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- PDB-4llo: Structure of the eag domain-CNBHD complex of the mouse EAG1 channel -

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基本情報

登録情報
データベース: PDB / ID: 4llo
タイトルStructure of the eag domain-CNBHD complex of the mouse EAG1 channel
要素(Potassium voltage-gated channel subfamily H member 1) x 2
キーワードTRANSPORT PROTEIN / Voltage-gated potassium channel
機能・相同性
機能・相同性情報


Voltage gated Potassium channels / regulation of presynaptic cytosolic calcium ion concentration / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / nuclear inner membrane / phosphatidylinositol bisphosphate binding / regulation of synaptic vesicle exocytosis / parallel fiber to Purkinje cell synapse / voltage-gated potassium channel complex / potassium ion transmembrane transport ...Voltage gated Potassium channels / regulation of presynaptic cytosolic calcium ion concentration / delayed rectifier potassium channel activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / nuclear inner membrane / phosphatidylinositol bisphosphate binding / regulation of synaptic vesicle exocytosis / parallel fiber to Purkinje cell synapse / voltage-gated potassium channel complex / potassium ion transmembrane transport / cellular response to calcium ion / postsynaptic density membrane / regulation of cell population proliferation / presynaptic membrane / early endosome membrane / perikaryon / calmodulin binding / axon / dendrite / plasma membrane
類似検索 - 分子機能
Potassium channel, voltage-dependent, EAG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain ...Potassium channel, voltage-dependent, EAG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / Beta-Lactamase / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Voltage-gated delayed rectifier potassium channel KCNH1
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.995 Å
データ登録者Haitin, Y. / Carlson, A.E. / Zagotta, W.N.
引用ジャーナル: Nature / : 2013
タイトル: The structural mechanism of KCNH-channel regulation by the eag domain.
著者: Haitin, Y. / Carlson, A.E. / Zagotta, W.N.
履歴
登録2013年7月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年8月28日Provider: repository / タイプ: Initial release
改定 1.12013年9月25日Group: Database references
改定 1.22023年9月20日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
改定 1.32024年10月9日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Potassium voltage-gated channel subfamily H member 1
B: Potassium voltage-gated channel subfamily H member 1
C: Potassium voltage-gated channel subfamily H member 1
D: Potassium voltage-gated channel subfamily H member 1
E: Potassium voltage-gated channel subfamily H member 1
F: Potassium voltage-gated channel subfamily H member 1
G: Potassium voltage-gated channel subfamily H member 1
H: Potassium voltage-gated channel subfamily H member 1


分子量 (理論値)分子数
合計 (水以外)142,5928
ポリマ-142,5928
非ポリマー00
18,3391018
1
A: Potassium voltage-gated channel subfamily H member 1
B: Potassium voltage-gated channel subfamily H member 1


分子量 (理論値)分子数
合計 (水以外)35,6482
ポリマ-35,6482
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10 kcal/mol
Surface area14610 Å2
手法PISA
2
C: Potassium voltage-gated channel subfamily H member 1
D: Potassium voltage-gated channel subfamily H member 1


分子量 (理論値)分子数
合計 (水以外)35,6482
ポリマ-35,6482
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area13850 Å2
手法PISA
3
E: Potassium voltage-gated channel subfamily H member 1
F: Potassium voltage-gated channel subfamily H member 1


分子量 (理論値)分子数
合計 (水以外)35,6482
ポリマ-35,6482
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9 kcal/mol
Surface area14570 Å2
手法PISA
4
G: Potassium voltage-gated channel subfamily H member 1
H: Potassium voltage-gated channel subfamily H member 1


分子量 (理論値)分子数
合計 (水以外)35,6482
ポリマ-35,6482
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-9 kcal/mol
Surface area13820 Å2
手法PISA
単位格子
Length a, b, c (Å)162.380, 162.380, 100.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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要素

#1: タンパク質
Potassium voltage-gated channel subfamily H member 1 / Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel ...Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel subunit Kv10.1


分子量: 20130.373 Da / 分子数: 4
断片: mEAG1 cyclic nucleotide-binding homology domain (unp residues 552-724)
由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Eag, Kcnh1 / プラスミド: pETM11 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL-21 (DE3) / 参照: UniProt: Q60603
#2: タンパク質
Potassium voltage-gated channel subfamily H member 1 / Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel ...Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel subunit Kv10.1


分子量: 15517.721 Da / 分子数: 4 / 断片: mEAG1 eag domain (unp residues 6-136) / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Eag, Kcnh1 / プラスミド: pETM11 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL-21 (DE3) / 参照: UniProt: Q60603
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1018 / 由来タイプ: 天然 / : H2O
Has protein modificationY

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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: 2.68 Å3/Da / 溶媒含有率: 54.12 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 18% (w/v) PEG 3350, 1.8% (v/v) Tacsimate, 0.01M MnCl2 and 0.09M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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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: ALS / ビームライン: 8.2.1 / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2012年9月24日
放射モノクロメーター: Double crystal, Si(111) / 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: 1 Å / 相対比: 1
反射解像度: 1.995→42.71 Å / Num. all: 102374 / Num. obs: 102374 / % possible obs: 100 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / 冗長度: 11.8 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.5
反射 シェル解像度: 2→2.1 Å / 冗長度: 9.4 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
BOSデータ収集
PHASER位相決定
PHENIX(phenix.refine: dev_1269)精密化
MOSFLMデータ削減
SCALAデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 4F8A
解像度: 1.995→42.71 Å / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 2.7 / 位相誤差: 19.74 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.1974 5113 5 %Random
Rwork0.1669 ---
obs0.1684 102309 99.97 %-
all-102374 --
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 41.6 Å2
精密化ステップサイクル: LAST / 解像度: 1.995→42.71 Å
タンパク質核酸リガンド溶媒全体
原子数8871 0 0 1018 9889
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.0079057
X-RAY DIFFRACTIONf_angle_d1.04312256
X-RAY DIFFRACTIONf_dihedral_angle_d12.6193186
X-RAY DIFFRACTIONf_chiral_restr0.0771402
X-RAY DIFFRACTIONf_plane_restr0.0031559
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.995-2.01770.27641760.24183223X-RAY DIFFRACTION100
2.0177-2.04140.24771720.23153217X-RAY DIFFRACTION100
2.0414-2.06630.28481880.21373202X-RAY DIFFRACTION100
2.0663-2.09250.25841600.2033253X-RAY DIFFRACTION100
2.0925-2.120.21541590.19363227X-RAY DIFFRACTION100
2.12-2.1490.23131760.18813229X-RAY DIFFRACTION100
2.149-2.17970.21861620.18563238X-RAY DIFFRACTION100
2.1797-2.21230.23141720.18113199X-RAY DIFFRACTION100
2.2123-2.24680.22971600.18813278X-RAY DIFFRACTION100
2.2468-2.28370.24411630.1923237X-RAY DIFFRACTION100
2.2837-2.3230.19112020.17083187X-RAY DIFFRACTION100
2.323-2.36530.18741770.17213191X-RAY DIFFRACTION100
2.3653-2.41080.20751700.17333262X-RAY DIFFRACTION100
2.4108-2.460.2131750.17823215X-RAY DIFFRACTION100
2.46-2.51350.21421710.17613243X-RAY DIFFRACTION100
2.5135-2.57190.20641730.17933219X-RAY DIFFRACTION100
2.5719-2.63620.24561700.18393234X-RAY DIFFRACTION100
2.6362-2.70750.22181540.18083245X-RAY DIFFRACTION100
2.7075-2.78720.19471620.17673270X-RAY DIFFRACTION100
2.7872-2.87710.21521620.16823227X-RAY DIFFRACTION100
2.8771-2.97990.22151830.17153236X-RAY DIFFRACTION100
2.9799-3.09920.21921850.17143198X-RAY DIFFRACTION100
3.0992-3.24020.18511700.16553278X-RAY DIFFRACTION100
3.2402-3.41090.21751570.16193241X-RAY DIFFRACTION100
3.4109-3.62450.16061790.15313225X-RAY DIFFRACTION100
3.6245-3.90420.16781480.14743290X-RAY DIFFRACTION100
3.9042-4.29680.16051600.13433268X-RAY DIFFRACTION100
4.2968-4.91780.171810.12983260X-RAY DIFFRACTION100
4.9178-6.19280.18171750.16613273X-RAY DIFFRACTION100
6.1928-42.71960.19371710.18933331X-RAY DIFFRACTION100
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.0853-1.0141-0.18222.46250.61691.02720.09260.5532-0.0282-0.4080.0292-0.0821-0.13610.0455-0.07890.3132-0.04280.00410.3127-0.01040.2409-37.919840.9985-22.7779
22.6570.52520.72253.9143-0.15581.7819-0.03770.1045-0.2192-0.23630.1960.08340.29290.0429-0.130.1911-0.0087-0.00130.1886-0.02790.1879-41.527133.8862-18.9818
32.83132.0738-0.09432.2020.93542.1063-0.0690.58070.3756-0.84110.31930.0622-0.3767-0.34810.03610.22650.0073-0.01090.10910.10030.2878-53.837251.791-16.6914
42.2216-0.1377-0.86452.33490.45421.4841-0.01580.08740.1579-0.08310.08490.2076-0.0599-0.1933-0.08360.1884-0.0004-0.00770.15540.0390.1749-54.046545.6273-11.3096
51.3994-0.6819-0.2761.8036-0.17261.7857-0.06950.0749-0.05660.03210.11830.3128-0.0165-0.23220.01180.2001-0.0426-0.02320.19960.0330.2898-57.57439.2088-12.3958
68.72750.8496-2.44784.68554.23045.015-0.4016-0.6157-1.1332-0.7499-0.2738-0.57040.89820.26880.2931.1576-0.25370.14180.6004-0.12580.8422-47.460352.39714.4146
70.36080.64171.15321.13722.05153.698-0.90020.63021.2393-1.3713-0.6187-0.932-1.24131.2070.73480.6791-0.22040.01590.83510.29970.8778-42.157444.56959.9297
83.5683-1.68411.67071.48260.15894.5949-0.2402-0.15570.01050.21640.01310.0358-0.7385-0.4148-0.02810.4175-0.06230.0950.21780.08040.2232-59.220247.65556.6794
91.3120.85931.14064.2869-2.3383.98020.2040.301-0.0406-0.554-0.4376-0.81080.26270.91870.22580.3099-0.00970.09270.27170.08140.2573-50.404438.51455.4634
101.5654-1.23370.06824.0621-0.25312.95330.14660.16630.0002-0.0847-0.3544-0.32630.20920.12330.17880.4399-0.01030.06310.2680.00210.277-57.325637.7822.9656
112.281-0.1819-1.95611.9267-2.03727.67440.2403-0.3263-0.27730.2278-0.03780.0832-0.2038-0.2203-0.24230.2557-0.04050.02380.27910.03240.2366-63.907432.889114.84
122.56410.529-0.54478.7419-2.54925.09750.09790.15680.3751-0.16750.15420.7577-0.9983-0.8723-0.19050.3890.08620.07830.3271-0.02320.301-65.927544.108518.7685
131.76240.777-0.1423.3236-0.54561.02580.0881-0.18420.03050.63140.0114-0.5327-0.3117-0.1809-0.07850.4748-0.039-0.01940.2384-0.00710.2088-59.023143.051318.9149
141.68420.0595-0.03750.818-0.93021.1625-0.0135-0.01570.2553-0.8167-0.0129-0.3217-0.38320.23480.13920.5126-0.13760.01920.2104-0.00010.2273-55.220241.758113.7574
151.9972-0.6103-0.83073.554-0.67842.5730.1118-0.14580.40040.1465-0.3174-0.8595-0.34540.18740.19270.403-0.1143-0.01080.27650.0160.3184-51.362142.034614.7267
164.09831.00020.91663.29960.62674.6576-0.00710.6131-0.0006-0.50710.14440.1794-0.35350.1754-0.10050.29820.0094-0.04780.2746-0.02290.3466-61.9227-0.5288-36.3335
172.6989-0.4738-0.75652.480.99331.6724-0.09320.0785-0.145-0.0924-0.05220.2868-0.0278-0.21820.13920.2147-0.0048-0.02450.1699-0.02720.2639-61.91875.8174-30.8086
183.1487-1.5776-2.56217.37390.8362.18440.25040.53740.5637-1.5410.5078-0.5379-0.552-0.0482-0.10680.3792-0.12180.11310.286-0.12740.2202-43.35398.6797-41.7728
191.56431.0012-0.01730.93680.51271.5593-0.0431-00.0248-0.2250.3065-0.5092-0.11540.2526-0.1580.22-0.04430.0690.2181-0.08420.2937-43.76719.4591-31.8581
204.7038-0.6331-2.51192.2575-0.1761.52920.36080.70540.7534-0.7233-0.04140.1656-1.01970.4259-0.2120.6065-0.11380.10590.51530.02240.5179-50.588621.5563-37.5269
212.04410.70430.1692.9136-1.13810.56650.16380.16880.0158-0.41320.0419-0.7101-0.13690.38430.8240.2202-0.04210.13490.2777-0.06980.361-39.2443.008-36.1213
223.9428-0.41220.09432.14690.14482.63850.32150.41710.3421-1.0268-0.21510.0568-0.2112-0.0181-0.04280.32770.0178-0.03940.17210.02230.2102-59.536111.6833-36.6963
233.06710.90930.06670.3926-0.26144.24960.1782-0.0150.08710.0971-0.0870.516-0.57920.2623-0.12470.26740.01690.02670.1655-0.02450.2784-63.967117.5583-26.1386
241.33860.8287-0.02260.5668-0.11230.6848-0.1030.06730.8148-0.2420.3315-0.343-0.23530.09820.04660.2467-0.11360.1020.2293-0.10770.4707-40.828918.4979-31.0211
250.02240.2402-0.12443.3021-0.84460.81410.14080.11730.12-0.2468-0.627-0.79220.21510.4742-0.1460.14210.20120.06851.3341-0.39140.9682-16.481420.5054-29.3482
261.350.0517-1.4091.15620.52715.1356-0.04130.1746-0.53620.54080.3519-0.54070.6058-0.09380.33610.65510.0706-0.36210.272-0.20220.5967-36.18023.7693-17.6607
272.94292.7831-0.9233.39690.27642.62070.2984-0.3842-0.18490.50650.2699-0.5860.21891.2618-0.27590.31680.0296-0.13580.4494-0.29580.5613-32.131112.264-22.4419
281.1386-0.1825-1.32841.51261.14362.26130.3427-0.4075-0.25580.36070.1678-0.20050.83010.4508-0.11320.3793-0.0224-0.14740.18360.01430.3244-41.371812.2556-16.0023
292.3940.69410.43510.4911-0.58952.23170.2004-0.1404-0.15650.12820.4315-0.8742-0.2741.9776-0.24650.3306-0.0472-0.12780.6844-0.41390.6084-28.065417.022-8.0185
302.1104-0.5632-1.51320.5220.40411.11410.452-0.32890.08120.14630.1784-0.63340.59051.1260.68090.49250.2531-0.20410.7132-0.26740.6145-27.22979.9818-8.9101
310.5-0.4175-0.50591.17720.57640.65560.52910.3634-0.2084-0.31830.1717-0.63620.5430.56160.48150.44530.2444-0.140.5896-0.27410.4942-32.7128.3971-12.1095
324.18780.5027-1.38660.68810.49394.12310.5806-0.5346-0.34580.27290.2885-0.09890.71840.2722.66420.62610.3202-0.25020.4149-0.22820.6686-32.12335.7084-13.135
333.3659-0.47920.51192.26070.18971.0932-0.0209-0.48340.06010.43090.19920.07790.2758-0.1287-0.15610.45390.0103-0.01880.3554-0.03350.3055-55.91061.418829.6245
343.20090.57060.5433.2986-0.15141.42930.0194-0.0067-0.10160.1828-0.0127-0.29910.05360.0787-0.05150.2724-0.003-0.0350.2032-0.01820.2132-53.1428.695825.7982
350.71810.00030.32336.05012.74821.82430.329-0.2451-0.12191.1175-0.40130.34190.3247-0.41880.00760.2356-0.06210.07420.29820.03210.2502-74.71356.393123.2405
362.1772-0.48580.66362.5365-0.51831.57530.0758-0.077-0.04980.25050.01280.15670.0908-0.103-0.05890.1962-0.030.03740.20120.00870.1974-69.961410.289817.6528
372.91440.77770.44622.95530.31751.6670.1153-0.45330.3410.4953-0.34390.3575-0.0668-0.16710.15760.3043-0.04710.03360.2531-0.04690.1755-59.696212.988529.563
384.00210.1330.22942.9675-0.50175.04980.3011-0.25880.65810.4432-0.0474-0.1997-0.05770.7481-0.35970.3287-0.05340.01790.2825-0.02330.2621-51.578221.446424.3341
392.103-0.62211.26940.6461-0.57961.68940.02210.30310.370.1662-0.16810.0995-0.14420.02310.07350.2164-0.03320.04120.2581-0.02510.2759-73.982518.222913.7214
403.3256-0.7224-0.16843.59311.85450.96650.00790.0350.5349-0.0239-0.88351.2408-0.3771-1.8522-0.40490.2580.06990.05110.9873-0.14530.4963-92.484518.1045-0.3134
418.18562.55981.76363.3107-1.63652.2854-0.1462-0.17151.7731-1.0164-0.1535-0.6904-1.13710.0025-0.15551.3262-0.17010.03790.457-0.03720.7433-72.73910.9942.8997
420.35290.30080.62010.50610.92291.7088-0.4524-0.6328-1.16780.1259-0.27130.64990.464-0.05570.16990.64680.15630.2740.45380.23260.8076-62.18362.2712-2.7721
432.9282-0.8898-0.1371.1280.17881.956-0.1595-0.0824-0.3989-0.06120.03230.26610.1988-0.2980.17620.1836-0.02780.06990.21120.03980.2299-74.70912.7747-0.3234
445.38321.483-2.45223.5278-0.96563.83810.0721-0.7719-0.11470.3181-0.2074-0.3406-0.09760.7030.06950.2128-0.00710.02810.25020.06380.2463-62.14812.32481.1793
455.10460.9553-0.18041.19220.44662.1091-0.1882-0.3736-0.25430.250.0056-0.0605-0.1586-0.02330.22090.2378-0.05740.03040.278-0.020.2494-66.236517.97723.5482
463.66810.25370.20453.2096-1.08946.9492-0.11990.1490.40280.03090.03250.1137-0.3671-0.30320.10250.19280.00380.0340.16970.01160.2096-66.797226.107-8.4357
476.65644.6664-2.26154.0675-1.42475.33810.00910.28870.9340.07760.14780.8631-0.5966-1.0292-0.36670.16160.04150.04010.3679-0.02890.2585-76.413620.0177-12.515
481.10960.3852-0.14991.9951-0.46611.2167-0.03260.4283-0.3731-0.31930.0822-0.30040.141-0.1556-0.00650.2444-0.05380.06370.2681-0.06080.1794-71.023115.6077-12.4988
492.40981.5434-0.75522.3023-0.93031.24170.2655-0.154-0.22880.5068-0.2861-0.13290.1913-0.05970.09110.2223-0.04830.06420.1573-0.02740.1943-64.537416.5146-8.2694
505.04292.03220.71863.63990.00260.4045-0.2543-0.1435-0.37160.0884-0.19740.37380.3196-0.2528-0.57510.5926-0.39350.20810.4693-0.14590.7252-83.9553-0.5135-1.755
512.01070.6936-0.0291.3894-0.85382.0236-0.18810.1169-0.4931-0.0367-0.0713-0.17070.3604-0.00760.37240.3618-0.01140.07920.2579-0.0040.3327-65.241410.4082-8.0951
523.76950.0613-0.34683.5131-0.01222.52720.1498-0.78090.31510.66730.0125-0.05210.2754-0.0854-0.18960.4003-0.0664-0.02010.4721-0.0410.3206-40.613746.714143.2904
533.7145-2.0147-0.99976.33930.69182.8492-0.0382-0.0577-0.2096-0.5431-0.08190.7406-0.32240.28990.14610.2473-0.0411-0.04030.3482-0.03480.2059-47.217641.021129.8631
548.1467-1.95091.9482.2323-0.17732.4891-0.2109-0.92470.62040.51770.0226-0.0583-0.2512-0.41080.20030.3408-0.09860.01870.2755-0.07840.2293-44.361643.916842.1328
551.0048-0.2733-0.64950.9438-1.30652.98220.5138-0.6125-0.28830.49830.0451-0.01830.5091-0.61721.00450.6033-0.2106-0.29430.42490.07390.2722-35.389527.158648.5414
562.2033-0.16280.1282.4607-0.17581.54360.3582-0.0636-0.38060.4191-0.1064-0.30420.35930.1153-0.21510.3686-0.0256-0.13180.26680.00260.2558-36.315226.715638.6713
572.8713-1.20550.9741.2907-1.37991.5081-0.0181-0.9389-0.54910.56660.26710.27540.3426-0.7802-0.14060.7503-0.1674-0.05930.62180.06650.4722-50.029823.952344.3486
582.04321.7747-0.59811.5403-0.55510.24050.1962-0.4744-0.6781-0.0792-0.1407-0.21670.5513-0.1103-0.08910.364-0.0193-0.15460.23120.09640.3893-28.498427.619643.0019
594.6353-0.720.74912.3321-0.48112.57960.1989-0.6956-0.14670.3894-0.27020.32280.1631-0.27220.10120.3119-0.10320.0310.4209-0.06930.2631-48.395637.169443.361
602.0484-0.20980.35614.1242-0.9456.13450.29340.1675-0.247-0.1854-0.22610.78930.9854-0.9720.00840.2355-0.0524-0.0250.2949-0.02270.2359-55.744336.498532.7171
611.6199-1.98490.44994.0321-1.78891.27190.4658-0.0029-0.910.4794-0.18350.49420.57660.2415-0.27640.4965-0.0267-0.20650.30330.02610.4512-41.255618.536137.9104
620.13880.4975-0.08974.17980.4590.3016-0.1-0.8496-0.57250.28170.0052-0.14181.2160.55770.0851.01080.0836-0.35210.6340.0811.0833-27.64260.043736.9563
631.5447-0.32311.96240.21830.10294.0729-0.01760.2658-0.26030.23090.326-0.70490.05350.59380.02530.4396-0.1223-0.0520.7299-0.34840.6288-27.123324.261724.5732
640.84-0.0252-0.01151.8642-0.29713.68580.24810.0856-0.6656-0.10680.4069-0.65350.78691.1545-0.43190.38510.0505-0.21520.3996-0.21180.5699-31.028216.049929.2299
654.42720.35021.57993.84621.63945.24330.0005-0.4490.20760.4467-0.0389-0.3532-0.2856-0.03330.0630.3605-0.16180.11630.3282-0.04650.3437-34.391327.967419.1933
663.17320.68910.31732.7906-0.32992.88860.48660.2266-0.0888-0.44780.2876-0.1448-0.73170.2664-0.41450.3221-0.12840.05180.3064-0.06490.2543-40.028224.173323.8076
674.9488-0.9004-0.75334.8091-1.37793.0172-0.21790.53540.03960.19421.0934-0.26430.7920.7516-0.55260.27680.0418-0.10760.5062-0.18080.4915-35.169916.020325.7836
681.41840.034-0.40120.5016-0.11960.14740.22970.2064-0.80420.09320.3001-0.01851.22910.9045-0.26930.60240.2429-0.19510.5948-0.23330.5733-31.01659.462815.7215
691.25680.25240.06440.2754-0.42470.87610.157-0.1872-0.54960.11110.3858-0.80480.75891.12430.64490.2280.2974-0.42230.8866-0.50650.7335-25.353813.357216.0315
702.5857-2.35990.51234.60132.84016.10660.00890.0297-0.1654-0.10010.14450.13530.10560.1236-0.18030.2543-0.049-0.05930.4842-0.00760.3711-42.189822.135812.2143
711.14310.14260.21990.5337-0.26820.22620.766-0.5924-0.45290.21460.5698-0.72780.53120.96741.98950.15820.0958-0.32271.092-0.46320.7381-23.028417.526921.4414
722.26050.28610.25480.66350.09911.5790.28470.4498-0.1352-0.15130.3949-0.2476-0.03610.65022.48930.0708-0.1079-0.04340.9928-0.41170.5382-25.752720.386219.3046
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 548 through 576 )
2X-RAY DIFFRACTION2chain 'A' and (resid 577 through 602 )
3X-RAY DIFFRACTION3chain 'A' and (resid 603 through 616 )
4X-RAY DIFFRACTION4chain 'A' and (resid 617 through 666 )
5X-RAY DIFFRACTION5chain 'A' and (resid 667 through 720 )
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 22 )
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 28 )
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 53 )
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 67 )
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 76 )
12X-RAY DIFFRACTION12chain 'B' and (resid 77 through 88 )
13X-RAY DIFFRACTION13chain 'B' and (resid 89 through 100 )
14X-RAY DIFFRACTION14chain 'B' and (resid 101 through 122 )
15X-RAY DIFFRACTION15chain 'B' and (resid 123 through 136 )
16X-RAY DIFFRACTION16chain 'C' and (resid 550 through 576 )
17X-RAY DIFFRACTION17chain 'C' and (resid 577 through 602 )
18X-RAY DIFFRACTION18chain 'C' and (resid 603 through 616 )
19X-RAY DIFFRACTION19chain 'C' and (resid 617 through 648 )
20X-RAY DIFFRACTION20chain 'C' and (resid 649 through 658 )
21X-RAY DIFFRACTION21chain 'C' and (resid 659 through 666 )
22X-RAY DIFFRACTION22chain 'C' and (resid 667 through 683 )
23X-RAY DIFFRACTION23chain 'C' and (resid 684 through 694 )
24X-RAY DIFFRACTION24chain 'C' and (resid 695 through 709 )
25X-RAY DIFFRACTION25chain 'C' and (resid 710 through 717 )
26X-RAY DIFFRACTION26chain 'D' and (resid 25 through 34 )
27X-RAY DIFFRACTION27chain 'D' and (resid 35 through 46 )
28X-RAY DIFFRACTION28chain 'D' and (resid 47 through 67 )
29X-RAY DIFFRACTION29chain 'D' and (resid 68 through 88 )
30X-RAY DIFFRACTION30chain 'D' and (resid 89 through 100 )
31X-RAY DIFFRACTION31chain 'D' and (resid 101 through 122 )
32X-RAY DIFFRACTION32chain 'D' and (resid 123 through 134 )
33X-RAY DIFFRACTION33chain 'E' and (resid 548 through 576 )
34X-RAY DIFFRACTION34chain 'E' and (resid 577 through 602 )
35X-RAY DIFFRACTION35chain 'E' and (resid 603 through 616 )
36X-RAY DIFFRACTION36chain 'E' and (resid 617 through 666 )
37X-RAY DIFFRACTION37chain 'E' and (resid 667 through 683 )
38X-RAY DIFFRACTION38chain 'E' and (resid 684 through 694 )
39X-RAY DIFFRACTION39chain 'E' and (resid 695 through 709 )
40X-RAY DIFFRACTION40chain 'E' and (resid 710 through 718 )
41X-RAY DIFFRACTION41chain 'F' and (resid 17 through 22 )
42X-RAY DIFFRACTION42chain 'F' and (resid 23 through 28 )
43X-RAY DIFFRACTION43chain 'F' and (resid 29 through 41 )
44X-RAY DIFFRACTION44chain 'F' and (resid 42 through 53 )
45X-RAY DIFFRACTION45chain 'F' and (resid 54 through 67 )
46X-RAY DIFFRACTION46chain 'F' and (resid 68 through 76 )
47X-RAY DIFFRACTION47chain 'F' and (resid 77 through 88 )
48X-RAY DIFFRACTION48chain 'F' and (resid 89 through 100 )
49X-RAY DIFFRACTION49chain 'F' and (resid 101 through 117 )
50X-RAY DIFFRACTION50chain 'F' and (resid 118 through 122 )
51X-RAY DIFFRACTION51chain 'F' and (resid 123 through 136 )
52X-RAY DIFFRACTION52chain 'G' and (resid 549 through 576 )
53X-RAY DIFFRACTION53chain 'G' and (resid 577 through 586 )
54X-RAY DIFFRACTION54chain 'G' and (resid 587 through 602 )
55X-RAY DIFFRACTION55chain 'G' and (resid 603 through 616 )
56X-RAY DIFFRACTION56chain 'G' and (resid 617 through 648 )
57X-RAY DIFFRACTION57chain 'G' and (resid 649 through 658 )
58X-RAY DIFFRACTION58chain 'G' and (resid 659 through 666 )
59X-RAY DIFFRACTION59chain 'G' and (resid 667 through 683 )
60X-RAY DIFFRACTION60chain 'G' and (resid 684 through 694 )
61X-RAY DIFFRACTION61chain 'G' and (resid 695 through 709 )
62X-RAY DIFFRACTION62chain 'G' and (resid 710 through 717 )
63X-RAY DIFFRACTION63chain 'H' and (resid 26 through 34 )
64X-RAY DIFFRACTION64chain 'H' and (resid 35 through 46 )
65X-RAY DIFFRACTION65chain 'H' and (resid 47 through 53 )
66X-RAY DIFFRACTION66chain 'H' and (resid 54 through 60 )
67X-RAY DIFFRACTION67chain 'H' and (resid 61 through 67 )
68X-RAY DIFFRACTION68chain 'H' and (resid 68 through 88 )
69X-RAY DIFFRACTION69chain 'H' and (resid 89 through 100 )
70X-RAY DIFFRACTION70chain 'H' and (resid 101 through 105 )
71X-RAY DIFFRACTION71chain 'H' and (resid 106 through 122 )
72X-RAY DIFFRACTION72chain 'H' and (resid 123 through 135 )

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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