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- PDB-5fjv: Crystal structure of the extracellular domain of alpha2 nicotinic... -

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基本情報

登録情報
データベース: PDB / ID: 5fjv
タイトルCrystal structure of the extracellular domain of alpha2 nicotinic acetylcholine receptor in pentameric assembly
要素NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-2
キーワードACETYLCHOLINE-BINDING PROTEIN / NACHR / EXTRACELLULAR DOMAIN / NICOTINIC ACETYLCHOLINE RECEPTOR / EPIBATIDINE / AGONIST / ALPHA2
機能・相同性
機能・相同性情報


Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / acetylcholine receptor activity / synaptic transmission, cholinergic / nervous system process / acetylcholine-gated monoatomic cation-selective channel activity / neurotransmitter receptor activity / plasma membrane => GO:0005886 / monoatomic ion transport ...Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / acetylcholine receptor activity / synaptic transmission, cholinergic / nervous system process / acetylcholine-gated monoatomic cation-selective channel activity / neurotransmitter receptor activity / plasma membrane => GO:0005886 / monoatomic ion transport / monoatomic ion transmembrane transport / regulation of membrane potential / response to nicotine / chemical synaptic transmission / postsynaptic membrane / membrane => GO:0016020 / neuron projection / synapse / signal transduction / plasma membrane
類似検索 - 分子機能
Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain ...Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
EPIBATIDINE / Neuronal acetylcholine receptor subunit alpha-2
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 / 分子置換 / 解像度: 3.2 Å
データ登録者Giastas, P. / Kouvatsos, N. / Chroni-Tzartou, D. / Tzartos, S.J.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2016
タイトル: Crystal Structure of a Human Neuronal Nachr Extracellular Domain in Pentameric Assembly: Ligand-Bound Alpah2 Homopentamer.
著者: Kouvatsos, N. / Giastas, P. / Chroni-Tzartou, D. / Poulopoulou, C. / Tzartos, S.J.
履歴
登録2015年10月13日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年8月10日Provider: repository / タイプ: Initial release
改定 1.12016年8月17日Group: Database references
改定 1.22016年9月28日Group: Database references
改定 1.32024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-2
B: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-2
C: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-2
D: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-2
E: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,49510
ポリマ－125,4525
非ポリマー1,0435
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16970 Å2
ΔGint-76.6 kcal/mol
Surface area42430 Å2
手法PISA
単位格子
Length a, b, c (Å)101.524, 116.559, 129.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-2 / ALPHA2 ECD NACHR


分子量: 25090.400 Da / 分子数: 5 / 断片: EXTRACELLULAR DOMAIN, RESIDUES 59-265 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 器官: BRAIN / 発現宿主: PICHIA PASTORIS (菌類) / 株 (発現宿主): X33 / 参照: UniProt: Q15822
#2: 化合物
ChemComp-EPJ / EPIBATIDINE / (2R)-2-(6-CHLOROPYRIDIN-3-YL)-7-AZABICYCLO[2.2.1]HEPTANE / エピバチジン


分子量: 208.687 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C11H13ClN2 / コメント: alkaloid*YM

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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: 3.05 Å3/Da / 溶媒含有率: 59.74 % / 解説: NONE
結晶化pH: 5.5 / 詳細: 100 MM BICINE PH 9.5, 20% PEG 8000

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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: SLS / ビームライン: X06DA / 波長: 1
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2013年8月30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: 1 Å / 相対比: 1
反射解像度: 3.2→47.26 Å / Num. obs: 26037 / % possible obs: 99.9 % / Observed criterion σ(I): 2.6 / 冗長度: 6.6 % / Biso Wilson estimate: 85.43 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.2
反射 シェル解像度: 3.2→3.37 Å / 冗長度: 7 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 1UV6

1uv6


解像度: 3.2→47.263 Å / SU ML: 0.53 / σ(F): 1.35 / 位相誤差: 32.95 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3079 1299 5 %
Rwork0.2237 --
obs0.2279 25981 99.94 %
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: 3.2→47.263 Å
タンパク質核酸リガンド溶媒全体
原子数8514 0 70 0 8584
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0128860
X-RAY DIFFRACTIONf_angle_d1.97712085
X-RAY DIFFRACTIONf_dihedral_angle_d15.8713199
X-RAY DIFFRACTIONf_chiral_restr0.0881286
X-RAY DIFFRACTIONf_plane_restr0.0091516
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.32820.37051430.29292685X-RAY DIFFRACTION100
3.3282-3.47960.4141660.29482693X-RAY DIFFRACTION100
3.4796-3.6630.40541360.27632711X-RAY DIFFRACTION100
3.663-3.89240.3311470.24612702X-RAY DIFFRACTION100
3.8924-4.19280.33021360.22952728X-RAY DIFFRACTION100
4.1928-4.61440.26171410.19462722X-RAY DIFFRACTION100
4.6144-5.28130.25961480.18132755X-RAY DIFFRACTION100
5.2813-6.65090.30421410.23032776X-RAY DIFFRACTION100
6.6509-47.26820.28211410.20632910X-RAY DIFFRACTION100
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)
10.1827-0.0057-0.03440.18530.09510.0413-0.0633-0.08251.0341-0.14730.21910.12510.8725-0.3791-0.00091.01640.17510.04180.59840.10070.732-14.610918.9941-20.566
20.96010.4163-0.40530.5502-0.2210.1678-0.50060.45690.4269-0.12240.6435-0.80180.3067-1.540.01971.0541-0.023-0.30.68340.03580.55370.180118.5714-9.8171
30.6283-0.2314-0.08110.63930.11820.0252-0.7713-1.4979-0.48460.34140.4542-0.0296-0.1672-0.89690.02151.31730.05850.01520.87080.01320.3955-7.01252.10932.8483
40.0075-0.0339-0.03150.19480.21560.2353-0.39980.3744-0.21180.51070.1870.16270.98290.8523-0.00031.17190.2892-0.04821.04810.14270.6798-0.9715-19.40331.5621
50.32340.197-0.11120.31870.02160.0796-0.6893-0.7585-0.26081.30811.18790.31170.1874-0.66580.02520.98230.2596-0.04820.84750.2850.6242-7.28680.2412-1.7248
60.0180.0141-0.06180.1445-0.07440.19720.1575-0.37040.85730.69610.3767-0.648-1.0851-0.5595-0.00541.03950.2923-0.02920.9375-0.01650.9887-10.243721.3516-8.8878
70.1164-0.0994-0.09950.07370.07020.09471.1046-0.02920.2943-0.50820.035-0.4924-0.60240.1734-0.00311.1126-0.12260.10310.72520.19050.961-20.112820.3573-13.8431
80.04390.0690.15010.5636-0.02780.3017-0.0043-0.29930.0427-0.2831-0.13230.1019-0.6355-0.4556-0.00160.91440.0967-0.06660.65520.05740.4569-2.98166.9034-9.416
90.10480.1557-0.20030.3227-0.23180.3487-0.4256-0.7036-0.5464-0.09880.1009-0.67170.08210.2687-0.04820.56080.1665-0.36991.01490.48750.95745.9097-6.9816-2.7221
100.11260.1249-0.22280.1757-0.29520.4475-0.6339-0.2234-0.8320.3040.34930.07522.254-0.09340.03670.72630.15280.14540.59330.01030.7779-7.57631.842-11.4266
110.39360.281-0.02880.1955-0.05190.6987-0.2356-0.6956-0.0750.01960.3598-0.2849-0.762-0.05870.00010.94610.27860.09410.74130.04330.7532-8.48954.4646-5.6042
120.1342-0.0935-0.0340.068-0.00510.09230.27530.54440.28540.1584-0.5843-0.17970.01060.3337-0.03031.13420.3315-0.45521.31520.08461.66952.6495-18.530111.3947
135.59463.2704-3.02526.8711-0.51441.947-0.25660.5388-1.6072-0.0559-0.52190.99550.4324-0.19-0.46760.9077-0.01910.06091.66660.22671.0299-2.9361-23.290314.8712
140.20240.1037-0.12650.43040.20490.26540.18190.03140.2205-0.27030.8954-0.13010.0913-0.40850.01690.75250.2584-0.30190.69120.04980.6435.13521.5382.6101
151.5784-1.06840.13320.8644-0.25630.2122-0.5636-0.26790.86710.5996-0.1213-0.2006-1.0967-0.3253-0.0691.42770.3305-0.25890.771-0.22460.6278-0.68749.65055.256
161.52330.48430.61192.16140.45560.2822-0.89040.3851-0.9418-0.0428-0.7924-0.75840.83650.7869-2.88182.5584-0.8391.08640.76970.58891.7876-12.7104-1.47368.1956
170.74150.12041.18021.05-0.01381.9139-0.55981.5165-0.5751-0.52730.6389-0.334-0.0616-0.57330.40250.8691-0.12940.77681.59760.21951.5542-11.8336-14.85995.9877
181.05820.09550.72460.00510.1543.5489-0.35250.14880.25380.06870-0.4378-0.05670.1704-4.15881.96480.3126-0.0721.0327-0.19270.14463.9521.882511.564
190.72010.62480.11190.54680.09570.0122-0.49130.943-0.6820.19460.1083-0.7816-1.6271-0.1883-0.02071.102-0.1163-0.41190.6919-0.03540.694414.05316.42965.4655
200.0603-0.040.0020.41710.11680.01450.2492-0.6016-0.37341.05260.73060.19670.14910.40930.00630.96780.6422-0.21261.13140.24670.8104-4.389-12.74959.8972
210.55390.1837-0.02760.26850.36340.64990.9109-0.893-0.5816-1.5749-0.8368-0.883-0.8220.5932-0.00440.91240.0548-0.08440.50460.15421.04638.508324.1185-11.8903
221.5693-0.1719-1.2170.23080.19560.95670.63680.73990.8223-0.18470.00080.631-1.1320.12270.15761.3583-0.0695-0.43330.94880.10660.658617.198615.4006-21.4078
230.92051.36680.32192.12021.14174.30420.24050.1298-0.61550.25620.264-0.87010.6148-0.02530.88180.3836-0.4745-0.17330.56160.67561.857730.893211.088-16.4608
241.2636-0.6314-0.81450.34090.13752.2021-0.2087-0.51640.59030.23170.1964-0.36140.74050.5730.33880.19540.1406-0.61480.63610.16191.013420.7374-4.2928-1.6662
250.11820.034-0.27910.20440.27091.26311.11390.4206-1.3486-0.6667-0.2959-0.1541-0.1218-1.40980.06310.9704-0.0679-0.23950.8192-0.21511.406114.2981-24.2725-5.4541
260.50830.2323-0.28090.1296-0.12620.59120.338-0.0104-0.3880.3753-0.2486-1.19550.5317-0.5568-0.04280.4530.0543-0.34980.58170.07810.706716.4956-9.3452-3.8011
270.1275-0.1131-0.04260.10760.03570.00480.0849-0.04810.25531.0399-0.1005-0.3797-1.14420.5043-0.00131.2416-0.1253-0.40920.8054-0.04551.155322.549515.3776-10.9333
280.05810.0067-0.00350.1721-0.09950.0858-0.5881-0.0496-0.1192-0.36960.42930.326-1.04180.1768-0.00541.22550.2426-0.22670.7275-0.08081.519915.073125.1228-2.7672
291.79291.95450.29573.70931.88681.729-0.2036-0.1018-0.48-0.71550.6372-0.3378-0.5658-0.18520.90590.8118-0.0285-0.58040.53940.13570.536917.49394.3596-13.6364
30-0.0101-0.0236-0.01980.16340.10470.0703-0.0423-0.1775-0.3226-1.3870.15260.4766-0.4999-0.05390.00440.71990.1088-0.15270.78610.05230.532714.73-9.017-13.8145
310.13850.1482-0.1070.14030.01970.5238-0.1673-0.29410.55130.7184-0.2339-0.6363-0.13750.14920.00180.7134-0.0278-0.33870.6534-0.20120.816617.77112.5716-6.3757
320.21320.11160.02850.95240.69940.55170.0729-0.58850.3316-0.83280.2888-0.4266-0.4227-0.04930.01750.5327-0.0997-0.43080.4767-0.13540.717115.0784-5.6649-7.6448
330.2328-0.63110.50591.822-1.58881.79760.4651-0.5774-0.5256-0.8534-0.5781-0.7030.85790.46990.03620.8264-0.0515-0.28210.70570.53191.79422.034-28.83160.8851
340.4891-0.1466-0.08510.0546-0.05350.7613-0.38850.6627-0.67790.09890.3585-1.10740.0381-0.09590.08810.93660.1562-0.29460.42680.08210.956925.3099-16.2024-4.35
350.0352-0.0341-0.06220.03240.01720.1148-0.90470.25770.19160.26290.7015-0.9034-0.47890.91090.00470.6593-0.0682-0.11840.67710.04131.082530.25210.0695-17.2873
360.0802-0.09410.01790.29630.45451.04770.9177-1.19171.05191.63140.56811.3792-0.77470.05760.10560.96440.0368-0.24370.9899-0.23712.343727.84360.11951.7865
370.34410.6558-0.13921.2054-0.42460.5591-1.22-0.28680.80550.56770.72030.22560.652-0.6943-0.33541.11740.40540.04950.87670.70221.299716.9787-12.35386.7781
380.30320.17260.08360.06910.03650.0195-0.2758-0.7809-0.09540.1147-0.0633-0.0032-0.09670.303-0.006-0.46990.4024-1.54710.61330.50191.622234.2947-8.5443-10.3774
390.9334-0.4843-0.02640.5456-0.10340.0260.25230.5164-0.85770.1099-0.0656-0.73060.2295-0.15020.0169-0.0256-0.2987-0.5290.7338-0.40651.54132.754-6.9599-16.5648
402.71880.0646-0.96490.70941.0952.1186-0.68360.15670.2470.0858-0.1935-0.5658-0.41860.4974-6.07511.19450.1915-0.06580.73280.46631.285521.1396-20.43595.8028
411.7241-0.61660.08890.23480.06020.3549-0.31870.11522.4373-0.03630.1684-0.3594-1.25020.5813-0.07351.6104-0.38370.39970.61020.07151.684925.30516.0016-30.3104
420.3918-0.9146-0.01444.08342.13763.44180.2385-0.5570.1879-1.3385-0.94270.4825-1.4236-0.2277-0.49990.914-0.3758-0.08231.00620.17580.842516.90285.1175-40.2274
430.53720.3609-0.53010.79920.21991.1056-0.16570.30720.0527-0.57680.2612-0.2541-0.34340.5150.66681.4494-0.44850.52710.72390.12840.433924.9296-6.8374-44.9815
440.1452-0.0050.04280.24460.07390.03760.98610.3803-0.38550.4140.8497-0.5039-0.08180.0363-0.00280.89560.1383-0.30780.7369-0.1831.306825.3773-19.1637-23.3737
450.755-0.0860.29431.0274-0.58760.41020.57411.59040.1253-0.24290.81870.69550.0508-0.94160.15241.238-0.3911-0.0350.9293-0.01960.776213.8301-31.8081-18.8753
460.1928-0.13290.06120.23890.10860.17150.27230.1043-0.1963-0.6957-0.3456-0.9954-0.1006-0.07840.00250.4822-0.0964-0.05650.4207-0.07960.982123.7147-15.881-25.5698
470.6440.1674-0.47520.0437-0.12170.36950.6228-0.4270.3302-0.2084-0.4132-0.40620.14810.90570.02610.77440.0190.22750.97480.16010.948427.28874.0301-39.5879
480.27540.07370.13230.01660.03090.06221.06040.54350.078-0.00270.83990.2759-1.02040.70120.01581.3652-0.31370.00271.21270.5841.534434.288412.959-31.361
490.10450.0454-0.12060.18760.0680.19110.02020.37531.3388-0.050.1586-0.31230.2446-0.0754-0.00230.4845-0.15730.09090.6959-0.03631.053819.8125-0.5992-31.6133
500.6382-0.20090.42630.1809-0.03540.36660.99751.0983-0.7612-0.0272-0.73511.5361-0.371-0.62160.03670.6466-0.28970.03990.8651-0.0440.908813.5872-20.1577-30.4008
510.04030.0030.12920.0672-0.03610.41080.1377-0.5886-1.21730.3648-0.56630.81910.1583-0.48930.00170.6217-0.0475-0.09460.68470.07531.337716.0886-8.5799-25.4897
520.2260.1486-0.23540.66790.31940.8425-0.21690.08470.5003-0.2430.63-1.25970.48190.13650.09890.1915-0.23640.05710.9734-0.00061.089826.515-3.7073-30.1103
530.19570.58060.4491.94571.73652.10540.3753-0.14880.4971-0.3120.04570.00331.6899-0.1333-0.01350.8430.1472-0.29140.7784-0.08751.134417.2343-29.7443-25.7023
540.1758-0.02820.0560.0012-0.00690.0194-0.35110.7649-0.4196-0.7991-1.0441-0.46670.33090.79460.00191.33040.3477-0.14590.8694-0.11081.622723.9308-41.8595-24.1504
550.5737-0.1263-0.07630.60950.43010.40610.51710.1897-0.43-0.6251-0.2916-1.35090.48530.76250.00670.6176-0.00940.16090.8036-0.0340.721918.3846-17.8692-38.7666
560.1893-0.0232-0.10470.0248-0.03220.11050.20590.06510.60560.24321.0584-0.4883-0.7646-0.3285-0.00230.92210.1629-0.00161.1628-0.11610.895532.2489-16.8691-35.0388
577.6629-4.0647-5.31732.68833.6626.11260.10590.64932.3941-0.3120.7723-0.6881-0.97161.13920.74540.7407-0.1642-0.36741.4106-0.48321.44230.3596-22.5358-17.9749
583.1929-1.81480.43292.6313-0.32910.09140.82970.20390.4293-2.0085-0.2094-1.378-0.25760.21980.48530.9599-0.18820.37990.6847-0.16840.854422.7918-25.4996-38.2458
590.01610.03060.00620.0308-0.01180.03530.09350.4753-1.0677-0.9098-0.255-0.3405-0.1967-0.6067-0.00920.61410.13980.17861.01340.05980.587515.8931-19.8766-44.3382
602.5175-1.48421.41482.3226-0.8530.79310.5621-1.18120.0929-0.92890.53140.2589-1.3661-0.95050.13550.72920.2194-0.20930.8738-0.34631.214227.0625-31.5042-21.797
610.02990.0010.05180.0413-0.10030.25371.0059-0.02680.9978-0.0168-0.63210.54730.2622-0.0946-0.00520.90710.00180.02861.02530.02440.6369.34415.1301-49.4528
620.6321-0.9420.69572.8353-0.95380.7594-0.27220.24030.61210.12070.84870.5519-1.8193-0.59220.11391.17680.08460.00780.67850.03660.2728-4.71992.4269-42.5418
631.0449-0.054-0.07720.05890.0680.0803-0.41270.7764-0.2699-0.5852-0.02490.1193-0.32960.4742-0.459-0.252-0.5407-1.10710.8537-0.2551-0.2959-9.7465-11.3286-48.2367
640.07950.0506-0.00560.0786-0.04170.03730.83880.7507-0.6184-0.30720.36420.12150.89970.5524-0.00020.8074-0.0226-0.0880.6623-0.23830.71934.6618-28.1495-32.6899
650.41740.0642-0.46410.6269-0.61260.97630.4322-0.1337-0.52260.28380.41640.56650.55550.17580.01370.5854-0.0105-0.03040.66330.06550.5540.4922-28.9781-25.9323
661.0445-0.40630.09510.9136-0.45250.26490.05650.5865-0.4103-0.98020.20890.4741-0.3490.6039-0.0341.08690.1183-0.38170.7303-0.12680.1108-2.4206-8.8396-47.6699
672.07541.45440.5123.3830.93812.0340.59920.28530.42080.16810.7371-0.3434-1.31991.02690.55941.6404-0.38390.68351.2992-0.00210.40368.1389-0.2422-57.453
680.26140.39030.24221.04440.23780.51870.24340.0242-0.18330.1413-0.325-0.5642-0.1654-0.4315-0.32651.1717-0.13950.34690.61010.0297-0.15498.1061-4.7864-44.8115
690.0612-0.08020.06780.1608-0.11990.06610.53890.3577-0.27980.60590.60040.13990.0240.05050.00740.53690.0480.07080.4755-0.01760.3192-5.3841-11.0207-37.4576
700.0536-0.09540.25830.1308-0.37921.1403-1.0502-0.0881-0.91931.11810.53161.2193-0.8376-0.051-0.01670.68060.03030.18490.59540.01990.876-6.0778-19.5189-26.711
710.62590.3037-0.10020.8073-0.76810.8215-0.4329-0.3493-0.5698-0.0566-0.7842-0.32870.7327-0.1392-0.06130.90870.06340.1350.7036-0.09580.34975.7529-10.2353-37.937
720.783-0.0494-0.08160.3110.31930.3478-0.05640.3067-0.0172-0.7738-0.0471-0.3269-0.57260.0899-0.00130.501-0.0828-0.10940.7609-0.17540.41432.9406-13.5897-42.4823
731.7086-0.66560.76357.07510.19690.63860.1835-1.8992-2.09590.77530.0873-0.34761.37920.29570.18271.87620.9782-0.1241.30810.75580.7113-5.6331-35.0514-24.1393
740.5470.2314-0.01640.2130.13280.1681-0.09180.01540.6317-0.31230.6246-0.4773-0.27240.06260.70841.9753-0.7504-0.95921.08960.31571.7012-5.7557-42.1016-27.964
751.35620.47970.56150.34540.35490.36950.3109-0.2281-0.3131-0.82450.50420.69390.208-1.15140.00030.6548-0.0592-0.05740.64540.12740.573-11.3544-17.9293-38.9306
766.9832-2.31275.55260.7868-2.04586.4107-0.50580.7202-0.1975-0.5498-0.5780.62210.04770.3628-1.99571.49860.922-0.06240.2326-0.01781.00792.4138-28.6767-44.9074
770.42250.48930.06680.55360.080.01241.50.0388-0.08330.5983-0.2696-1.1765-0.27131.07840.01711.17540.141-0.18911.1226-0.11311.04856.5341-36.2218-32.0235
781.78860.51240.39140.2209-0.01720.2533-0.59690.32530.9821-0.7358-0.02171.3742-0.5480.1095-0.09861.0336-0.1723-0.56190.73210.12571.0193-14.028-26.2611-39.1822
790.25380.2876-0.42030.2912-0.42520.6283-0.2896-0.11820.1386-0.0511-0.28390.05390.1504-0.4332-0.09750.56790.0229-0.40270.7412-0.04890.9721-17.2168-18.9442-36.6311
800.3087-0.36610.23550.7288-0.04480.35120.3711-0.3033-1.89630.20160.75280.54710.7026-0.17690.12270.5513-0.091-0.38860.82040.40181.56360.3943-40.3673-31.0386
811.8771-0.94340.40560.457-0.20130.0909-0.9345-0.51790.32520.81730.158-0.87180.24520.8405-0.09420.98540.142-0.12820.51860.05380.1344-14.03166.9022-42.9174
822.7028-1.0874-0.55540.44490.20610.1108-0.42380.7464-1.0241-0.48380.3531.0738-2.6376-0.3324-0.02141.0301-0.1022-0.37630.714-0.04380.8385-13.981710.9243-27.0694
834.9277-0.06460.138-0.0013-0.00250.00240.101-0.65590.9736-0.0743-0.34850.4814-0.4803-0.992-0.45430.26510.89490.30050.99890.16160.4594-26.18047.5286-20.4875
840.2251-0.26340.29740.87770.06240.4467-0.07740.1246-0.70370.13140.18590.9717-0.59060.30680.00360.3617-0.01270.03830.68880.13110.594-16.7208-18.9323-18.8374
850.4320.3556-0.29690.3937-0.050.44760.2422-0.4563-0.5561-0.2663-0.04350.21410.271-0.07110.00410.4433-0.02770.07660.58450.08410.7011-12.1481-19.4215-14.9638
860.0815-0.07280.03110.1323-0.07960.05550.04550.62940.43520.41-0.27070.3437-0.8644-0.3772-0.00080.6510.0735-0.06150.68580.23680.7169-23.31144.5307-28.7689
870.0673-0.00670.01250.0206-0.00650.02770.29620.92820.35010.3998-1.1876-1.36920.1392-0.11340.0051.02260.3548-0.11090.9510.23721.0505-23.73694.3358-44.5067
880.3291-0.1153-0.25020.4384-0.11090.4502-0.08510.55730.6166-0.0576-0.18890.60590.5185-0.1812-0.00350.7351-0.0306-0.03840.63130.07940.8135-14.8655-0.1893-30.6576
890.22640.17380.08660.13790.09240.0455-0.2394-0.1330.0031.3426-0.0921-0.5438-0.55660.345-0.02360.42070.0452-0.0060.54520.20430.7946-11.3724-9.9302-11.6697
900.1302-0.2176-0.11090.30810.18150.1085-0.14440.3635-1.19970.27020.91470.7113-0.27651.330.14870.4579-0.0641-0.15550.66520.08150.4013-10.7962-7.3099-25.3304
910.1363-0.0919-0.08460.06530.06770.16440.40820.07770.23510.28180.30271.01160.0744-0.3796-0.00210.43340.0562-0.10660.64280.11650.8089-22.1806-1.9971-31.824
92-0.0347-0.04150.01420.2082-0.09390.0911-0.057-0.3888-0.82690.4684-0.13410.0043-0.13380.21660.00380.4818-0.0680.08090.8560.25950.4454-12.3123-20.5623-12.0519
930.08590.00850.10130.5786-0.2880.1984-0.5161-0.9679-1.01631.28650.10260.15550.5110.0522-0.12250.87050.19290.34120.72620.50441.268-18.2502-28.7291-6.4871
940.8999-0.59280.38061.6527-0.48650.20610.1199-0.2564-0.04040.79580.20270.6353-1.43580.00780.01560.77970.07310.07660.82070.15790.3165-19.4177-0.499-11.7524
950.05230.1621-0.09061.0401-0.7210.50210.77210.5114-0.53290.8139-0.176-0.5001-0.5145-0.61780.07310.50510.05580.11380.93540.22350.9592-27.4497-5.2141-17.9863
960.3168-0.5417-0.8631.24530.33846.4360.41850.67560.4161-1.0506-0.4432-0.2591-1.6897-0.3284-0.78541.06930.0344-0.90890.44691.44411.8008-24.4762-20.1396-25.299
970.1373-0.1583-0.07930.17320.10920.07760.2483-0.32840.29460.40970.143-1.1447-0.13070.3135-0.00450.7397-0.25510.20580.71820.21281.435-16.3367-29.6904-19.3544
98-0.00390.11120.00741.28850.17920.0087-0.21090.24750.0435-0.4547-0.05290.68370.1959-0.65020.010.77420.36830.61691.13720.29440.9287-26.9588-13.052-10.0656
990.4024-0.1257-0.23530.4649-0.24010.3731-0.0234-0.2686-0.527-0.0809-0.1075-0.09310.15440.1801-0.17290.23220.87540.70961.03850.28460.8953-21.10830.0464-3.583
1001.06820.37521.41761.84711.1662.8230.474-1.3146-0.86990.4726-0.50020.68740.8588-0.981-1.82050.4298-0.11340.08630.78060.34720.7892-20.2415-26.8632-12.4892
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:9)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 10:26)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 27:35)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 36:47)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 48:58)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 59:66)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 67:75)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 76:89)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 90:98)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 99:106)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 107:122)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 123:130)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 131:138)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 139:150)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 151:158)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 159:166)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 167:177)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 178:186)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 187:195)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 196:207)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 1:9)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 10:18)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 19:27)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 28:37)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 38:45)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 46:54)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 55:65)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 66:74)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 75:90)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 91:102)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 103:114)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 115:123)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 124:135)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 136:143)
35X-RAY DIFFRACTION35(CHAIN B AND RESID 144:155)
36X-RAY DIFFRACTION36(CHAIN B AND RESID 156:163)
37X-RAY DIFFRACTION37(CHAIN B AND RESID 164:177)
38X-RAY DIFFRACTION38(CHAIN B AND RESID 178:187)
39X-RAY DIFFRACTION39(CHAIN B AND RESID 188:199)
40X-RAY DIFFRACTION40(CHAIN B AND RESID 200:207)
41X-RAY DIFFRACTION41(CHAIN C AND RESID 1:9)
42X-RAY DIFFRACTION42(CHAIN C AND RESID 10:21)
43X-RAY DIFFRACTION43(CHAIN C AND RESID 22:29)
44X-RAY DIFFRACTION44(CHAIN C AND RESID 30:38)
45X-RAY DIFFRACTION45(CHAIN C AND RESID 39:46)
46X-RAY DIFFRACTION46(CHAIN C AND RESID 47:56)
47X-RAY DIFFRACTION47(CHAIN C AND RESID 57:65)
48X-RAY DIFFRACTION48(CHAIN C AND RESID 66:74)
49X-RAY DIFFRACTION49(CHAIN C AND RESID 75:86)
50X-RAY DIFFRACTION50(CHAIN C AND RESID 87:95)
51X-RAY DIFFRACTION51(CHAIN C AND RESID 96:105)
52X-RAY DIFFRACTION52(CHAIN C AND RESID 106:120)
53X-RAY DIFFRACTION53(CHAIN C AND RESID 121:128)
54X-RAY DIFFRACTION54(CHAIN C AND RESID 129:137)
55X-RAY DIFFRACTION55(CHAIN C AND RESID 138:154)
56X-RAY DIFFRACTION56(CHAIN C AND RESID 155:162)
57X-RAY DIFFRACTION57(CHAIN C AND RESID 163:174)
58X-RAY DIFFRACTION58(CHAIN C AND RESID 175:188)
59X-RAY DIFFRACTION59(CHAIN C AND RESID 189:198)
60X-RAY DIFFRACTION60(CHAIN C AND RESID 199:207)
61X-RAY DIFFRACTION61(CHAIN D AND RESID 1:11)
62X-RAY DIFFRACTION62(CHAIN D AND RESID 12:20)
63X-RAY DIFFRACTION63(CHAIN D AND RESID 21:30)
64X-RAY DIFFRACTION64(CHAIN D AND RESID 31:39)
65X-RAY DIFFRACTION65(CHAIN D AND RESID 40:53)
66X-RAY DIFFRACTION66(CHAIN D AND RESID 54:62)
67X-RAY DIFFRACTION67(CHAIN D AND RESID 63:71)
68X-RAY DIFFRACTION68(CHAIN D AND RESID 72:81)
69X-RAY DIFFRACTION69(CHAIN D AND RESID 82:89)
70X-RAY DIFFRACTION70(CHAIN D AND RESID 90:98)
71X-RAY DIFFRACTION71(CHAIN D AND RESID 99:107)
72X-RAY DIFFRACTION72(CHAIN D AND RESID 108:121)
73X-RAY DIFFRACTION73(CHAIN D AND RESID 122:130)
74X-RAY DIFFRACTION74(CHAIN D AND RESID 131:138)
75X-RAY DIFFRACTION75(CHAIN D AND RESID 139:157)
76X-RAY DIFFRACTION76(CHAIN D AND RESID 158:167)
77X-RAY DIFFRACTION77(CHAIN D AND RESID 168:176)
78X-RAY DIFFRACTION78(CHAIN D AND RESID 177:187)
79X-RAY DIFFRACTION79(CHAIN D AND RESID 188:199)
80X-RAY DIFFRACTION80(CHAIN D AND RESID 200:207)
81X-RAY DIFFRACTION81(CHAIN E AND RESID 1:10)
82X-RAY DIFFRACTION82(CHAIN E AND RESID 11:19)
83X-RAY DIFFRACTION83(CHAIN E AND RESID 20:27)
84X-RAY DIFFRACTION84(CHAIN E AND RESID 28:41)
85X-RAY DIFFRACTION85(CHAIN E AND RESID 42:55)
86X-RAY DIFFRACTION86(CHAIN E AND RESID 56:63)
87X-RAY DIFFRACTION87(CHAIN E AND RESID 64:72)
88X-RAY DIFFRACTION88(CHAIN E AND RESID 73:85)
89X-RAY DIFFRACTION89(CHAIN E AND RESID 86:96)
90X-RAY DIFFRACTION90(CHAIN E AND RESID 97:106)
91X-RAY DIFFRACTION91(CHAIN E AND RESID 107:115)
92X-RAY DIFFRACTION92(CHAIN E AND RESID 116:130)
93X-RAY DIFFRACTION93(CHAIN E AND RESID 131:142)
94X-RAY DIFFRACTION94(CHAIN E AND RESID 143:151)
95X-RAY DIFFRACTION95(CHAIN E AND RESID 152:159)
96X-RAY DIFFRACTION96(CHAIN E AND RESID 160:167)
97X-RAY DIFFRACTION97(CHAIN E AND RESID 168:176)
98X-RAY DIFFRACTION98(CHAIN E AND RESID 177:185)
99X-RAY DIFFRACTION99(CHAIN E AND RESID 186:196)
100X-RAY DIFFRACTION100(CHAIN E AND RESID 197:207)

+
万見について

-
お知らせ

-
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://pdbjlvh1.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

+
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