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- PDB-4lgd: Structural Basis for Autoactivation of Human Mst2 Kinase and Its ... -

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基本情報

登録情報
データベース: PDB / ID: 4lgd
タイトルStructural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5
要素
  • Ras association domain family member 5, RASSF5
  • Serine/threonine-protein kinase 3
キーワードSIGNALING PROTEIN / Hippo / Mst autoactivation / RASSF / SARAH domain / dimerization
機能・相同性
機能・相同性情報


regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of lymphocyte proliferation / positive regulation of hippo signaling / lymphocyte proliferation / endocardium development / negative regulation of organ growth ...regulation of cell differentiation involved in embryonic placenta development / cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of lymphocyte proliferation / positive regulation of hippo signaling / lymphocyte proliferation / endocardium development / negative regulation of organ growth / hippo signaling / transcription regulator activator activity / regulation of protein localization to nucleus / Signaling by Hippo / protein localization to centrosome / organ growth / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / JNK cascade / protein serine/threonine kinase activator activity / central nervous system development / epithelial cell proliferation / positive regulation of protein ubiquitination / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / protein import into nucleus / negative regulation of epithelial cell proliferation / microtubule / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / magnesium ion binding / signal transduction / protein-containing complex / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
Helix Hairpins - #4270 / Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / : / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 ...Helix Hairpins - #4270 / Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / : / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / SARAH domain / SARAH domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / : / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / p53-like tetramerisation domain superfamily / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Ubiquitin-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase 3 / Ras association domain-containing protein 5
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 / molecular replacement-SAD / 解像度: 3.05 Å
データ登録者Luo, X. / Ni, L. / Tomchick, D.R.
引用ジャーナル: Structure / 年: 2013
タイトル: Structural Basis for Autoactivation of Human Mst2 Kinase and Its Regulation by RASSF5.
著者: Ni, L. / Li, S. / Yu, J. / Min, J. / Brautigam, C.A. / Tomchick, D.R. / Pan, D. / Luo, X.
履歴
登録2013年6月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年9月18日Provider: repository / タイプ: Initial release
改定 1.12013年10月30日Group: Database references
改定 1.22017年8月9日Group: Source and taxonomy / カテゴリ: entity_src_gen
改定 1.32017年11月15日Group: Refinement description / カテゴリ: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
改定 1.42018年2月28日Group: Data collection / Experimental preparation / Refinement description
カテゴリ: diffrn_radiation / exptl_crystal ...diffrn_radiation / exptl_crystal / exptl_crystal_grow / software
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ..._diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_pH_range
改定 1.52023年9月20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 / struct_ref_seq_dif / struct_site
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_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 / _struct_ref_seq_dif.details / _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: Serine/threonine-protein kinase 3
B: Serine/threonine-protein kinase 3
C: Serine/threonine-protein kinase 3
D: Serine/threonine-protein kinase 3
E: Ras association domain family member 5, RASSF5
F: Ras association domain family member 5, RASSF5
G: Ras association domain family member 5, RASSF5
H: Ras association domain family member 5, RASSF5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)201,41528
ポリマ－198,3598
非ポリマー3,05620
水00
1
A: Serine/threonine-protein kinase 3
E: Ras association domain family member 5, RASSF5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,2165
ポリマ－49,5902
非ポリマー6273
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-26 kcal/mol
Surface area23710 Å2
手法PISA
2
C: Serine/threonine-protein kinase 3
G: Ras association domain family member 5, RASSF5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,2627
ポリマ－49,5902
非ポリマー6735
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-31 kcal/mol
Surface area23590 Å2
手法PISA
3
D: Serine/threonine-protein kinase 3
H: Ras association domain family member 5, RASSF5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,4318
ポリマ－49,5902
非ポリマー8426
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-18 kcal/mol
Surface area21960 Å2
手法PISA
4
B: Serine/threonine-protein kinase 3
F: Ras association domain family member 5, RASSF5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,5058
ポリマ－49,5902
非ポリマー9156
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
A: Serine/threonine-protein kinase 3
B: Serine/threonine-protein kinase 3
E: Ras association domain family member 5, RASSF5
F: Ras association domain family member 5, RASSF5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,72113
ポリマ－99,1804
非ポリマー1,5419
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-75 kcal/mol
Surface area41720 Å2
手法PISA
6
C: Serine/threonine-protein kinase 3
D: Serine/threonine-protein kinase 3
G: Ras association domain family member 5, RASSF5
H: Ras association domain family member 5, RASSF5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,69415
ポリマ－99,1804
非ポリマー1,51411
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-88 kcal/mol
Surface area40920 Å2
手法PISA
単位格子
Length a, b, c (Å)123.403, 237.136, 95.862
Angle α, β, γ (deg.)90.000, 100.700, 90.000
Int Tables number5
Space group name H-MC121

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要素

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タンパク質 / タンパク質・ペプチド , 2種, 8分子 ABCDEFGH

#1: タンパク質
Serine/threonine-protein kinase 3 / Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein kinase Krs-1 / Serine/threonine-protein kinase 3 36kDa subunit / MST2/N / Serine/threonine-protein kinase 3 20kDa subunit / MST2/C


分子量: 43626.164 Da / 分子数: 4
断片: kinase domain, SARAH domain, UNP residues 1-313, 428-491
変異: D146N / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: STK3, KRS1, MST2 / プラスミド: pET29 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: Q13188, non-specific serine/threonine protein kinase
#2: タンパク質・ペプチド
Ras association domain family member 5, RASSF5 / New ras effector 1 / Regulator for cell adhesion and polarization enriched in lymphoid tissues / RAPL


分子量: 5963.654 Da / 分子数: 4 / 断片: SARAH domain, UNP residues 365-413 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RASSF5, NORE1, RAPL / プラスミド: pGEX-6p / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q8WWW0

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非ポリマー , 4種, 20分子

#3: 化合物
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP


分子量: 506.196 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H17N6O12P3
コメント: AMP-PNP, エネルギー貯蔵分子類似体*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: 4 / 由来タイプ: 合成 / 式: Mg
#5: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 9 / 由来タイプ: 合成 / 式: SO4
#6: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Na

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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
IDマシュー密度 (Å3/Da)溶媒含有率 (%)
13.4764.59
23.4764.59
結晶化温度: 293 K / 手法: 蒸気拡散法
詳細: 0.1 M Bis-Tris propane, 200 mM Na2SO4, 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH範囲: 8.5

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データ収集

回折
ID平均測定温度 (K)Crystal-ID
11001
21002
放射光源
由来サイトビームラインID波長
シンクロトロンAPS 19-ID10.97929
シンクロトロンAPS 19-ID20.97921
検出器
タイプID検出器日付詳細
ADSC QUANTUM 315r1CCD2011年2月12日MONOCHROMATOR
ADSC QUANTUM 315r2CCD2011年3月14日MONOCHROMATOR
放射
IDモノクロメータープロトコル単色(M)・ラウエ(L)散乱光タイプWavelength-ID
1SAGITALLY FOCUSED SI(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED SI(111)SINGLE WAVELENGTHMx-ray1
放射波長
ID波長 (Å)相対比
10.979291
20.979211
反射解像度: 3.05→46.049 Å / Num. obs: 50456 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / 冗長度: 4.1 % / Biso Wilson estimate: 71.84 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.4
Reflection scaleGroup code: 1
反射 シェル解像度: 3.05→3.1 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.6 / % possible all: 90.7

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
PHENIX1.8_1069精密化
PDB_EXTRACT3.11データ抽出
PHASES位相決定
精密化構造決定の手法: molecular replacement-SAD
開始モデル: PDB ENTRY 4LG4

4lg4


解像度: 3.05→30 Å / SU ML: 0.29 / σ(F): 0 / 位相誤差: 32.15 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.244 2524 5 %
Rwork0.199 --
obs0.202 50374 98.6 %
all-65746 -
溶媒の処理減衰半径: 0.99 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: 135.9 Å2
精密化ステップサイクル: LAST / 解像度: 3.05→30 Å
タンパク質核酸リガンド溶媒全体
原子数12609 0 176 0 12785
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00613027
X-RAY DIFFRACTIONf_angle_d0.6117577
X-RAY DIFFRACTIONf_dihedral_angle_d14.5575083
X-RAY DIFFRACTIONf_chiral_restr0.0361935
X-RAY DIFFRACTIONf_plane_restr0.0022230
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0532-3.11190.39331240.29382308X-RAY DIFFRACTION85
3.1119-3.17530.35341320.30452498X-RAY DIFFRACTION93
3.1753-3.24430.33681420.29322618X-RAY DIFFRACTION98
3.2443-3.31970.2981330.25872672X-RAY DIFFRACTION99
3.3197-3.40260.30381310.24082690X-RAY DIFFRACTION99
3.4026-3.49440.28991390.22222690X-RAY DIFFRACTION100
3.4944-3.59710.27561430.20232682X-RAY DIFFRACTION100
3.5971-3.7130.23631650.1912691X-RAY DIFFRACTION100
3.713-3.84540.25841270.18912698X-RAY DIFFRACTION100
3.8454-3.9990.25841330.17342701X-RAY DIFFRACTION100
3.999-4.18060.22471480.17742702X-RAY DIFFRACTION100
4.1806-4.40030.2091490.16732665X-RAY DIFFRACTION100
4.4003-4.6750.21821310.16422691X-RAY DIFFRACTION100
4.675-5.03440.22421590.18962694X-RAY DIFFRACTION100
5.0344-5.5380.2411310.20722713X-RAY DIFFRACTION100
5.538-6.33260.2881360.21592721X-RAY DIFFRACTION100
6.3326-7.95280.21771360.20442713X-RAY DIFFRACTION100
7.9528-29.6520.20061650.17682703X-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)
10.27550.06180.13470.19430.03320.1136-0.70480.5229-0.6099-0.5725-0.1386-0.13110.95320.3967-0.07032.70331.10190.051.7573-0.11561.874433.3768-71.101316.7739
20.0903-0.0702-0.04240.0510.00070.0248-0.7201-0.27260.13750.4030.03730.08630.51990.138402.89810.15350.25291.7597-0.07881.374935.7405-57.487814.5636
30.0760.03050.05020.00180.00330.0453-0.1556-0.3079-0.3530.01790.205-0.226-0.056-0.3078-0.00032.05810.62510.09760.9359-0.10641.431936.8545-61.519825.6929
40.08520.19920.00360.43570.3570.68830.22160.0702-0.38860.28170.68260.73850.99520.07490.2952.23270.49050.08780.9103-0.12290.917122.7867-58.176528.4377
50.480.00020.21780.2385-0.14480.14540.23971.098-0.19430.46980.17950.03360.63210.58590.04821.82740.50130.1010.9005-0.13011.002928.9479-50.983225.1448
60.66770.28110.14750.84860.40190.5844-0.4799-0.2444-0.1590.99520.56230.3008-0.2350.22540.92631.72020.47440.42290.53350.18650.721418.249-41.937531.2699
70.0508-0.05680.05360.0413-0.01140.00750.22710.23410.29350.7457-0.6096-0.1932-0.3355-0.46440.00012.48180.07130.11911.12440.10691.653511.2766-71.775418.3566
8-0.00790.00890.0482-0.0071-0.02360.0291-0.6448-0.4206-0.40660.25830.10360.3161-0.09070.2706-0.00012.15370.00750.20121.0069-0.04071.369821.3249-81.8802-0.6008
90.02750.00180.02790.0236-0.0110.0110.62820.31550.26880.12390.59450.0663-0.0381-0.3440.0020.7893-0.21320.26151.00810.0952.09119.9015-63.4374-11.2906
100.0076-0.0093-0.0289-0.00560.0070.0293-0.2274-0.0909-0.03180.1478-0.4462-0.1969-0.04720.10700.9849-0.0234-0.07640.9835-0.24921.81160.8238-41.2496-21.5916
110.2353-0.0032-0.25590.3001-0.07710.1818-0.0626-0.5043-0.3081-0.2062-0.030.02280.33160.175700.9080.1541-0.06540.645-0.07410.670923.4163-31.6941-23.8233
120.3317-0.2056-0.2990.40120.2430.52840.0284-0.16460.075-0.3257-0.061-0.12910.3860.0981-0.00020.52470.112-0.01020.60450.02490.551722.2771-25.2343-12.8967
130.0247-0.2366-0.21461.25521.01961.0466-0.27990.26740.1341.305-0.09930.39621.9350.0272-0.02860.07750.17720.16340.63470.04240.570117.6769-24.6851.6615
140.00290.0193-0.01010.0029-0.0180.0259-0.1527-0.3069-0.17180.698-0.22610.420.38690.1928-01.31510.26090.09170.90630.01640.706927.0791-25.333814.899
150.28730.2339-0.31940.78330.1210.44040.2802-0.13460.08231.32350.03210.2578-0.41040.13840.08080.3040.27230.18470.6302-0.03860.578318.6211-8.73797.8759
160.4461-0.0601-0.01190.3441-0.21620.5153-0.31350.39390.1481-0.3591-0.1899-0.45020.78650.12760.00320.15140.21320.13140.9901-0.12920.843740.9563-19.9535-14.5696
170.00820.001-0.00370.00510.0003-0.0061-0.0030.1827-0.026-0.09560.1107-0.0009-0.0588-0.1175-02.02550.18470.54992.02580.20372.15252.4416-43.2949-28.075
180.0044-0.0070.00640.0023-0.0033-0-0.0032-0.1989-0.00940.05970.1085-0.10530.0629-0.0207-01.51170.12820.34432.74830.50441.801655.2402-48.6452-13.1814
19-0.01230.01810.02450.02850.05310.0257-0.4697-0.50450.1766-0.02050.37330.14920.0442-0.1496-02.65620.59420.29012.0480.24481.676555.4657-53.849510.1501
200.30280.12050.23570.0833-0.10610.3132-0.6082-0.31140.48440.49880.23240.0088-0.934-0.2185-0.00011.05960.0873-0.1540.9447-0.2321.073533.400337.86834.1304
210.0090.535-0.23090.8288-0.10170.6761-0.3033-0.06840.0598-0.34720.2771-0.0201-0.06480.1424-0.00030.67710.1181-0.13780.6164-0.03420.685626.906523.099522.5197
220.79490.3877-0.24660.79330.17080.5294-0.17890.22780.1479-1.02720.35750.31040.163-0.00950.00130.96510.0337-0.13060.62090.11730.627616.915921.857614.6154
230.1641-0.127-0.16470.16680.41610.96370.370.0529-0.1479-0.81480.50360.5037-1.2092-0.46020.12281.14430.0595-0.32040.90960.28161.26685.097543.104647.1477
24-0.00610.0146-0.0109-0.0126-0.01290.0477-0.120.3355-0.16090.2387-0.7870.63090.2765-0.1480.00010.48840.0179-0.04151.0294-0.12931.171-13.700813.498760.6545
250.1460.02520.06430.21260.03610.48950.19690.01120.00930.11-0.15330.0646-0.68730.1423-0.00560.22330.0954-0.02150.621-0.02830.7098.04793.248367.5427
260.2756-0.0539-0.38190.0556-0.12080.5808-0.53270.1458-0.0568-0.03310.4035-0.14910.511-0.2924-0.03370.4772-0.0997-0.14590.6194-0.03780.53963.18773.622658.3747
270.1933-0.21740.25090.0742-0.2890.46790.17920.15410.08330.9462-0.15760.14651.0868-0.1519-0.01520.3040.292-0.10860.7655-0.02350.500913.8924-14.441852.0799
280.39130.412-0.19650.28030.2080.29780.1477-0.12290.0201-0.1393-0.01980.1009-0.20160.10700.53980.139-0.02350.4963-0.00450.40529.7545-4.202742.3007
290.3581-0.23670.16020.46340.43760.5669-0.09670.15930.0152-0.16180.04810.0070.92660.216300.94340.18950.05480.6593-0.01560.551415.4503-15.919936.0141
300.0090.163-0.0151-0.01870.10070.0137-0.2366-0.8858-0.56620.04660.0566-0.1771-0.09260.0567-0.00050.90180.1143-0.01991.1404-0.03080.538925.6015-8.967165.9416
310.0279-0.0107-0.00340.0070.0030.01480.5718-0.2120.0182-0.062-0.111-0.0020.03640.1378-0.00021.02120.28890.00582.21610.03121.363141.438620.123862.7501
320.01060.02350.01710.0102-0.00470.00680.0253-0.0812-0.22660.10920.49440.4789-0.29620.1550.00010.767-0.1633-0.12971.7674-0.24431.122752.360727.598140.7763
330.16630.12520.03270.10330.10410.2268-0.15660.1309-0.14480.2544-0.20620.20550.08710.26530.00011.10770.06640.19340.9338-0.06021.211314.0945-48.9809-17.1816
340.00850.0114-0.02660.02560.01730.02780.42220.0979-0.06480.06240.68860.0925-0.35730.42540.00012.08330.05860.22380.92150.0741.161726.29-78.9945-8.6353
350.1390.0748-0.04870.07290.04710.02940.4354-0.1193-0.4286-0.1867-0.12380.25310.08160.21420.00463.39781.69320.73542.4893-0.02341.430947.4217-59.1034.9299
360.00070.0043-0.00230.0066-0.00570.003-0.06490.05340.01940.0478-0.09440.2306-0.04980.0717-00.8249-0.1406-0.20570.9908-0.09240.7589-6.49328.007453.6329
370.35921.265-0.2641.45060.02581.8811-0.1224-0.19940.3187-0.58570.5420.9153-1.7333-0.27960.2045-0.029-0.2936-0.39790.52750.05820.88946.518333.501356.5771
380.00920.00750.0059-0.00040.0011-0.00120.0660.04530.0213-0.19020.29860.2893-0.1741-0.0758-0.00011.01050.2448-0.08521.4593-0.1791.174243.554923.429935.527
390.08680.11240.09460.00660.07760.0614-0.50810.4404-0.27891.3610.05350.6965-0.02720.4226-0.01761.35990.0550.23091.1836-0.26081.23836.941429.054457.3256
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 140 )
5X-RAY DIFFRACTION5chain 'A' and (resid 141 through 176 )
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 287 )
7X-RAY DIFFRACTION7chain 'A' and (resid 288 through 313 )
8X-RAY DIFFRACTION8chain 'A' and (resid 437 through 453 )
9X-RAY DIFFRACTION9chain 'A' and (resid 454 through 474 )
10X-RAY DIFFRACTION10chain 'A' and (resid 475 through 488 )
11X-RAY DIFFRACTION11chain 'B' and (resid 10 through 39 )
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 139 )
13X-RAY DIFFRACTION13chain 'B' and (resid 140 through 216 )
14X-RAY DIFFRACTION14chain 'B' and (resid 217 through 233 )
15X-RAY DIFFRACTION15chain 'B' and (resid 234 through 283 )
16X-RAY DIFFRACTION16chain 'B' and (resid 284 through 313 )
17X-RAY DIFFRACTION17chain 'B' and (resid 443 through 455 )
18X-RAY DIFFRACTION18chain 'B' and (resid 456 through 463 )
19X-RAY DIFFRACTION19chain 'B' and (resid 464 through 488 )
20X-RAY DIFFRACTION20chain 'C' and (resid 12 through 75 )
21X-RAY DIFFRACTION21chain 'C' and (resid 76 through 216 )
22X-RAY DIFFRACTION22chain 'C' and (resid 217 through 313 )
23X-RAY DIFFRACTION23chain 'C' and (resid 437 through 473 )
24X-RAY DIFFRACTION24chain 'C' and (resid 474 through 490 )
25X-RAY DIFFRACTION25chain 'D' and (resid 11 through 63 )
26X-RAY DIFFRACTION26chain 'D' and (resid 64 through 99 )
27X-RAY DIFFRACTION27chain 'D' and (resid 100 through 139 )
28X-RAY DIFFRACTION28chain 'D' and (resid 140 through 216 )
29X-RAY DIFFRACTION29chain 'D' and (resid 217 through 283 )
30X-RAY DIFFRACTION30chain 'D' and (resid 284 through 313 )
31X-RAY DIFFRACTION31chain 'D' and (resid 455 through 473 )
32X-RAY DIFFRACTION32chain 'D' and (resid 474 through 489 )
33X-RAY DIFFRACTION33chain 'E' and (resid 367 through 399 )
34X-RAY DIFFRACTION34chain 'E' and (resid 400 through 413 )
35X-RAY DIFFRACTION35chain 'F' and (resid 370 through 398 )
36X-RAY DIFFRACTION36chain 'G' and (resid 366 through 373 )
37X-RAY DIFFRACTION37chain 'G' and (resid 374 through 413 )
38X-RAY DIFFRACTION38chain 'H' and (resid 366 through 373 )
39X-RAY DIFFRACTION39chain 'H' and (resid 374 through 405 )

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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