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- PDB-6i4g: Crystal Structure of Plasmodium falciparum actin I (H74Q) in the ... -

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基本情報

登録情報
データベース: PDB / ID: 6i4g
タイトルCrystal Structure of Plasmodium falciparum actin I (H74Q) in the Mg-K-ATP state
要素
  • Actin-1アクチン
  • Gelsolin
キーワードCONTRACTILE PROTEIN / hydrolase (加水分解酵素) / filamentous / glideosome / cytoskeleton (細胞骨格)
機能・相同性
機能・相同性情報


glial filament / plastid inheritance / 分裂 (生物学) / apical ectoplasmic specialization / basal ectoplasmic specialization / Caspase-mediated cleavage of cytoskeletal proteins / Platelet degranulation / symbiont-medited actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / striated muscle atrophy ...glial filament / plastid inheritance / 分裂 (生物学) / apical ectoplasmic specialization / basal ectoplasmic specialization / Caspase-mediated cleavage of cytoskeletal proteins / Platelet degranulation / symbiont-medited actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / Neutrophil degranulation / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / entry into host cell by a symbiont-containing vacuole / actin filament capping / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / positive regulation of p38MAPK cascade / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / positive regulation of cardiac muscle hypertrophy / hepatocyte apoptotic process / cilium assembly / 筋形質 / phagocytic vesicle / vesicle-mediated transport / cytoskeleton organization / ruffle / cellular response to cadmium ion / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / response to muscle stretch / Neutrophil degranulation / central nervous system development / actin filament organization / マイクロフィラメント / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / protein destabilization / structural constituent of cytoskeleton / cellular response to type II interferon / actin filament binding / マイクロフィラメント / lamellipodium / 髄鞘 / actin binding / actin cytoskeleton organization / amyloid fibril formation / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / extracellular region / ATP binding / 細胞核 / 細胞膜 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain ...Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / アクチン / Actin family / アクチン / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / 2-メルカプトエタノール / : / THIOCYANATE ION / Gelsolin / Actin-1
類似検索 - 構成要素
生物種Plasmodium falciparum (マラリア病原虫)
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: 2 Å
データ登録者Kumpula, E.-P. / Lopez, A.J. / Tajedin, L. / Han, H. / Kursula, I.
資金援助 フィンランド, ノルウェー, 3件
組織認可番号国
Academy of Finland フィンランド
Sigrid Juselius Foundation フィンランド
Research Council of Norway ノルウェー
引用ジャーナル: Plos Biol. / 年: 2019
タイトル: Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation.
著者: Kumpula, E.P. / Lopez, A.J. / Tajedin, L. / Han, H. / Kursula, I.
履歴
登録2018年11月9日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年6月26日Provider: repository / タイプ: Initial release
改定 1.12024年1月24日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Actin-1
B: Actin-1
G: Gelsolin
H: Gelsolin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)114,09318
ポリマ－112,4994
非ポリマー1,59414
水7,188399
1
A: Actin-1
H: Gelsolin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,9788
ポリマ－56,2502
非ポリマー7296
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-47 kcal/mol
Surface area20780 Å2
手法PISA
2
B: Actin-1
G: Gelsolin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)57,11510
ポリマ－56,2502
非ポリマー8658
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-49 kcal/mol
Surface area20660 Å2
手法PISA
単位格子
Length a, b, c (Å)68.610, 110.620, 138.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 8 through 28 or resid 31...A8 - 28
121(chain 'A' and (resid 8 through 28 or resid 31...A31 - 36
131(chain 'A' and (resid 8 through 28 or resid 31...A39
141(chain 'A' and (resid 8 through 28 or resid 31...A53 - 57
1401(chain 'A' and (resid 8 through 28 or resid 31...A59 - 63
151(chain 'A' and (resid 8 through 28 or resid 31...A66 - 95
161(chain 'A' and (resid 8 through 28 or resid 31...A97 - 116
171(chain 'A' and (resid 8 through 28 or resid 31...A118 - 153
181(chain 'A' and (resid 8 through 28 or resid 31...A156 - 206
191(chain 'A' and (resid 8 through 28 or resid 31...A208 - 239
1101(chain 'A' and (resid 8 through 28 or resid 31...A241 - 250
1111(chain 'A' and (resid 8 through 28 or resid 31...A252 - 281
1391(chain 'A' and (resid 8 through 28 or resid 31...A283 - 323
1121(chain 'A' and (resid 8 through 28 or resid 31...A326 - 334
1131(chain 'A' and (resid 8 through 28 or resid 31...A336 - 338
1141(chain 'A' and (resid 8 through 28 or resid 31...A340 - 359
1151(chain 'A' and (resid 8 through 28 or resid 31...A361 - 373
2161(chain 'B' and (resid 8 through 28 or resid 31...B8 - 28
2171(chain 'B' and (resid 8 through 28 or resid 31...B31 - 36
2181(chain 'B' and (resid 8 through 28 or resid 31...B39
2191(chain 'B' and (resid 8 through 28 or resid 31...B53 - 57
2201(chain 'B' and (resid 8 through 28 or resid 31...B59 - 63
2211(chain 'B' and (resid 8 through 28 or resid 31...B66 - 95
2221(chain 'B' and (resid 8 through 28 or resid 31...B97 - 116
2231(chain 'B' and (resid 8 through 28 or resid 31...B118 - 153
2241(chain 'B' and (resid 8 through 28 or resid 31...B156 - 206
2251(chain 'B' and (resid 8 through 28 or resid 31...B208 - 239
2261(chain 'B' and (resid 8 through 28 or resid 31...B241 - 250
2271(chain 'B' and (resid 8 through 28 or resid 31...B252 - 281
2281(chain 'B' and (resid 8 through 28 or resid 31...B283 - 323
2291(chain 'B' and (resid 8 through 28 or resid 31...B326 - 334
2301(chain 'B' and (resid 8 through 28 or resid 31...B336 - 338
2311(chain 'B' and (resid 8 through 28 or resid 31...B340 - 359
2321(chain 'B' and (resid 8 through 28 or resid 31...B361 - 373
1332(chain 'G' and (resid 26 through 146 or resid 148 through 149))G26 - 75
1342(chain 'G' and (resid 26 through 146 or resid 148 through 149))G79 - 145
1352(chain 'G' and (resid 26 through 146 or resid 148 through 149))G148 - 149
2362(chain 'H' and (resid 26 through 75 or resid 79 through 146 or resid 148 through 149))H26 - 75
2372(chain 'H' and (resid 26 through 75 or resid 79 through 146 or resid 148 through 149))H79 - 145
2382(chain 'H' and (resid 26 through 75 or resid 79 through 146 or resid 148 through 149))H148 - 149

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 2種, 4分子 ABGH

#1: タンパク質 Actin-1 / アクチン / Actin I


分子量: 42037.656 Da / 分子数: 2 / 変異: H74Q / 由来タイプ: 組換発現
由来: (組換発現) Plasmodium falciparum (マラリア病原虫)
遺伝子: PFL2215w
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q8I4X0
#2: タンパク質 Gelsolin / / Actin-depolymerizing factor / ADF / Brevin


分子量: 14211.929 Da / 分子数: 2 / 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: Gsn, Gsb / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P13020

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非ポリマー , 7種, 413分子

#3: 化合物 ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP / アデノシン三リン酸


分子量: 507.181 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / コメント: ATP, エネルギー貯蔵分子*YM
#4: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#5: 化合物 ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 2 / 由来タイプ: 合成 / 式: K
#6: 化合物 ChemComp-BME / BETA-MERCAPTOETHANOL / 2-メルカプトエタノ-ル / 2-メルカプトエタノール


分子量: 78.133 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H6OS
#7: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Ca
#8: 化合物 ChemComp-SCN / THIOCYANATE ION / チオシアン酸アニオン / チオシアン酸塩


分子量: 58.082 Da / 分子数: 1 / 由来タイプ: 合成 / 式: CNS
#9: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 399 / 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: 2.3 Å3/Da / 溶媒含有率: 46.63 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.8
詳細: 11% PEG3350, 0.1M BIS-TRIS pH 5.8, 0.2M K-SCN; streak seeded; 20% PEG400 used for cryoprotection

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I04-1 / 波長: 0.916 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年10月24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: 0.916 Å / 相対比: 1
反射解像度: 2→48.8 Å / Num. obs: 132341 / % possible obs: 95.64 % / 冗長度: 5.3 % / Biso Wilson estimate: 33.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1655 / Rpim(I) all: 0.07289 / Rrim(I) all: 0.1814 / Net I/σ(I): 5.57
反射 シェル解像度: 2→2.071 Å / 冗長度: 4.3 % / Rmerge(I) obs: 1.851 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 12840 / CC1/2: 0.437 / Rpim(I) all: 0.9164 / Rrim(I) all: 2.075 / % possible all: 92.84

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
XDSデータ削減
XSCALE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: 4CBU

4cbu


解像度: 2→48.8 Å / SU ML: 0.3244 / 交差検証法: FREE R-VALUE / σ(F): 1.92 / 位相誤差: 30.5041
Rfactor反射数%反射
Rfree0.2569 2634 2 %
Rwork0.2165 --
obs0.2173 131937 95.65 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 48.14 Å2
精密化ステップサイクル: LAST / 解像度: 2→48.8 Å
タンパク質核酸リガンド溶媒全体
原子数7521 0 85 399 8005
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0057841
X-RAY DIFFRACTIONf_angle_d0.618910643
X-RAY DIFFRACTIONf_chiral_restr0.04721159
X-RAY DIFFRACTIONf_plane_restr0.00391371
X-RAY DIFFRACTIONf_dihedral_angle_d9.94554661
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.38531340.36676617X-RAY DIFFRACTION92.81
2.04-2.080.43131320.35166649X-RAY DIFFRACTION92.93
2.08-2.120.37391350.32156639X-RAY DIFFRACTION93.64
2.12-2.160.30341340.29476682X-RAY DIFFRACTION93.69
2.16-2.210.27881380.27976720X-RAY DIFFRACTION94.2
2.21-2.270.32011320.27036701X-RAY DIFFRACTION94.51
2.27-2.330.29441380.26556668X-RAY DIFFRACTION94.42
2.33-2.40.25431340.2566723X-RAY DIFFRACTION94.29
2.4-2.480.32121340.25226717X-RAY DIFFRACTION94.41
2.48-2.570.28411410.23636728X-RAY DIFFRACTION94.22
2.57-2.670.31881340.2356759X-RAY DIFFRACTION95.1
2.67-2.790.2831410.22976793X-RAY DIFFRACTION95.5
2.79-2.940.24571390.236764X-RAY DIFFRACTION95.35
2.94-3.120.33151410.22856868X-RAY DIFFRACTION96.16
3.12-3.360.26381450.20896942X-RAY DIFFRACTION97.82
3.36-3.70.1941470.18797061X-RAY DIFFRACTION99.35
3.7-4.240.22191450.16767103X-RAY DIFFRACTION99.74
4.24-5.330.19921470.16097101X-RAY DIFFRACTION99.77
5.33-48.810.2361430.20827068X-RAY DIFFRACTION99.46
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)
10.673119796620.429482317876-0.03393930360640.858448744332-0.06425763512940.1313193089530.0829901529063-0.188049645540.1282424190130.214774348422-0.03983392411180.05302928200110.0399806547805-0.009048030371787.74624870166E-60.293528420509-0.01061613505580.009215469846610.320630838066-0.0175867931120.3137637935124.02938777166-14.5446544955-26.4905226601
21.17528930191-0.2345232307960.8275707386450.8340002217890.03255800064041.6184809828-0.0113434826953-0.107084700875-0.01928569021230.187270987520.0258966020512-0.04712860822770.0312571430446-0.002005414391380.0001789635179430.362235967727-0.0114754725475-0.008569224113120.3384894872310.02185537379970.2930966472760.849750172085-36.8016173645-15.0933300463
30.7570277118080.773192093764-0.2941415441721.188983647010.2684565660820.464642278356-0.06619614988750.04649973097950.262441781846-0.2001023637120.005072759140960.009001594440810.0560489773782-0.1852451707856.50089394856E-50.333748854465-0.0233417834837-0.01569774984930.3693054091250.007947778134750.3182085603291.30343822371-14.9180371933-39.9426537716
40.733568632249-0.5450646497740.2640987184820.85742051330.1034136760650.7407934005380.09634802517430.0379413130573-0.1191731268310.0117437307404-0.05344789280580.08285594112620.0599527013934-0.01459834172380.009670676532210.2383441217260.0112612459761-0.01193624876840.266791672544-0.007979930652170.286690377938.2525166886-27.196263323-42.6926951969
50.834807067444-0.162138032186-0.8249214291950.6559318112770.05408097694550.345298792715-0.105808721251-0.0123915247286-0.1653962499690.0229653973672-0.0164248900320.05781967457990.181762655507-0.273145525409-0.0004881029372760.186504591779-0.0200333233893-0.01193433360190.232690704689-0.03900662459490.17458254917830.1938008544-12.3313118424-52.7705163472
60.9701827441310.33810054718-0.6567227282680.9605736382270.7899414036641.278299239120.0146296853641-0.08587725382850.139040453667-0.02931384125720.1442686844640.0102993665736-0.0992460323286-0.02089564682030.07247822490610.1883902937380.007957971327630.01342729335950.1076824057850.01652801110260.15697418968136.1366218847-5.20203643113-57.3647862382
70.1981462743820.1586760341560.1101245054830.3518279895230.07144000618780.09262948398750.08022839217030.1747348851380.185746550045-0.116442468248-0.0919337402293-0.0578812056735-0.2252247362090.209191671361-7.6184442163E-50.4520763436260.04002910923580.02697407731720.345245220433-0.01013928250460.39651602434232.33952022732.77652405109-44.1086683881
80.174995267232-0.55167571972-0.2864282468410.7641567028440.3867528280740.6185731540410.05392917054020.149305438275-0.1286788526850.2852412537080.1493962312080.3315571138170.12240212353-0.309487155088-0.0002113514583360.291060335788-0.04408424644260.005006939589120.2764939127450.05673814260050.30650718772135.7295907969-26.2123885947-29.1226264031
90.0549482115199-0.0551264600635-0.2723619606310.05299130436740.2571370896761.35850199588-0.2089044697010.177338933526-0.06586655347910.262062794011-0.6134031546250.799167196772-0.104114960196-0.158086808599-0.3437649613840.335546169004-0.1210573200360.01235305294980.333697603920.02343044499770.78190084534735.8034749509-19.1106094505-13.5398149869
100.4469541235840.07645510993380.2972444472560.227271157432-0.2241708437810.3960893361850.111594153379-0.2350764937690.05790076867230.135098909516-0.130860892192-0.00956317945234-0.2416738588810.0489722161861-0.007654705235590.288772519247-0.07096866896520.00806711714590.435955479922-0.01873606145650.17870452388338.0538455127-8.93463616802-10.3565800494
110.4028088327980.246410196133-0.005319600008320.305322809024-0.254618323310.2445840519360.121707601233-0.390950676077-0.08596665232170.482845697040.175913528384-0.3100948249260.1125067817160.146955893.52565643017E-50.45194327474-0.0566071231803-0.00441816104410.441004206072-0.004224419381520.33622322439147.6749795157-5.74687108227-14.7659696259
120.584424144251-0.7593159067640.5352559359871.21743385419-0.8383821859930.8727526785440.492601290834-0.1032965069970.6221169405550.243499638591-0.323581022490.1809494118290.259145342252-0.216551395371-0.1093177900460.308004509313-0.1214494065980.02931988812460.424435738439-0.09097934298390.33060251994336.7366354647-3.23675394692-14.2012789515
130.294025243680.08126783973020.368458993660.4477100537420.04007690072930.416823286257-0.195318872663-0.3685840121330.1764915792460.203644105239-0.03326602007660.114984702670.0523959093225-0.357364329991-0.01526593376240.399499148693-0.01936631930690.04258726591370.444328900828-0.04512266360980.30590584327135.8126382328-2.60571998396-18.0085064932
140.01484967753080.11791773504-0.103569793280.473450230543-0.3046939572390.2623893136160.434201682646-0.1128290952050.007250932788960.0843644085771-0.16687428769-0.156809788708-0.5777965394060.1234054509570.002193294592960.25375920327-0.03256488070960.01142489012510.268041374020.01577310314170.28576859535537.2806987623-11.993636672-22.6112015537
150.27087582032-0.1844074617290.07126800743880.7838862235040.02918039154920.1128006228180.0446245532759-0.02296245629690.6140319435570.526734182207-0.0004705111769320.41735935364-0.175587484003-0.4986274454030.002069820441240.3695651200370.03761744930610.04235631703930.361802977814-0.04280858371840.44696106991834.42311043070.895034367602-20.05205344
160.2573404647890.07680814126420.4755219341550.05416841348680.1811761005970.9348900475810.0997376320285-0.9049270054350.5773537979730.6571229295190.1771477317620.5116925601750.0121929732125-1.560045191850.05232677305730.5255435156960.04904904403420.08432161966740.643794041228-0.08715795592650.50627289765545.85129215956.63724970279-13.7491368606
170.202701908415-0.1782272337490.07819825759980.147528640728-0.06531530194670.02011486641040.139859123461-0.1491332778940.581081048204-0.41772945453-0.669515350121-0.0390965904444-0.176380444839-0.138500883528-0.0011394829950.288043525199-0.02806409781810.01446320476060.340864642548-0.006571955078890.41302146439753.8702926404-9.0410662328-24.399942997
180.004164304237670.00734222276478-0.005891225744860.07196696879510.0193092766877-0.00744934677190.05897906349080.1810061796751.06348778384-0.120824998511-0.552019771089-0.1998412055250.3869413610820.2226419255490.001820370713480.740740981041-0.01075179235970.04177853890320.8235715718760.01927816481060.591782570031.16824819822-22.4740657564-56.1580166559
190.33626511101-0.0161460158363-0.04556397652880.06700365019040.05697485660360.0378196688428-0.4715394232410.6006463917890.522271658796-0.1901974569510.2930219636020.0667166448027-0.1515859432060.0959325918588-0.01450876731160.5467720310860.0759191193029-0.135391788820.8229302981840.07513107081640.357033202538-1.89852423283-31.4258178915-64.0405257397
204.857233822880.326860995414-1.074189520550.0338539477259-0.07622962621170.2362440085680.1598142043511.1070465209-0.0979241593641-0.547844426871-0.0394800513116-0.0353391155688-0.239645863244-0.1452779764210.1891059669310.3745215021180.0180593625530.01272566694230.2268334343390.00136619173740.2198370015817.98392325519-33.7543913828-55.7765869776
210.475691402623-0.07120279377470.08419972167560.9640000764290.8298037907211.17698003127-0.03141409891730.2548173792470.537032517906-0.2047312822850.828896445178-0.811242212574-0.1895695716350.6985360623070.0326711869090.429610521012-0.05164277131910.02670705098490.355853986516-0.001156692045840.39655045411812.6024672631-31.4630510068-55.8473985674
220.2805506918760.04435306445740.1991211886610.3329718735970.1226803037290.2344166856210.4688844236020.621975157249-0.434445925657-0.166456949948-0.18099172869-0.08791667603180.5767449490960.3224768742360.005961632599550.3198947939540.00751034262294-0.01771286172770.374397092665-0.02532450205780.3023494149947.18742665069-39.0705473699-54.7017518051
230.159867731124-0.559239241644-0.1415800967121.45264927798-0.08095637604920.279023915146-0.1690101938840.0151242336467-0.2365864518120.341637360150.120333172859-0.00824912504386-0.12481992105-0.12675165683-0.3106777919370.138569381443-0.05509735168420.05498009294970.340693394742-0.03454731188690.25534408073-0.906207002995-38.7981802854-52.6002000628
240.1896407588150.21901138636-0.0385018352360.54682938028-0.07997481138130.1059129973660.0612680481233-0.4327688547820.4920318439210.1086623541680.00269324308095-0.0785811228547-0.0389685406406-0.1206533458720.0007427886481040.2907781783090.008019862780220.04691346934260.3473657412990.002608450216280.3237275336242.94527668602-29.0396209025-46.5337588868
250.06315197153420.2416792624350.1148226159150.6518333166190.4987593125770.2642047076030.278631940247-0.0386402974866-0.0725109946686-0.42448502403-0.3222301291950.02171483396260.3198066926970.0816696193645-0.0004050058386110.413182677164-0.01747738050810.01455684245190.3727418046050.03735068811940.354785327936-0.508839968877-39.8583180513-47.7777826133
260.0362363751115-0.0446446185672-0.003627384917760.04830792234350.01755321186110.0153952880656-0.268180371539-0.146908128833-0.333971321533-0.1197750511410.531910001940.3484935753770.301942778667-0.235873755941-0.0006940570231760.4215420800660.0252707121762-0.03061014418150.547586006921-0.09223620111990.4043651489371.60056630548-47.3008295564-53.7639373268
270.405355040661-0.00874365112151-0.1170062714730.0177493426711-0.05062638962690.265706008314-0.150993772337-0.0165359695399-0.276413453371-0.4277706247390.253315065739-0.232590081941-0.106547790390.65774800821-0.005809338922290.405022537395-0.0590772700321-0.04492954554130.446200537886-0.06654176182120.37093118194311.4090842813-47.9619217263-55.5844716893
281.31923499774-1.32592476469-1.004498797571.372900254481.069974932312.220312659460.538518076554-0.397448238727-0.1317004612140.17956834007-0.484555505651-0.127308646149-0.106222676815-1.322239723080.09272997586150.397080896114-0.0113244022567-0.01854404303790.591299562912-0.0665500578580.51080717396119.4698990462-32.2354787468-44.8288692982
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 335 )
3X-RAY DIFFRACTION3chain 'A' and (resid 336 through 374 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 166 )
5X-RAY DIFFRACTION5chain 'B' and (resid 167 through 197 )
6X-RAY DIFFRACTION6chain 'B' and (resid 198 through 309 )
7X-RAY DIFFRACTION7chain 'B' and (resid 310 through 335 )
8X-RAY DIFFRACTION8chain 'B' and (resid 336 through 373 )
9X-RAY DIFFRACTION9chain 'G' and (resid 2 through 7 )
10X-RAY DIFFRACTION10chain 'G' and (resid 8 through 23 )
11X-RAY DIFFRACTION11chain 'G' and (resid 24 through 42 )
12X-RAY DIFFRACTION12chain 'G' and (resid 43 through 50 )
13X-RAY DIFFRACTION13chain 'G' and (resid 51 through 70 )
14X-RAY DIFFRACTION14chain 'G' and (resid 71 through 87 )
15X-RAY DIFFRACTION15chain 'G' and (resid 88 through 109 )
16X-RAY DIFFRACTION16chain 'G' and (resid 110 through 117 )
17X-RAY DIFFRACTION17chain 'G' and (resid 118 through 125 )
18X-RAY DIFFRACTION18chain 'H' and (resid 2 through 7 )
19X-RAY DIFFRACTION19chain 'H' and (resid 8 through 15 )
20X-RAY DIFFRACTION20chain 'H' and (resid 16 through 23 )
21X-RAY DIFFRACTION21chain 'H' and (resid 24 through 34 )
22X-RAY DIFFRACTION22chain 'H' and (resid 35 through 51 )
23X-RAY DIFFRACTION23chain 'H' and (resid 52 through 70 )
24X-RAY DIFFRACTION24chain 'H' and (resid 71 through 87 )
25X-RAY DIFFRACTION25chain 'H' and (resid 88 through 103 )
26X-RAY DIFFRACTION26chain 'H' and (resid 104 through 109 )
27X-RAY DIFFRACTION27chain 'H' and (resid 110 through 117 )
28X-RAY DIFFRACTION28chain 'H' and (resid 118 through 125 )

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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