.2919-2.7592-3.2313.06472.18382.78111.2698-0.61580.91863.2566-0.12212.0984-66.2886-52.527165.6794
663.98490.89443.95793.26863.72895.139-0.71370.48770.8335-0.23980.16910.97621.52090.10190.73692.4555-0.21480.3212.12940.17762.0014-71.6845-48.253880.4671
675.2844-2.39342.32515.29323.66456.7627-0.55981.7401-1.6889-1.0971.05913.2677-0.9741-1.37990.84032.2081-0.44170.24842.39220.00442.4624-64.1991-61.007650.1041
685.90175.29590.8754.8080.09812.4704-3.79910.1249-7.24690.10910.22953.72482.1331.20460.90782.4813-0.18740.23323.03480.1451.8939-60.955-53.482257.7039
697.5447-4.7817-5.72113.61713.92075.5124-2.85840.5472-1.64984.53223.05641.2471-2.75872.9123-0.27962.49820.58390.57511.60490.53182.0618-48.3437-61.317160.6681
705.6048-3.13542.7714.63031.06284.05581.06711.7606-2.1431.5721-3.1897-5.3498-0.85493.811-1.40242.85020.11060.03922.16580.37972.2285-44.3268-68.193453.7281
714.6116-4.4331.51416.29551.01825.98261.96411.0815-5.9587-5.24342.6056-4.9281-1.42920.2126-0.19342.16030.46231.06032.6001-0.36133.8891-41.1579-57.849552.745
722.1142-2.12817.87032.00832.01543.3549-1.88172.3143-10.5497-2.49014.68230.0399-7.45513.2051-1.22944.40320.64140.67422.8764-0.22073.3618-46.9094-48.954156.2986
735.0698-2.52520.73253.8122.67255.2184-0.45794.06273.0324-3.46772.93552.3253-3.86034.1084-1.75653.0342-0.30890.52381.96740.15423.4249-53.435-54.844751.2128
744.115-4.5472-2.70385.34813.41742.98470.00910.2405-0.2756-2.2758-0.1232-4.07712.083-0.3727-1.33353.7424-0.04170.79752.5168-0.05662.0249-52.9868-65.725744.994
752.11281.23432.10012.6922.27642.4264-0.33061.9685-2.33131.13830.22831.1698-0.88480.20681.85683.2016-0.26980.54122.6376-0.04631.9629-56.222-68.86456.6048
763.54123.82532.27916.84874.89954.33391.42171.3287-1.1580.9488-1.12571.69322.00290.47320.28952.29350.22240.39052.13510.17292.4112-63.9541-63.183863.1151
775.31540.1017-4.24743.58932.34435.4354-0.2032.06271.3746-2.4995-1.2258-3.18920.45473.0941.60882.2922-0.20390.40912.4660.52862.3587-29.233-16.339839.832
782.074910.01070.13221.87575.23624.23081.81511.27445.52730.6158-5.4067-2.02661.05171.0596-0.11212.5536-0.8090.40382.57760.31461.816-29.59-24.538847.4026
792.6507-1.2390.44383.20890.33448.5466-2.5925-1.6134-0.23081.69322.94771.0359-0.1833-2.7993-0.82482.38860.41450.15772.3873-0.02241.8841-46.0418-20.380548.238
805.8619-2.9612-1.24292.63932.87915.213-1.05930.21813.518-8.02420.87816.9711-4.7476-1.52060.03192.44530.4719-1.03053.29590.24254.8974-49.6057-27.651142.3341
811.94790.49910.3872.7933-2.85033.6356-3.2052-2.10734.80860.09461.41484.02136.8086-0.6983-0.18382.57260.65480.05393.30950.67813.7954-41.0113-33.876245.8973
825.3615-3.3713-3.98294.31990.112710.0019-0.37391.1751-2.9896-2.78121.2143-3.96021.3092-2.2182-0.85443.2329-0.1881-0.43551.3380.4322.8381-37.0143-25.981640.8796
832.2153-5.36680.43747.90310.85130.17161.04143.2172-1.2079-4.08630.56733.5688-6.49591.2819-0.65264.8892-0.0435-0.07592.37060.53691.7425-41.3372-15.996434.6634
846.7605-6.70415.12828.8344-6.45794.6315-2.6644-1.57413.45641.3175-2.4051-1.4405-2.8287-2.642.10863.25680.3134-0.05932.88740.15582.0468-39.5507-11.90946.3164
855.13553.1371-4.19454.3644-2.92065.062.15353.06021.02262.6855-0.8652-1.6664-4.8585-1.42320.32682.16770.05770.14282.93990.3272.2938-30.3559-14.404652.9233
864.60633.17514.32622.94733.09573.5777-2.46431.50842.3793-1.3152-0.28060.7585-2.42-0.31010.27972.29830.2288-0.02232.5170.4612.912-70.2078-33.518334.5896
872.6461-1.44341.09642.40111.37272.8423-0.85565.03781.3004-1.5558-0.6342.42680.0823-0.38111.11571.83710.49320.1142.98720.11231.7503-62.0795-32.321242.1949
884.6771.76012.68314.71584.54246.74422.5559-0.7535-1.69272.3191-2.384-1.18893.0613-1.09150.19672.4238-0.43360.17091.96620.40521.6565-63.2046-49.215843.1085
893.18191.31431.24485.79443.37652.3180.9339.3741-4.0796-1.97880.42041.67270.18583.0186-1.12083.82570.3798-0.23192.6528-0.93063.424-55.3336-51.479737.133
903.7276-3.16362.46383.4548-0.98352.67834.77430.1793-3.28110.946-2.8011.7671-2.64217.8221-2.15653.397-0.5797-0.27152.48920.23312.9411-50.8381-41.898140.672
919.3584.54436.78632.0103-7.19181.92590.3884.7256.0564-7.97992.441-0.91912.9865.8968-0.32531.0932-0.4360.19663.7255-0.67823.3217-59.2882-39.439935.6713
921.53953.0886-1.02822.0349-4.36621.418-0.8561.751-2.10742.7204-1.1727-1.23441.9635-4.80720.36042.2221-0.53010.58054.6591-0.63061.7118-68.3065-45.504529.4975
933.4160.0313-3.52573.29391.43684.9647-1.5351-1.46710.94780.8072-1.65413.95942.6047-1.33720.92872.9429-0.39930.58633.1481-0.16442.4934-72.6479-44.417841.1008
945.00121.42954.65723.50261.86686.0032.7454-3.09491.2702-3.3338-1.61411.46391.5825-1.6908-1.3512.635-0.10690.33192.4635-0.05352.1732-71.8594-34.902347.5921
956.6166-1.5314.16134.52562.87395.77162.26363.45372.8284-1.8076-1.59081.72711.35812.02030.54632.7309-0.0120.11012.36120.64832.3902-57.4833-17.216755.3169
965.3185-5.5236-0.3236.5781.10732.4995-1.3017-1.17293.6897-2.85890.99244.11441.89820.013-1.60912.33410.46930.24782.43550.12762.0929-50.6911-21.687762.862
974.0074.92771.48474.2992.11352.28681.60860.6976-1.467-0.99362.1935-0.14964.69-0.3186-2.15292.0048-0.25520.17112.27920.07911.9436-60.5399-32.746965.8515
983.8774-0.18172.68675.48355.24375.52842.33162.3503-3.4082-0.7737-0.94331.1140.8533-2.2416-2.56652.1711-0.12520.0782.32960.06952.4482-62.5533-38.311758.3113
992.03992.0643-2.1682.3448-2.222.40642.4604-0.66381.05911.3314-0.82757.19013.38883.0236-0.99183.2176-0.1792-0.20933.62390.21933.5703-48.6772-36.323861.4258
1002.9874-1.7098-0.33094.5081-4.56567.77560.23042.07742.1142-3.25780.5563-3.2251-0.5091-1.8738-1.10791.86720.414-0.10023.00170.142.8719-53.3071-28.882156.3591
1017.9089-2.05541.93346.15274.41415.0784-0.76830.4556-1.42020.68871.10581.415-1.8313-5.4829-1.92573.28241.1606-0.38764.00160.04512.1053-64.0691-27.336850.1699
1023.50521.39152.81462.6146-0.22552.62161.6566-0.64062.6654-1.015-2.26990.9046-0.3051-0.56120.46882.43390.11550.26013.01160.2171.8321-66.6298-23.641861.7652
1035.3615-4.00530.03015.96172.14183.2663-2.5942-1.34551.6834-1.84881.338-1.31482.0871-2.27840.84922.3353-0.23080.01582.45390.11792.3994-59.7195-17.079868.3035
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON MICROSCOPY1chain 'G' and (resid 1 through 11 )
2ELECTRON MICROSCOPY2chain 'G' and (resid 12 through 16 )
3ELECTRON MICROSCOPY3chain 'G' and (resid 17 through 34 )
4ELECTRON MICROSCOPY4chain 'G' and (resid 35 through 41 )
5ELECTRON MICROSCOPY5chain 'G' and (resid 42 through 46 )
6ELECTRON MICROSCOPY6chain 'G' and (resid 47 through 63 )
7ELECTRON MICROSCOPY7chain 'G' and (resid 64 through 75 )
8ELECTRON MICROSCOPY8chain 'G' and (resid 76 through 85 )
9ELECTRON MICROSCOPY9chain 'L' and (resid 1 through 34 )
10ELECTRON MICROSCOPY10chain 'L' and (resid 35 through 41 )
11ELECTRON MICROSCOPY11chain 'L' and (resid 42 through 46 )
12ELECTRON MICROSCOPY12chain 'L' and (resid 47 through 63 )
13ELECTRON MICROSCOPY13chain 'L' and (resid 64 through 85 )
14ELECTRON MICROSCOPY14chain 'K' and (resid 1 through 11 )
15ELECTRON MICROSCOPY15chain 'K' and (resid 12 through 16 )
16ELECTRON MICROSCOPY16chain 'K' and (resid 17 through 34 )
17ELECTRON MICROSCOPY17chain 'K' and (resid 35 through 41 )
18ELECTRON MICROSCOPY18chain 'K' and (resid 42 through 46 )
19ELECTRON MICROSCOPY19chain 'K' and (resid 47 through 58 )
20ELECTRON MICROSCOPY20chain 'K' and (resid 59 through 63 )
21ELECTRON MICROSCOPY21chain 'K' and (resid 64 through 75 )
22ELECTRON MICROSCOPY22chain 'K' and (resid 76 through 85 )
23ELECTRON MICROSCOPY23chain 'J' and (resid 1 through 11 )
24ELECTRON MICROSCOPY24chain 'J' and (resid 12 through 16 )
25ELECTRON MICROSCOPY25chain 'J' and (resid 17 through 29 )
26ELECTRON MICROSCOPY26chain 'J' and (resid 30 through 34 )
27ELECTRON MICROSCOPY27chain 'J' and (resid 35 through 41 )
28ELECTRON MICROSCOPY28chain 'J' and (resid 42 through 46 )
29ELECTRON MICROSCOPY29chain 'J' and (resid 47 through 58 )
30ELECTRON MICROSCOPY30chain 'J' and (resid 59 through 75 )
31ELECTRON MICROSCOPY31chain 'J' and (resid 76 through 85 )
32ELECTRON MICROSCOPY32chain 'I' and (resid 1 through 11 )
33ELECTRON MICROSCOPY33chain 'I' and (resid 12 through 16 )
34ELECTRON MICROSCOPY34chain 'I' and (resid 17 through 29 )
35ELECTRON MICROSCOPY35chain 'I' and (resid 30 through 34 )
36ELECTRON MICROSCOPY36chain 'I' and (resid 35 through 41 )
37ELECTRON MICROSCOPY37chain 'I' and (resid 42 through 46 )
38ELECTRON MICROSCOPY38chain 'I' and (resid 47 through 58 )
39ELECTRON MICROSCOPY39chain 'I' and (resid 59 through 63 )
40ELECTRON MICROSCOPY40chain 'I' and (resid 64 through 75 )
41ELECTRON MICROSCOPY41chain 'I' and (resid 76 through 85 )
42ELECTRON MICROSCOPY42chain 'H' and (resid 1 through 11 )
43ELECTRON MICROSCOPY43chain 'H' and (resid 12 through 16 )
44ELECTRON MICROSCOPY44chain 'H' and (resid 17 through 29 )
45ELECTRON MICROSCOPY45chain 'H' and (resid 30 through 34 )
46ELECTRON MICROSCOPY46chain 'H' and (resid 35 through 41 )
47ELECTRON MICROSCOPY47chain 'H' and (resid 42 through 46 )
48ELECTRON MICROSCOPY48chain 'H' and (resid 47 through 58 )
49ELECTRON MICROSCOPY49chain 'H' and (resid 59 through 63 )
50ELECTRON MICROSCOPY50chain 'H' and (resid 64 through 75 )
51ELECTRON MICROSCOPY51chain 'H' and (resid 76 through 85 )
52ELECTRON MICROSCOPY52chain 'F' and (resid 1 through 11 )
53ELECTRON MICROSCOPY53chain 'F' and (resid 12 through 16 )
54ELECTRON MICROSCOPY54chain 'F' and (resid 17 through 29 )
55ELECTRON MICROSCOPY55chain 'F' and (resid 30 through 41 )
56ELECTRON MICROSCOPY56chain 'F' and (resid 42 through 58 )
57ELECTRON MICROSCOPY57chain 'F' and (resid 59 through 75 )
58ELECTRON MICROSCOPY58chain 'F' and (resid 76 through 85 )
59ELECTRON MICROSCOPY59chain 'E' and (resid 1 through 11 )
60ELECTRON MICROSCOPY60chain 'E' and (resid 12 through 16 )
61ELECTRON MICROSCOPY61chain 'E' and (resid 17 through 29 )
62ELECTRON MICROSCOPY62chain 'E' and (resid 30 through 41 )
63ELECTRON MICROSCOPY63chain 'E' and (resid 42 through 46 )
64ELECTRON MICROSCOPY64chain 'E' and (resid 47 through 58 )
65ELECTRON MICROSCOPY65chain 'E' and (resid 59 through 63 )
66ELECTRON MICROSCOPY66chain 'E' and (resid 64 through 85 )
67ELECTRON MICROSCOPY67chain 'D' and (resid 1 through 11 )
68ELECTRON MICROSCOPY68chain 'D' and (resid 12 through 16 )
69ELECTRON MICROSCOPY69chain 'D' and (resid 17 through 29 )
70ELECTRON MICROSCOPY70chain 'D' and (resid 30 through 34 )
71ELECTRON MICROSCOPY71chain 'D' and (resid 35 through 41 )
72ELECTRON MICROSCOPY72chain 'D' and (resid 42 through 46 )
73ELECTRON MICROSCOPY73chain 'D' and (resid 47 through 58 )
74ELECTRON MICROSCOPY74chain 'D' and (resid 59 through 63 )
75ELECTRON MICROSCOPY75chain 'D' and (resid 64 through 75 )
76ELECTRON MICROSCOPY76chain 'D' and (resid 76 through 85 )
77ELECTRON MICROSCOPY77chain 'C' and (resid 1 through 11 )
78ELECTRON MICROSCOPY78chain 'C' and (resid 12 through 16 )
79ELECTRON MICROSCOPY79chain 'C' and (resid 17 through 34 )
80ELECTRON MICROSCOPY80chain 'C' and (resid 35 through 41 )
81ELECTRON MICROSCOPY81chain 'C' and (resid 42 through 46 )
82ELECTRON MICROSCOPY82chain 'C' and (resid 47 through 58 )
83ELECTRON MICROSCOPY83chain 'C' and (resid 59 through 63 )
84ELECTRON MICROSCOPY84chain 'C' and (resid 64 through 75 )
85ELECTRON MICROSCOPY85chain 'C' and (resid 76 through 85 )
86ELECTRON MICROSCOPY86chain 'B' and (resid 1 through 11 )
87ELECTRON MICROSCOPY87chain 'B' and (resid 12 through 16 )
88ELECTRON MICROSCOPY88chain 'B' and (resid 17 through 34 )
89ELECTRON MICROSCOPY89chain 'B' and (resid 35 through 41 )
90ELECTRON MICROSCOPY90chain 'B' and (resid 42 through 46 )
91ELECTRON MICROSCOPY91chain 'B' and (resid 47 through 58 )
92ELECTRON MICROSCOPY92chain 'B' and (resid 59 through 63 )
93ELECTRON MICROSCOPY93chain 'B' and (resid 64 through 75 )
94ELECTRON MICROSCOPY94chain 'B' and (resid 76 through 85 )
95ELECTRON MICROSCOPY95chain 'A' and (resid 1 through 11 )
96ELECTRON MICROSCOPY96chain 'A' and (resid 12 through 16 )
97ELECTRON MICROSCOPY97chain 'A' and (resid 17 through 29 )
98ELECTRON MICROSCOPY98chain 'A' and (resid 30 through 41 )
99ELECTRON MICROSCOPY99chain 'A' and (resid 42 through 46 )
100ELECTRON MICROSCOPY100chain 'A' and (resid 47 through 58 )
101ELECTRON MICROSCOPY101chain 'A' and (resid 59 through 63 )
102ELECTRON MICROSCOPY102chain 'A' and (resid 64 through 75 )
103ELECTRON MICROSCOPY103chain 'A' and (resid 76 through 85 )

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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