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- PDB-4pkh: Complex of ADP-actin With the N-terminal Actin-Binding Domain of ... -

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基本情報

登録情報
データベース: PDB / ID: 4pkh
タイトルComplex of ADP-actin With the N-terminal Actin-Binding Domain of Tropomodulin
要素
  • Actin, alpha skeletal muscle
  • Gelsolin,Tropomodulin-1 chimera
キーワードContractile Protein/Actin-Binding Protein / Tmod / Actin Filament / Pointed-End Capping Protein / Tropomyosin / Contractile Protein / Actin-binding Protein / Contractile Protein-Actin-Binding Protein complex
機能・相同性
機能・相同性情報


pointed-end actin filament capping / lens fiber cell development / myofibril assembly / 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 ...pointed-end actin filament capping / lens fiber cell development / myofibril assembly / 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 / actin cap / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / Striated Muscle Contraction / Sensory processing of sound by outer hair cells of the cochlea / podosome / relaxation of cardiac muscle / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / myosin heavy chain binding / hepatocyte apoptotic process / tropomyosin binding / cortical cytoskeleton / troponin I binding / filamentous actin / myofibril / mesenchyme migration / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / sarcoplasm / skeletal muscle thin filament assembly / actin monomer binding / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / stress fiber / skeletal muscle fiber development / phagocytic vesicle / titin binding / muscle contraction / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / adult locomotory behavior / sarcomere / central nervous system development / actin filament organization / filopodium / actin filament / protein destabilization / 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 / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / cell body / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / cytoskeleton / hydrolase activity / protein domain specific binding / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Tropomodulin / Tropomodulin / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat ...Tropomodulin / Tropomodulin / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / 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. / Actin / Actin family / Actin / Leucine-rich repeat domain superfamily / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / Gelsolin / Tropomodulin-1 / Actin, alpha skeletal muscle
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Oryctolagus cuniculus (ウサギ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.15 Å
データ登録者Rao, J.N. / Dominguez, R.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM073791 米国
引用ジャーナル: Science / 年: 2014
タイトル: Actin cytoskeleton. Mechanism of actin filament pointed-end capping by tropomodulin.
著者: Rao, J.N. / Madasu, Y. / Dominguez, R.
履歴
登録2014年5月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年7月30日Provider: repository / タイプ: Initial release
改定 1.12014年8月6日Group: Database references
改定 1.22017年9月6日Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
カテゴリ: citation / entity_src_gen ...citation / entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
改定 1.32019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年9月27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 / refine_hist / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_conn.ptnr2_label_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: Actin, alpha skeletal muscle
B: Gelsolin,Tropomodulin-1 chimera
D: Actin, alpha skeletal muscle
E: Gelsolin,Tropomodulin-1 chimera
F: Actin, alpha skeletal muscle
G: Gelsolin,Tropomodulin-1 chimera
I: Actin, alpha skeletal muscle
J: Gelsolin,Tropomodulin-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)253,87524
ポリマ－251,6858
非ポリマー2,19016
水9,872548
1
A: Actin, alpha skeletal muscle
B: Gelsolin,Tropomodulin-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,4696
ポリマ－62,9212
非ポリマー5474
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-66 kcal/mol
Surface area22640 Å2
手法PISA
2
D: Actin, alpha skeletal muscle
E: Gelsolin,Tropomodulin-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,4696
ポリマ－62,9212
非ポリマー5474
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-55 kcal/mol
Surface area20630 Å2
手法PISA
3
F: Actin, alpha skeletal muscle
G: Gelsolin,Tropomodulin-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,4696
ポリマ－62,9212
非ポリマー5474
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-61 kcal/mol
Surface area22930 Å2
手法PISA
4
I: Actin, alpha skeletal muscle
J: Gelsolin,Tropomodulin-1 chimera
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)63,4696
ポリマ－62,9212
非ポリマー5474
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-58 kcal/mol
Surface area20910 Å2
手法PISA
単位格子
Length a, b, c (Å)69.222, 135.136, 140.549
Angle α, β, γ (deg.)90.00, 94.41, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Actin, alpha skeletal muscle / Alpha-actin-1


分子量: 42096.953 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 組織: Skeletal Muscle / 参照: UniProt: P68135
#2: タンパク質
Gelsolin,Tropomodulin-1 chimera / AGEL / Actin-depolymerizing factor / ADF / Brevin / Erythrocyte tropomodulin / E-Tmod


分子量: 20824.406 Da / 分子数: 4
Fragment: Gelsolin (UNP residues 12-136), GGSGGSGGS linker, Tmod1 Actin-binding site 1 (UNP residues 50-101)
由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GSN, TMOD1, D9S57E, TMOD / プラスミド: pTYB11 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P06396, UniProt: P28289
#3: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM
#4: 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: 12 / 由来タイプ: 合成 / 式: Ca
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 548 / 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

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試料調製

結晶マシュー密度: 2.6 Å3/Da / 溶媒含有率: 52.77 %
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 0.18 M sodium fluoride, 11% w/v PEG3350, 1% v/v PEG1000, 1% v/v PEG400
PH範囲: 7.5

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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: NSLS / ビームライン: X6A / 波長: 1.0781 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2013年3月6日
放射モノクロメーター: channel cut 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: 1.0781 Å / 相対比: 1
反射解像度: 2.15→46 Å / Num. obs: 138122 / % possible obs: 98.7 % / 冗長度: 5.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.03
反射 シェル解像度: 2.15→2.28 Å / 冗長度: 5.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.8.4_1496)精密化
HKL-2000データスケーリング
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 1EQY

1eqy


解像度: 2.15→44.9 Å / SU ML: 0.41 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 36.48 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3262 2017 1.46 %
Rwork0.2742 --
obs0.2749 138063 98.41 %
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: 2.15→44.9 Å
タンパク質核酸リガンド溶媒全体
原子数15772 0 120 548 16440
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01816281
X-RAY DIFFRACTIONf_angle_d1.72922082
X-RAY DIFFRACTIONf_dihedral_angle_d18.3396008
X-RAY DIFFRACTIONf_chiral_restr0.0712411
X-RAY DIFFRACTIONf_plane_restr0.012836
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1473-2.2010.38961400.33879456X-RAY DIFFRACTION96
2.201-2.26050.36791570.32989754X-RAY DIFFRACTION99
2.2605-2.3270.3831220.33819754X-RAY DIFFRACTION99
2.327-2.40210.39321670.33079724X-RAY DIFFRACTION99
2.4021-2.4880.39241430.31859706X-RAY DIFFRACTION99
2.488-2.58760.35591390.31329726X-RAY DIFFRACTION99
2.5876-2.70530.39881350.3079747X-RAY DIFFRACTION99
2.7053-2.84790.34651520.29199670X-RAY DIFFRACTION98
2.8479-3.02630.33391470.28669711X-RAY DIFFRACTION98
3.0263-3.25990.34741380.27649597X-RAY DIFFRACTION98
3.2599-3.58790.31071470.25719631X-RAY DIFFRACTION97
3.5879-4.10670.29821340.24179715X-RAY DIFFRACTION98
4.1067-5.17280.2751460.23129869X-RAY DIFFRACTION100
5.1728-44.92070.30581500.27199986X-RAY DIFFRACTION99
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)
11.7014-0.4959-0.66571.95581.01194.32480.2064-0.60660.27240.5531-0.17370.3798-0.4049-0.085-0.07270.3747-0.03760.15710.3738-0.09290.2889-24.90211.9513186.4066
22.4848-0.2745-0.44582.14210.81213.11430.1201-0.59450.26020.31710.03050.0769-0.24690.064-0.12090.2208-0.02220.05760.2382-0.0460.2145-17.21217.4456177.8672
31.051-0.8868-0.47181.51470.78851.34740.0277-0.08360.3207-0.25730.02360.266-0.6493-0.6799-0.07270.52960.31610.06810.6865-0.06950.7315-36.342827.0267174.3462
40.4575-0.69710.12362.00570.57451.222-0.1176-0.18170.7049-0.0188-0.020.0288-0.3888-0.3322-0.24610.84220.42440.1620.441-0.0170.8514-35.199932.1559170.6161
51.5992-0.414-1.48070.94030.44411.38020.49850.70190.7076-0.2967-0.25110.0436-0.9394-0.515-0.31340.47720.48870.28950.21730.22270.726-26.406620.8758157.4264
62.76580.0639-1.39041.1360.28633.59190.1104-0.0922-0.01860.0333-0.0190.06750.16560.1649-0.12010.22720.01820.00130.2255-0.0760.2531-17.68623.8646168.5909
71.692-0.8685-1.12555.07041.06220.799-0.118-0.2262-0.00450.45560.3501-0.5280.6740.43510.13790.72570.2956-0.23830.3908-0.32260.6177-12.8119-13.2727159.5718
82.9759-0.0543-1.58193.17131.35583.4866-0.34020.0775-0.70730.1810.18590.02570.50870.0262-0.23230.3568-0.0408-0.11010.1849-0.10660.3975-19.0176-12.216151.2191
92.46540.45911.24332.81330.55131.04-0.06240.3447-0.55920.2245-0.04970.34950.8549-0.4248-0.07760.3974-0.1607-0.00440.3082-0.09990.3992-25.5216-14.7302156.5427
100.1360.1630.59752.20891.0742.68910.06461.1768-0.6580.0621-0.15890.30860.3966-0.44590.18230.23310.0016-0.09260.4201-0.17520.3407-25.3668-9.0282149.0989
114.05890.5722-0.99852.26130.84753.8041-0.08540.287-0.2623-0.02680.0182-0.23450.4656-0.03740.07130.27920.0104-0.08690.2149-0.03070.2507-19.4351-3.3138148.2522
121.10380.96770.2831.2390.98234.44180.08720.6148-0.26140.00390.03850.0910.2889-0.1978-0.12060.22450.0053-0.03720.3465-0.06120.2061-21.6243-1.3059152.4889
132.68770.32970.34253.1971-2.4872.0711-0.09330.4578-0.4551-0.1543-0.1135-0.07021.1344-0.4542-0.48860.5078-0.0755-0.09570.257-0.23930.5927-32.8393-9.6933142.7526
144.60630.47082.36271.44710.62881.3169-0.0077-0.5978-0.74320.2139-0.1258-0.04520.7329-0.8432-0.16030.4125-0.137-0.06650.4109-0.03850.4771-35.0601-8.6997163.4409
151.54610.6007-1.98592.25220.27743.0961-0.52660.1226-0.02510.0949-0.1276-0.17690.1069-0.69120.10360.47580.43110.11670.9405-0.41061.026-47.130.7799193.3308
164.1536-4.47530.26654.8282-0.35520.6076-0.3784-0.07980.71280.4647-0.091-0.0707-0.3199-0.36610.54240.6164-0.27650.16031.2459-0.18731.2917-37.648415.9463201.639
170.18880.36010.06061.7254-1.12521.7988-0.548-0.8755-0.31420.179-0.15620.84170.2161-0.12040.37920.7765-0.32790.25460.9115-0.03140.8291-19.07543.715197.8294
180.3972-0.9752-0.81094.1521-0.61446.543-0.6696-0.8562-0.6755-0.078-0.0868-0.01251.1550.2660.83510.6556-0.11450.00260.49290.11370.4257-0.2075-0.7381187.0038
192.1073-0.4354-1.00083.42430.96363.36180.03920.67690.0374-0.5172-0.09270.37690.1139-0.43940.01830.29810.0007-0.10970.45360.01390.28319.0359-9.2514126.1011
201.83720.0672-1.19223.0031-0.24842.10070.00540.35620.0031-0.4024-0.0146-0.12880.08610.1112-0.01550.25210.0162-0.03690.3239-0.02230.218117.4349-9.2701129.1907
211.95821.02440.08333.25761.38342.2002-0.11810.1197-0.43770.2112-0.22290.27870.8227-0.51520.04230.4289-0.1920.0980.2702-0.12570.36652.2503-26.2277142.5463
222.63010.7037-0.5772.54110.26763.3987-0.00430.2249-0.13970.16810.0084-0.08930.092-0.09460.03340.20370.018-0.02330.1936-0.04050.163712.4211-9.7883145.7191
232.30472.02560.58975.2636-4.6349.53670.0104-0.42850.1584-0.5894-0.4052-0.7567-0.04010.89330.20890.3547-0.05630.11950.2205-0.05510.467422.369311.8286151.2808
242.2737-0.0997-0.63861.88050.83553.04420.0957-0.33940.3469-0.00280.0158-0.1109-0.26080.173-0.04890.2114-0.02080.02830.1914-0.06130.22311.23645.6739160.6867
252.78311.42750.11887.53282.67786.2785-0.32280.0644-0.6092-0.38350.2538-0.82110.5893-0.68640.35120.9406-0.0240.1390.66430.2591.0592-18.0522.7253109.9245
260.02880.3250.38753.46754.40325.82510.38710.3702-0.38820.3802-0.14740.00950.3677-0.37310.31870.71090.1756-0.09070.73770.04880.677-18.491217.9857127.9804
272.03520.9867-0.77184.63472.82934.2038-0.1595-0.451-0.1686-0.6761-0.25070.0303-0.2444-0.92030.30070.62780.0764-0.18780.7638-0.06260.8365-17.050618.7427119.8484
280.6879-0.07651.10852.06410.46161.87560.1983-0.28520.23180.28730.0625-0.7443-0.02330.1961-0.02410.6657-0.0105-0.06411.04950.08510.919-8.12445.6209112.1041
292.2546-0.3571-0.40791.2049-0.34221.7761-0.0487-0.53830.1633-0.15150.1059-0.9186-0.21360.69180.05030.71750.0285-0.11621.12330.10040.7892-12.245416.378494.6507
302.936-1.6193-0.14663.14521.31121.0725-0.0189-0.19310.23080.58930.34570.329-0.4738-0.03180.42291.4608-0.05930.06880.7183-0.08060.6683-29.028531.4371113.5378
311.58240.7495-0.31512.43930.08653.18480.0955-0.39690.47390.3612-0.30871.011-0.8386-0.67040.31481.08120.233-0.08890.915-0.11731.0358-37.765627.4553104.6166
320.752-1.23580.10812.30610.7183.17320.1081-0.50140.4189-0.7413-0.3426-0.2152-0.3423-0.6520.38151.26730.1375-0.17180.8618-0.04240.9531-27.722531.853101.5462
333.58440.87310.36330.8247-1.29523.2245-0.18550.23660.1797-1.06030.2164-0.3742-0.53730.36210.14110.84320.02220.03590.90080.01340.7717-12.977620.280184.2335
341.3066-0.43221.22022.8054-0.21041.1818-0.2257-0.11690.9242-0.6418-0.39550.258-0.43430.21640.24991.02610.1554-0.09970.9438-0.08920.7662-25.061520.416591.7614
351.18520.18861.49612.08690.73651.938-0.05120.291-0.05980.6231-0.1616-0.3292-0.13170.2915-0.01290.5681-0.0448-0.00990.95070.01570.6791-9.95183.905299.4244
361.22971.57530.48442.02350.64171.95920.03160.1844-0.48550.62610.0973-1.17130.63960.5684-0.35420.67270.25160.05060.85660.30731.705-3.2662-11.964392.9067
373.6394-0.1270.75822.05240.72422.93320.27180.932-0.2661-0.1616-0.2359-0.30850.3736-0.09150.05040.54650.10130.06740.9101-0.19010.9937-13.5012-7.967683.631
383.39761.3596-1.58762.5889-1.03253.05050.6285-0.06010.30740.6402-0.08650.61270.2617-0.5836-0.4780.6869-0.17550.02411.1253-0.05480.772-19.4187-4.344180.239
391.3462-1.2202-0.53461.4793-0.07141.04090.04980.17170.0488-0.8693-0.01470.4071-0.4014-0.1336-0.11121.3911-0.2644-0.29230.5317-0.15851.5645-46.380934.054118.3947
404.7432-0.10790.15610.07250.32242.1533-0.4614-1.2522-1.57840.1386-0.21080.02260.1673-0.77850.66440.8155-0.41260.10231.0348-0.08430.8975-38.206327.1808127.4994
412.9239-0.16741.83243.97042.27512.8790.14350.5209-0.2806-0.3304-0.3838-0.08120.1114-0.10890.36450.8768-0.01290.04281.19190.06510.66122.3081-10.018361.583
423.30971.04740.53452.0360.73793.23430.15780.29140.057-0.29930.0645-0.4391-0.4793-0.4546-0.08430.68550.0755-0.14950.77810.18640.71415.9687-25.462271.6386
433.56643.58352.33626.54911.00674.8343-0.06471.1582-0.1037-0.8929-0.2191-0.037-0.006-0.41520.21041.1004-0.0908-0.25561.09080.11350.90912.3059-25.92858.9293
442.54591.77560.4733.10721.20422.88870.09080.05340.1920.204-0.2439-0.00640.0252-0.38530.03960.861-0.04990.09620.9955-0.03010.80537.3286-26.814577.9174
454.09180.68070.08621.60591.54021.8899-0.2888-0.77980.85310.2874-0.0626-0.050.40830.67530.40310.77210.0353-0.17550.9640.17250.810624.8451-4.754674.6093
462.71530.7319-0.42472.1901-2.66264.41420.72231.10160.1074-0.7154-0.5348-0.49980.120.40180.0310.52550.32260.09771.2430.33491.258831.362910.292881.7727
477.0973-0.36092.03364.0887-1.8774.17221.065-0.06360.9369-0.3556-0.27780.3092-0.4313-0.8215-0.66630.73310.20050.11520.9481-0.16381.029619.528610.6991.5017
485.50910.73812.95472.3793-0.04095.15770.6151-0.7257-0.62930.394-0.2089-0.3642-0.0524-0.726-0.31440.7242-0.11310.02580.98810.10950.723323.36531.057190.4469
494.1478-0.87032.01424.7527-6.09238.05010.0424-1.1593-0.23380.12740.96560.8779-0.0336-1.9947-1.1770.66420.09950.08721.0522-0.24491.125210.94635.046394.7816
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 246 )
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 273 )
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 320 )
6X-RAY DIFFRACTION6chain 'A' and (resid 321 through 375 )
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 61 )
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 85 )
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 102 )
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 121 )
12X-RAY DIFFRACTION12chain 'B' and (resid 122 through 160 )
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 168 )
14X-RAY DIFFRACTION14chain 'B' and (resid 169 through 177 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1059 through 1071 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1072 through 1081 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1082 through 1091 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1092 through 1099 )
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 59 )
20X-RAY DIFFRACTION20chain 'D' and (resid 60 through 145 )
21X-RAY DIFFRACTION21chain 'D' and (resid 146 through 295 )
22X-RAY DIFFRACTION22chain 'D' and (resid 296 through 375 )
23X-RAY DIFFRACTION23chain 'E' and (resid 53 through 60 )
24X-RAY DIFFRACTION24chain 'E' and (resid 61 through 177 )
25X-RAY DIFFRACTION25chain 'F' and (resid 5 through 28 )
26X-RAY DIFFRACTION26chain 'F' and (resid 29 through 55 )
27X-RAY DIFFRACTION27chain 'F' and (resid 56 through 78 )
28X-RAY DIFFRACTION28chain 'F' and (resid 79 through 145 )
29X-RAY DIFFRACTION29chain 'F' and (resid 146 through 181 )
30X-RAY DIFFRACTION30chain 'F' and (resid 182 through 206 )
31X-RAY DIFFRACTION31chain 'F' and (resid 207 through 246 )
32X-RAY DIFFRACTION32chain 'F' and (resid 247 through 273 )
33X-RAY DIFFRACTION33chain 'F' and (resid 274 through 295 )
34X-RAY DIFFRACTION34chain 'F' and (resid 296 through 320 )
35X-RAY DIFFRACTION35chain 'F' and (resid 321 through 375 )
36X-RAY DIFFRACTION36chain 'G' and (resid 52 through 60 )
37X-RAY DIFFRACTION37chain 'G' and (resid 61 through 138 )
38X-RAY DIFFRACTION38chain 'G' and (resid 139 through 177 )
39X-RAY DIFFRACTION39chain 'G' and (resid 1058 through 1063 )
40X-RAY DIFFRACTION40chain 'G' and (resid 1064 through 1074 )
41X-RAY DIFFRACTION41chain 'I' and (resid 5 through 165 )
42X-RAY DIFFRACTION42chain 'I' and (resid 166 through 196 )
43X-RAY DIFFRACTION43chain 'I' and (resid 197 through 216 )
44X-RAY DIFFRACTION44chain 'I' and (resid 217 through 320 )
45X-RAY DIFFRACTION45chain 'I' and (resid 321 through 375 )
46X-RAY DIFFRACTION46chain 'J' and (resid 52 through 60 )
47X-RAY DIFFRACTION47chain 'J' and (resid 61 through 102 )
48X-RAY DIFFRACTION48chain 'J' and (resid 103 through 149 )
49X-RAY DIFFRACTION49chain 'J' and (resid 150 through 177 )

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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