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- PDB-5dpw: Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 -

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基本情報

登録情報
データベース: PDB / ID: 5dpw
タイトルCrystal structure of PLEKHM1 LIR in complex with human LC3C_8-125
要素
  • Microtubule-associated proteins 1A/1B light chain 3C
  • Pleckstrin homology domain-containing family M member 1
キーワードPROTEIN BINDING / Autophagy
機能・相同性
機能・相同性情報


protein exit from endoplasmic reticulum / late endosome to lysosome transport / aggrephagy / autophagosome-lysosome fusion / autolysosome membrane / lysosome localization / phosphatidylethanolamine binding / positive regulation of ruffle assembly / cellular response to nitrogen starvation / autophagy of mitochondrion ...protein exit from endoplasmic reticulum / late endosome to lysosome transport / aggrephagy / autophagosome-lysosome fusion / autolysosome membrane / lysosome localization / phosphatidylethanolamine binding / positive regulation of ruffle assembly / cellular response to nitrogen starvation / autophagy of mitochondrion / Macroautophagy / organelle membrane / autolysosome / autophagosome membrane / autophagosome maturation / autophagosome assembly / positive regulation of bone resorption / endomembrane system / cellular response to starvation / autophagosome / macroautophagy / cytoplasmic ribonucleoprotein granule / protein transport / late endosome membrane / cytoplasmic vesicle / microtubule / lysosome / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / nucleolus / metal ion binding / cytosol
類似検索 - 分子機能
Microtubule-associated protein 1A/1B light chain 3C / PLEKHM1, PH domain / : / : / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / RUN / RUN domain / RUN domain superfamily ...Microtubule-associated protein 1A/1B light chain 3C / PLEKHM1, PH domain / : / : / Rubicon Homology Domain / Rubicon Homology Domain / DUF4206 / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
Microtubule-associated proteins 1A/1B light chain 3C / Pleckstrin homology domain-containing family M member 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 解像度: 2.185 Å
データ登録者Ravichandran, A.C. / Suzuki, H. / Dobson, R.C.J.
引用ジャーナル: EMBO Rep. / 年: 2017
タイトル: Structural and functional analysis of the GABARAP interaction motif (GIM).
著者: Rogov, V.V. / Stolz, A. / Ravichandran, A.C. / Rios-Szwed, D.O. / Suzuki, H. / Kniss, A. / Lohr, F. / Wakatsuki, S. / Dotsch, V. / Dikic, I. / Dobson, R.C. / McEwan, D.G.
履歴
登録2015年9月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年9月28日Provider: repository / タイプ: Initial release
改定 1.12018年6月20日Group: Data collection / Database references / Derived calculations
カテゴリ: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
改定 1.22024年3月6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

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: Microtubule-associated proteins 1A/1B light chain 3C
B: Pleckstrin homology domain-containing family M member 1
C: Microtubule-associated proteins 1A/1B light chain 3C
D: Pleckstrin homology domain-containing family M member 1
E: Microtubule-associated proteins 1A/1B light chain 3C
F: Pleckstrin homology domain-containing family M member 1
G: Microtubule-associated proteins 1A/1B light chain 3C
H: Pleckstrin homology domain-containing family M member 1
I: Microtubule-associated proteins 1A/1B light chain 3C
J: Pleckstrin homology domain-containing family M member 1
K: Microtubule-associated proteins 1A/1B light chain 3C
L: Pleckstrin homology domain-containing family M member 1
M: Microtubule-associated proteins 1A/1B light chain 3C
N: Pleckstrin homology domain-containing family M member 1
O: Microtubule-associated proteins 1A/1B light chain 3C
P: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)124,43916
ポリマ－124,43916
非ポリマー00
水2,882160
1
A: Microtubule-associated proteins 1A/1B light chain 3C
B: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)15,5552
ポリマ－15,5552
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Microtubule-associated proteins 1A/1B light chain 3C
D: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)15,5552
ポリマ－15,5552
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Microtubule-associated proteins 1A/1B light chain 3C
F: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)15,5552
ポリマ－15,5552
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Microtubule-associated proteins 1A/1B light chain 3C
H: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)15,5552
ポリマ－15,5552
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I: Microtubule-associated proteins 1A/1B light chain 3C
J: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)15,5552
ポリマ－15,5552
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K: Microtubule-associated proteins 1A/1B light chain 3C
L: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)15,5552
ポリマ－15,5552
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
7
M: Microtubule-associated proteins 1A/1B light chain 3C
N: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)15,5552
ポリマ－15,5552
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
O: Microtubule-associated proteins 1A/1B light chain 3C
P: Pleckstrin homology domain-containing family M member 1


分子量 (理論値)分子数
合計 (水以外)15,5552
ポリマ－15,5552
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)54.140, 73.225, 89.048
Angle α, β, γ (deg.)89.96, 89.99, 77.31
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Microtubule-associated proteins 1A/1B light chain 3C / Autophagy-related protein LC3 C / Autophagy-related ubiquitin-like modifier LC3 C / MAP1 light ...Autophagy-related protein LC3 C / Autophagy-related ubiquitin-like modifier LC3 C / MAP1 light chain 3-like protein 3 / MAP1A/MAP1B light chain 3 C / MAP1A/MAP1B LC3 C / Microtubule-associated protein 1 light chain 3 gamma


分子量: 13808.062 Da / 分子数: 8 / 断片: UNP residues 8-125 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MAP1LC3C / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Bl21(de3) / 参照: UniProt: Q9BXW4
#2: タンパク質・ペプチド
Pleckstrin homology domain-containing family M member 1 / PH domain-containing family M member 1 / 162 kDa adapter protein / AP162


分子量: 1746.782 Da / 分子数: 8 / 断片: UNP residues 629-642 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PLEKHM1, KIAA0356 / プラスミド: pET30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Bl21(de3) / 参照: UniProt: Q9Y4G2
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 160 / 由来タイプ: 天然 / 式: H2O

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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: 2.77 Å3/Da / 溶媒含有率: 55.56 %
結晶化温度: 278 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年4月9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: 0.9537 Å / 相対比: 1
反射解像度: 2.185→38.61 Å / Num. obs: 68176 / % possible obs: 98.6 % / 冗長度: 6.6 % / Net I/σ(I): 13.4
反射 シェル解像度: 2.19→2.24 Å / % possible all: 97.8

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
XDSデータ削減
Aimlessデータスケーリング
MOLREP位相決定
精密化解像度: 2.185→38.61 Å / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 30.78 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2457 1423 2.09 %
Rwork0.1996 --
obs0.2006 68171 98.59 %
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
精密化ステップサイクル: LAST / 解像度: 2.185→38.61 Å
タンパク質核酸リガンド溶媒全体
原子数8264 0 0 160 8424
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0048483
X-RAY DIFFRACTIONf_angle_d0.79811459
X-RAY DIFFRACTIONf_dihedral_angle_d17.1313267
X-RAY DIFFRACTIONf_chiral_restr0.031263
X-RAY DIFFRACTIONf_plane_restr0.0041458
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1853-2.26340.30661130.28286684X-RAY DIFFRACTION96
2.2634-2.3540.30831320.28196636X-RAY DIFFRACTION96
2.354-2.46110.28341750.26366596X-RAY DIFFRACTION95
2.4611-2.59080.31651480.25086608X-RAY DIFFRACTION96
2.5908-2.7530.27171390.25336642X-RAY DIFFRACTION96
2.753-2.96530.26841380.2376702X-RAY DIFFRACTION97
2.9653-3.26340.26781290.21966705X-RAY DIFFRACTION97
3.2634-3.73480.26031290.20086685X-RAY DIFFRACTION97
3.7348-4.70230.20321470.14756727X-RAY DIFFRACTION97
4.7023-29.17650.18911430.15036747X-RAY DIFFRACTION98
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)
10.63730.83520.01721.13240.02180.0074-0.0349-0.2417-0.52920.0928-0.14830.07030.47190.03420.08210.6172-0.03030.16210.52520.06280.637413.224-65.734720.4327
20.00740.0886-0.05162.7101-1.64971.0210.1491-0.1520.3052-0.0633-0.0981-0.15-0.2057-0.037-0.02270.3074-0.04720.0950.4209-0.00170.721516.2981-54.739418.7002
34.36920.94312.40465.6708-1.47482.0501-0.2188-0.1375-0.13210.181-0.19030.2640.3194-0.31420.27310.5624-0.0636-0.20750.37240.10551.077511.4687-48.604310.8392
41.44760.6722-0.45191.7164-0.57962.0354-0.0133-0.0640.0096-0.1644-0.2059-0.2035-0.1624-0.03870.06750.3392-0.00390.15370.3567-0.02470.3114.1429-58.133514.6658
53.58661.496-1.76674.0004-1.25770.95760.0908-0.58460.00060.1391-0.05460.12650.0784-0.1976-0.00980.43280.02430.01910.596-0.07510.5498-1.8838-76.95620.4748
61.06050.1892-0.00110.87520.00090.30660.05770.02230.01370.11870.0895-0.4902-0.06570.2117-0.14290.4335-0.0020.15170.4122-0.09340.30292.8405-62.5810.7922
78.43360.95961.36183.06743.2845.7323-0.00890.26210.2241-0.1516-0.05990.0188-0.30180.0905-0.04350.39750.06350.04150.3551-0.02220.1147-7.3766-54.070311.6628
82.3498-0.67520.19172.44040.68252.71580.15340.1962-0.3542-0.04990.04610.16610.5405-0.3913-0.03910.58670.048-0.05510.4558-0.08850.0858-6.6704-68.338.6065
92.01671.01140.83242.77271.33770.90320.5292-0.25660.1560.06310.0004-0.03830.2950.215-0.31140.3776-0.0472-0.01340.471-0.03540.1866-4.8455-63.403622.8817
101.0870.1914-0.01050.4652-0.15511.57280.0828-0.21250.14280.11530.2435-0.04120.1062-0.08740.17950.45380.12970.19460.634-0.08330.0401-3.038-51.894621.1139
112.60180.3561-2.38352.9675-0.20382.5619-0.0965-0.39830.09960.11250.0449-0.23390.00470.3033-0.29610.25610.07460.12910.6116-0.18940.2126.1503-58.038121.2669
122.12640.2826-0.6422.4188-0.66284.88610.0418-0.14830.05060.1487-0.004-0.0175-0.0660.0666-0.00350.5361-0.05150.0380.51750.00110.0147-5.3877-71.270123.7718
132.87642.13450.64753.33920.28921.6068-0.05650.0114-0.0978-0.08340.1417-0.12170.21870.2731-0.02530.367-0.02810.05140.5471-0.07620.46545.7974-99.34219.9221
140.79930.7704-1.19131.8365-0.80961.8915-0.0148-0.00970.284-0.34330.0538-0.0352-0.24440.0621-0.01170.4041-0.09250.12310.382-0.02031.06785.3186-87.296513.9243
151.03770.2666-0.30282.5177-1.31651.61420.03280.25180.1655-0.19-0.1306-0.2951-0.2427-0.06560.00310.36670.04810.220.37960.01320.5044-4.3595-93.653113.6006
162.67050.81391.33191.88670.99380.89690.039-0.2898-0.0007-0.16280.1682-0.2363-0.0048-0.0119-0.13870.49990.08870.12090.4236-0.14320.6549-9.5593-110.91516.2325
172.26590.2450.66813.9028-0.48242.1710.34150.2938-0.17150.08280.1839-0.1139-0.11270.0583-0.42330.3963-0.0507-0.0240.44030.03780.6173-3.9884-94.3339.212
182.5504-2.28020.4032.7170.23122.66830.0879-0.11120.0987-0.11260.12830.0188-0.00880.2092-0.06350.32040.05040.22840.31990.04850.6031-14.6214-93.30619.7098
190.88460.24390.94291.24561.25671.8487-0.0991-0.03950.01260.11470.2120.35080.2919-0.313-0.02340.6377-0.01520.18120.5088-0.01390.4705-13.2503-106.61225.7411
204.7226-1.28561.36624.4040.35853.7956-0.01560.47710.1345-0.4915-0.04370.1717-0.2293-0.05130.0550.8255-0.1788-0.00621.1009-0.04651.3189-20.9944-108.31499.1236
212.72990.83920.33472.35210.80632.27260.2442-0.07710.05630.2938-0.1180.0270.06660.0267-0.18780.3033-0.01370.14210.4031-0.07060.5612-13.9956-98.450821.275
220.8908-0.49860.32170.3922-0.71152.57930.4147-0.5270.12340.04430.30980.1594-0.1021-0.0795-0.38950.37520.00160.19480.36570.02330.8517-12.9225-86.959218.4807
234.21680.9363-0.97844.6059-0.55352.25380.0998-0.53830.21730.2841-0.1555-0.1298-0.12580.1278-0.02330.2588-0.0350.17320.4744-0.11570.4598-2.5148-92.407620.6669
243.78091.4603-1.41373.3202-1.74896.66940.1954-0.35460.0430.4113-0.03770.1259-0.09690.0064-0.07280.6605-0.1040.32330.3536-0.08540.6676-13.8735-106.726722.8393
255.2543-1.4424-2.73871.16460.87465.02910.0572-0.13570.10340.06970.00740.0926-0.17320.0153-0.12790.6348-0.06590.4570.4252-0.04880.6385-26.7414-66.262940.7715
261.54510.97471.64952.06551.30174.0449-0.05480.1013-0.032-0.140.26740.09660.4491-0.2462-0.06460.4783-0.04830.13350.4689-0.04240.2134-30.9079-78.375239.0262
271.74120.5320.45543.490.65691.85950.10980.2865-0.0756-0.0852-0.08130.16830.2214-0.1057-0.0480.3463-0.05720.10340.4184-0.00620.2193-29.6881-75.435228.7332
280.06860.3002-0.60341.3987-2.87275.9233-0.064-0.23940.41050.27740.3091-0.0998-0.25450.1593-0.14651.0875-0.19860.08210.426-0.05530.4777-17.5445-55.361731.411
290.65890.99010.2013.4636-0.67870.5376-0.0593-0.22530.03680.1249-0.0690.2776-0.0895-0.1228-0.06140.5355-0.02990.33190.3599-0.06550.6128-29.4366-61.875628.7525
302.4658-1.3067-1.46471.49170.55872.58750.1081-0.1338-0.0971-0.3261-0.01550.02960.25930.0874-0.14490.30770.02050.05640.33720.03050.3141-26.2454-76.410321.5019
311.0267-0.8136-0.35111.38620.20760.83780.02140.13030.0604-0.08930.0599-0.02980.0533-0.11110.02390.39360.10450.1770.40020.02580.2264-25.5582-66.661118.9948
322.41230.7773-2.26980.2542-0.72862.13920.03020.08790.3617-0.10310.0994-0.3953-0.29060.2279-0.09110.5479-0.06920.12690.58380.1260.8538-23.2088-54.934417.7267
330.93720.3856-0.99751.1754-1.35413.00130.03590.09740.12450.01270.1076-0.0186-0.01450.12960.05780.3550.00890.1880.6072-0.10120.1701-16.3265-66.25426.1423
343.1541.43392.38743.71781.3567.8162-0.0268-0.34160.34860.1317-0.11150.2561-0.1376-0.33480.1520.5007-0.09640.09680.48530.08080.3094-12.8464-70.731326.282
350.06210.0254-0.22250.02410.02243.33-0.094-0.1275-0.02960.0210.0039-0.04790.24760.0863-0.02180.53510.03430.01740.4145-0.12730.139-18.4341-79.819526.775
360.53890.0461-0.16650.77660.26210.6460.0828-0.08190.2630.16160.1865-0.1259-0.03330.1761-0.01610.386-0.11490.23110.5487-0.12520.1577-18.0617-67.611731.6348
373.85311.52770.05091.56612.18585.00280.0277-0.17460.4330.1251-0.0465-0.1604-0.41620.10390.01520.6119-0.02370.18920.4218-0.06590.3957-34.404-101.075239.6693
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512.3650.9049-0.52182.6239-0.32311.19250.14890.0180.15150.33060.1579-0.28510.09180.0504-0.04460.48770.022-0.29980.2560.08380.6741-2.9076-70.8998-15.1231
526.15884.43234.62168.50180.60515.32830.0609-0.6740.08330.6329-0.1270.46060.1757-0.40520.02270.52480.0930.06730.3653-0.07090.5308-11.5734-89.5473-16.6238
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551.1512-0.0943-0.1322.4027-0.2611.27330.45780.2507-0.393-0.06330.107-0.01050.3356-0.1774-0.38910.42750.0148-0.06880.33620.01650.6751-5.1115-84.0219-25.7178
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602.57310.4271-0.68362.3780.47472.32470.2195-0.1786-0.18170.27260.09020.59030.1056-0.0962-0.1460.3802-0.0578-0.14680.28230.0780.666-17.7344-83.1645-16.0825
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621.32450.3727-0.02210.98560.05373.1387-0.1377-0.00450.005-0.11210.03920.06350.162-0.0128-0.19730.632-0.0884-0.21070.4807-0.05980.2097-7.9881-104.392-4.1641
635.16382.79280.73453.0020.89232.6072-0.0379-0.05360.1455-0.14720.07740.1033-0.1649-0.05740.04311.0053-0.2777-0.40780.45920.09880.6785-2.4612-97.0154-14.0556
641.64310.30020.05450.4492-0.0160.00540.20210.4088-0.0394-0.4235-0.04710.29310.0126-0.1873-0.09140.662-0.0874-0.20710.34180.13060.7161-4.3217-96.5675-19.8711
651.61621.8707-0.6713.9-1.41411.33460.0764-0.2741-0.35660.19410.03820.02190.1282-0.1228-0.01040.47080.0407-0.17650.29680.04450.4685-14.7442-112.5255-14.2712
662.7007-0.42860.40533.60270.27982.56460.1933-0.1371-0.1410.04760.22150.02970.3937-0.0489-0.05910.56560.017-0.32210.36920.17020.9089-13.8139-121.4715-16.6177
671.9011-0.17530.52491.7482-0.10221.9804-0.11970.16120.3276-0.4385-0.061-0.0272-0.22430.15920.08710.5524-0.0438-0.18280.34820.04650.2925-12.0817-106.9669-24.7867
684.14370.8857-0.24624.0857-0.75122.52110.09580.3258-0.3236-0.39240.06580.1455-0.0317-0.4613-0.10610.5017-0.0572-0.06130.4573-0.02771.1279-11.8523-122.5751-26.6491
691.8057-0.61190.02562.14490.0271.5396-0.1034-0.2019-0.30790.16780.21520.1826-0.0054-0.27150.07160.3161-0.0615-0.17830.3498-0.0010.6202-22.3234-113.1422-19.5596
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712.95551.84722.12673.44490.42181.9013-0.0689-0.31150.10450.3901-0.1230.2438-0.2274-0.09610.10380.6004-0.0316-0.24290.3167-0.02850.6307-15.2685-104.0193-10.5917
722.288-1.0583-1.51380.55640.46911.77510.3269-0.15730.01540.26780.34330.08460.0367-0.0523-0.40010.3844-0.0313-0.15120.26610.11460.8866-24.0096-118.3926-17.1405
733.99491.0892-0.33721.91652.26164.05-0.291-0.21340.16370.1047-0.0862-0.0079-0.44890.01850.20680.3909-0.0114-0.07640.4289-0.12670.5757-41.9084-76.7664-24.6608
742.64642.7299-0.83336.0781-0.83480.47820.0451-0.04230.1998-0.0873-0.2071-0.0398-0.04140.07260.1230.30770.0924-0.03620.5729-0.18430.8134-46.7588-81.3011-23.7113
750.52330.1949-0.36852.35942.73583.8787-0.0442-0.2041-0.1358-0.18460.02350.1136-0.0307-0.07840.01540.37340.0329-0.03910.3924-0.06410.988-44.4589-90.6561-28.4321
760.74010.42170.27793.79191.68411.83320.14180.1506-0.0165-0.123-0.11820.16260.1703-0.2268-0.02940.43080.0061-0.17250.31390.04760.752-35.4438-85.6751-30.3791
772.62.52031.41613.82261.12150.8289-0.2699-0.06410.1042-0.5254-0.15230.262-0.16910.01380.29470.44680.0416-0.07040.28270.04660.6551-31.2938-70.3368-30.0683
783.285-0.35440.95992.4667-0.82792.3728-0.20890.1674-0.3436-0.1406-0.0299-0.02860.2672-0.02650.14360.4449-0.0860.07790.3278-0.03280.3964-31.9869-89.8926-33.9296
793.8518-2.12760.18912.1951-0.09684.50860.2684-0.0504-0.2284-0.54640.0455-0.5162-0.12780.263-0.17610.31150.0110.05060.3267-0.13560.6216-23.6406-83.6984-33.8017
801.0918-1.19810.06211.3245-0.19571.7524-0.0845-0.14380.20450.0151-0.0955-0.3213-0.06630.17370.04690.5545-0.01490.08950.37140.00850.5257-24.9453-71.5753-38.0362
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823.09560.29730.34931.1060.7771.883-0.0791-0.04040.09120.02260.0210.1538-0.1069-0.13140.06260.3238-0.075-0.28530.28840.10690.947-24.9695-82.8721-20.8805
831.2546-1.1308-0.74981.43771.18392.11510.2103-0.1733-0.24550.05420.2286-0.2420.1445-0.1703-0.21110.42940.0042-0.21150.33630.12930.8911-27.6535-92.5363-24.0069
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871.06970.2950.01022.79440.92741.47880.1860.1362-0.09750.0268-0.0862-0.04230.1607-0.1402-0.09090.3547-0.0101-0.1480.31330.05940.4106-27.0086-50.1047-31.3729
882.87321.4729-0.0443.6672-1.16923.27880.006-0.0740.0432-0.1804-0.2009-0.0476-0.0007-0.06080.0880.6981-0.05260.03160.37570.21751.0865-20.213-31.1099-27.2349
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911.1250.7885-0.63311.6161-1.04272.64430.12830.19650.09090.0551-0.0284-0.0914-0.02350.1238-0.00450.5582-0.00380.17050.4305-0.00080.1827-18.3463-39.6586-38.4155
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962.29890.89640.19111.6977-0.33830.148-0.0718-0.02180.22670.44020.2762-0.2265-0.18-0.0138-0.14260.37360.0695-0.09090.2460.00040.4772-16.0601-36.7074-22.3057
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:8)
2X-RAY DIFFRACTION2(chain A and resid 9:18)
3X-RAY DIFFRACTION3(chain A and resid 19:22)
4X-RAY DIFFRACTION4(chain A and resid 23:34)
5X-RAY DIFFRACTION5(chain A and resid 35:39)
6X-RAY DIFFRACTION6(chain A and resid 40:52)
7X-RAY DIFFRACTION7(chain A and resid 53:58)
8X-RAY DIFFRACTION8(chain A and resid 59:74)
9X-RAY DIFFRACTION9(chain A and resid 75:85)
10X-RAY DIFFRACTION10(chain A and resid 86:100)
11X-RAY DIFFRACTION11(chain A and resid 101:108)
12X-RAY DIFFRACTION12(chain A and resid 109:115)
13X-RAY DIFFRACTION13(chain C and resid 1:11)
14X-RAY DIFFRACTION14(chain C and resid 12:22)
15X-RAY DIFFRACTION15(chain C and resid 23:34)
16X-RAY DIFFRACTION16(chain C and resid 35:43)
17X-RAY DIFFRACTION17(chain C and resid 44:52)
18X-RAY DIFFRACTION18(chain C and resid 53:63)
19X-RAY DIFFRACTION19(chain C and resid 64:70)
20X-RAY DIFFRACTION20(chain C and resid 71:74)
21X-RAY DIFFRACTION21(chain C and resid 75:86)
22X-RAY DIFFRACTION22(chain C and resid 87:98)
23X-RAY DIFFRACTION23(chain C and resid 99:108)
24X-RAY DIFFRACTION24(chain C and resid 109:115)
25X-RAY DIFFRACTION25(chain E and resid 1:7)
26X-RAY DIFFRACTION26(chain E and resid 8:20)
27X-RAY DIFFRACTION27(chain E and resid 21:33)
28X-RAY DIFFRACTION28(chain E and resid 34:39)
29X-RAY DIFFRACTION29(chain E and resid 40:47)
30X-RAY DIFFRACTION30(chain E and resid 48:56)
31X-RAY DIFFRACTION31(chain E and resid 57:66)
32X-RAY DIFFRACTION32(chain E and resid 67:74)
33X-RAY DIFFRACTION33(chain E and resid 75:80)
34X-RAY DIFFRACTION34(chain E and resid 81:87)
35X-RAY DIFFRACTION35(chain E and resid 88:100)
36X-RAY DIFFRACTION36(chain E and resid 101:115)
37X-RAY DIFFRACTION37(chain G and resid 1:6)
38X-RAY DIFFRACTION38(chain G and resid 7:18)
39X-RAY DIFFRACTION39(chain G and resid 19:23)
40X-RAY DIFFRACTION40(chain G and resid 24:36)
41X-RAY DIFFRACTION41(chain G and resid 37:45)
42X-RAY DIFFRACTION42(chain G and resid 46:56)
43X-RAY DIFFRACTION43(chain G and resid 57:71)
44X-RAY DIFFRACTION44(chain G and resid 72:75)
45X-RAY DIFFRACTION45(chain G and resid 76:80)
46X-RAY DIFFRACTION46(chain G and resid 81:95)
47X-RAY DIFFRACTION47(chain G and resid 96:100)
48X-RAY DIFFRACTION48(chain G and resid 101:115)
49X-RAY DIFFRACTION49(chain I and resid 1:6)
50X-RAY DIFFRACTION50(chain I and resid 7:21)
51X-RAY DIFFRACTION51(chain I and resid 22:35)
52X-RAY DIFFRACTION52(chain I and resid 36:41)
53X-RAY DIFFRACTION53(chain I and resid 42:46)
54X-RAY DIFFRACTION54(chain I and resid 47:59)
55X-RAY DIFFRACTION55(chain I and resid 60:73)
56X-RAY DIFFRACTION56(chain I and resid 74:83)
57X-RAY DIFFRACTION57(chain I and resid 84:94)
58X-RAY DIFFRACTION58(chain I and resid 95:101)
59X-RAY DIFFRACTION59(chain I and resid 102:108)
60X-RAY DIFFRACTION60(chain I and resid 109:115)
61X-RAY DIFFRACTION61(chain K and resid 1:4)
62X-RAY DIFFRACTION62(chain K and resid 5:18)
63X-RAY DIFFRACTION63(chain K and resid 19:22)
64X-RAY DIFFRACTION64(chain K and resid 23:26)
65X-RAY DIFFRACTION65(chain K and resid 27:35)
66X-RAY DIFFRACTION66(chain K and resid 36:46)
67X-RAY DIFFRACTION67(chain K and resid 47:64)
68X-RAY DIFFRACTION68(chain K and resid 65:72)
69X-RAY DIFFRACTION69(chain K and resid 73:85)
70X-RAY DIFFRACTION70(chain K and resid 86:99)
71X-RAY DIFFRACTION71(chain K and resid 100:107)
72X-RAY DIFFRACTION72(chain K and resid 108:115)
73X-RAY DIFFRACTION73(chain M and resid 1:4)
74X-RAY DIFFRACTION74(chain M and resid 5:11)
75X-RAY DIFFRACTION75(chain M and resid 12:20)
76X-RAY DIFFRACTION76(chain M and resid 21:35)
77X-RAY DIFFRACTION77(chain M and resid 36:46)
78X-RAY DIFFRACTION78(chain M and resid 47:53)
79X-RAY DIFFRACTION79(chain M and resid 54:64)
80X-RAY DIFFRACTION80(chain M and resid 65:71)
81X-RAY DIFFRACTION81(chain M and resid 72:77)
82X-RAY DIFFRACTION82(chain M and resid 78:87)
83X-RAY DIFFRACTION83(chain M and resid 88:99)
84X-RAY DIFFRACTION84(chain M and resid 100:115)
85X-RAY DIFFRACTION85(chain O and resid 1:6)
86X-RAY DIFFRACTION86(chain O and resid 7:20)
87X-RAY DIFFRACTION87(chain O and resid 21:35)
88X-RAY DIFFRACTION88(chain O and resid 36:41)
89X-RAY DIFFRACTION89(chain O and resid 42:54)
90X-RAY DIFFRACTION90(chain O and resid 55:61)
91X-RAY DIFFRACTION91(chain O and resid 62:69)
92X-RAY DIFFRACTION92(chain O and resid 70:77)
93X-RAY DIFFRACTION93(chain O and resid 78:94)
94X-RAY DIFFRACTION94(chain O and resid 95:99)
95X-RAY DIFFRACTION95(chain O and resid 100:108)
96X-RAY DIFFRACTION96(chain O and resid 109:115)

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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

-
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

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