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- PDB-5brm: Structural basis for Mob1-dependent activation of the core Mst-La... -

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基本情報

登録情報
データベース: PDB / ID: 5brm
タイトルStructural basis for Mob1-dependent activation of the core Mst-Lats kinase cascade in Hippo signaling
要素
  • MOB kinase activator 1A
  • Serine/threonine-protein kinase 3
キーワードTransferase/Signaling Protein / Mst2 / Mob1 / Hippo / Transferase-Signaling Protein complex
機能・相同性
機能・相同性情報


cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome ...cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome / organ growth / hepatocyte apoptotic process / protein kinase activator activity / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / epithelial cell proliferation / central nervous system development / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / magnesium ion binding / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
類似検索 - 分子機能
: / MOB kinase activator / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / SARAH domain / SARAH domain profile. ...: / MOB kinase activator / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / SARAH domain / SARAH domain profile. / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / p53-like tetramerisation domain superfamily / 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 / Mainly Alpha
類似検索 - ドメイン・相同性
Serine/threonine-protein kinase 3 / MOB kinase activator 1A
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: 2.651 Å
データ登録者Luo, X. / Ni, L.
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)GM085004 米国
引用ジャーナル: Genes Dev. / 年: 2015
タイトル: Structural basis for Mob1-dependent activation of the core Mst-Lats kinase cascade in Hippo signaling.
著者: Ni, L. / Zheng, Y. / Hara, M. / Pan, D. / Luo, X.
履歴
登録2015年5月31日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年7月8日Provider: repository / タイプ: Initial release
改定 1.12015年7月15日Group: Source and taxonomy
改定 1.22015年7月22日Group: Database references
改定 1.32017年9月20日Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
カテゴリ: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
改定 1.42019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023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 / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: MOB kinase activator 1A
B: MOB kinase activator 1A
C: MOB kinase activator 1A
D: MOB kinase activator 1A
E: MOB kinase activator 1A
F: MOB kinase activator 1A
G: Serine/threonine-protein kinase 3
H: Serine/threonine-protein kinase 3
I: Serine/threonine-protein kinase 3
J: Serine/threonine-protein kinase 3
K: Serine/threonine-protein kinase 3
L: Serine/threonine-protein kinase 3
M: Serine/threonine-protein kinase 3
N: Serine/threonine-protein kinase 3
O: Serine/threonine-protein kinase 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)158,75121
ポリマ－158,35915
非ポリマー3926
水1086
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)142.188, 142.188, 135.981
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
12chain I
22chain J
32chain K
42chain L

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPZNZNchain AAA - P52 - 30113
21ASPASPZNZNchain BBB - Q52 - 30113
31ASPASPZNZNchain CCC - R52 - 30113
41ASPASPZNZNchain DDD - S52 - 30113
51ASPASPZNZNchain EEE - T52 - 30113
61ASPASPZNZNchain FFF - U52 - 30113
12TPOTPOASPASPchain III378 - 3988 - 28
22TPOTPOASPASPchain JJJ378 - 3988 - 28
32TPOTPOASPASPchain KKK378 - 3988 - 28
42TPOTPOPHEPHEchain LLL378 - 3978 - 27

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B


分子量: 20724.754 Da / 分子数: 6 / 断片: UNP residues 41-216 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / 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: Q9H8S9
#2: タンパク質・ペプチド
Serine/threonine-protein kinase 3 / Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein kinase Krs-1


分子量: 3778.892 Da / 分子数: 9 / 断片: UNP residues 371-401 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
参照: UniProt: Q13188, non-specific serine/threonine protein kinase
#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 6 / 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: 2.51 Å3/Da / 溶媒含有率: 50.91 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 / 詳細: 2.4 M Na Malonate

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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: APS / ビームライン: 19-ID / 波長: 0.97929 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2013年4月11日 / 詳細: monochromator
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: 0.97929 Å / 相対比: 1
反射解像度: 2.65→40 Å / Num. obs: 46680 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / 冗長度: 11 % / Biso Wilson estimate: 38.38 Å2 / Rmerge(I) obs: 0.091 / Χ2: 0.963 / Net I/av σ(I): 25.585 / Net I/σ(I): 11.3 / Num. measured all: 512365
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.65-2.76.311.822320.93997.9
2.7-2.748.322800.83499.9
2.74-2.89.90.96723110.85699.9
2.8-2.8510.90.89622740.883100
2.85-2.9211.60.77122930.887100
2.92-2.9811.80.71222920.891100
2.98-3.0611.90.62123040.927100
3.06-3.1411.90.46522740.95499.8
3.14-3.2311.90.34523310.96999.9
3.23-3.34120.25723000.99199.8
3.34-3.4611.80.20722941.10199.7
3.46-3.6120.14423001.00799.4
3.6-3.7611.70.11522951.07999.2
3.76-3.9611.70.09323181.04899.5
3.96-4.2111.60.07323160.98699.4
4.21-4.5311.50.06523120.96599.4
4.53-4.9811.40.06123080.97299.4
4.98-5.711.40.06323721.03199.9
5.7-7.1811.50.05723780.87499.8
7.18-4010.60.05824270.99397.8

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
HKL-2000データスケーリング
PDB_EXTRACT3.15データ抽出
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1pi1

1pi1


解像度: 2.651→39.295 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.5 / 位相誤差: 27.15 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2681 2004 4.83 %random selection
Rwork0.2441 39468 --
obs0.2452 41472 89.28 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 172.2 Å2 / Biso mean: 56.5769 Å2 / Biso min: 10.42 Å2
精密化ステップサイクル: final / 解像度: 2.651→39.295 Å
タンパク質核酸リガンド溶媒全体
原子数8906 0 6 6 8918
Biso mean--39.39 31.94 -
残基数----1060
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0069179
X-RAY DIFFRACTIONf_angle_d0.99412387
X-RAY DIFFRACTIONf_chiral_restr0.0381305
X-RAY DIFFRACTIONf_plane_restr0.0051574
X-RAY DIFFRACTIONf_dihedral_angle_d13.0393355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A6092X-RAY DIFFRACTION12.277TORSIONAL
12B6092X-RAY DIFFRACTION12.277TORSIONAL
13C6092X-RAY DIFFRACTION12.277TORSIONAL
14D6092X-RAY DIFFRACTION12.277TORSIONAL
15E6092X-RAY DIFFRACTION12.277TORSIONAL
16F6092X-RAY DIFFRACTION12.277TORSIONAL
21I283X-RAY DIFFRACTION12.277TORSIONAL
22J283X-RAY DIFFRACTION12.277TORSIONAL
23K283X-RAY DIFFRACTION12.277TORSIONAL
24L283X-RAY DIFFRACTION12.277TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.651-2.71730.3611800.30121412149246
2.7173-2.79070.2957960.30691871196760
2.7907-2.87280.3461100.30362201231171
2.8728-2.96550.33651270.30692634276183
2.9655-3.07150.31881490.30942912306194
3.0715-3.19440.341540.28663116327099
3.1944-3.33970.2771620.27731433305100
3.3397-3.51570.29031600.249731303290100
3.5157-3.73580.25641580.24033119327799
3.7358-4.0240.26471590.22983130328999
4.024-4.42840.26731580.21353146330499
4.4284-5.06810.20411640.20131633327100
5.0681-6.38080.25751580.225332163374100
6.3808-39.29930.22971690.22743275344498
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)
10.89630.07920.10030.89530.15312.4566-0.1021-0.00080.0021-0.0107-0.03220.09970.1259-0.24350.01690.23840.0157-0.03490.2539-0.06340.04718.0532-57.4108-0.4959
26.3741.90621.56424.4660.48254.14290.06040.1327-0.1165-0.1236-0.09180.41690.104-0.45060.03250.1857-0.0316-0.10040.1996-0.13670.25231.7616-72.5646-0.9786
32.7607-0.8190.66771.2823-1.30631.3488-0.09880.58580.1912-0.4406-0.01840.4952-0.242-0.42990.05310.31350.0925-0.22320.4166-0.13920.3012-1.3222-60.5972-8.434
40.94340.17710.6110.79270.46911.6864-0.11740.02640.1035-0.047-0.10860.1528-0.0873-0.1688-0.22930.22920.003-0.05620.2558-0.1380.08148.7943-56.75833.1208
52.12290.48510.03710.40380.05051.06270.0244-0.32470.15070.1127-0.07990.0327-0.2149-0.18320.06210.3387-0.0393-0.0170.1773-0.03040.02836.0317-47.50125.5108
62.3856-0.28231.24890.6498-0.34233.3218-0.2044-0.37880.05530.1511-0.04310.1782-0.0472-0.41870.20440.4608-0.06740.08480.2149-0.080.12821.3334-54.442712.6791
70.83130.0737-0.23382.8954-0.46251.5253-0.05310.13270.0765-0.0902-0.0467-0.2501-0.00750.10720.07730.21770.08150.11560.20940.13850.146656.8243-40.3972.6172
81.9902-0.3380.22051.1316-0.33331.1166-0.203-0.3770.30410.24820.051-0.0815-0.1963-0.0782-0.0540.1831-0.0191-0.04480.36720.13540.312866.41-34.079514.3942
92.6579-0.13680.85843.96561.71754.3879-0.1527-0.5283-0.15990.80820.2533-0.68730.41750.5289-0.08490.4618-0.0623-0.03690.66940.31220.683176.7746-35.949411.5778
102.0914-0.07320.15231.67250.08430.6647-0.11550.3404-0.4658-0.2238-0.027-0.14950.25910.19210.47990.30220.12290.28640.43180.21060.556267.0003-46.7932-0.2094
110.6018-0.0559-0.00350.7147-0.03560.9579-0.0946-0.2764-0.14130.1819-0.0312-0.02960.0224-0.0271-0.14120.26120.09380.09720.23420.22010.060354.1547-41.695511.9916
121.1843-0.167-0.39510.9984-0.70192.1722-0.14220.1392-0.217-0.1702-0.126-0.1672-0.04030.0281-0.13640.2953-0.12270.15130.37830.01580.143447.8545-49.5769-4.6267
132.3805-2.10820.83973.85130.58111.17770.15650.2796-0.3576-0.1414-0.25870.36080.2596-0.07270.0730.6056-0.04330.20350.525-0.38230.765939.5935-68.7237-11.1909
149.55314.56030.21042.3237-0.92817.2-0.12140.56640.3952-0.5390.01910.0014-0.2090.17810.07490.8805-0.07010.21870.6193-0.140.516239.5361-55.9196-24.5689
155.2139-4.36964.72763.7308-4.18054.98-0.20950.12550.30750.0407-0.0455-0.2764-0.19950.0840.26351.0535-0.35010.28640.9205-0.31010.662238.6905-64.5748-21.6243
160.38970.0026-0.19010.78760.08431.3359-0.08160.2562-0.1782-0.3101-0.025-0.07560.0232-0.0573-0.02140.7315-0.13770.25190.7963-0.21670.332347.2204-56.2816-16.5137
171.2717-0.0298-0.40942.60160.29193.4114-0.12450.1349-0.0289-0.32540.121-0.1498-0.29950.55780.01440.79780.0290.15060.79340.19760.275752.0019-38.5166-15.3211
181.93250.2168-0.6750.5757-0.0632.0161-0.42480.2289-0.3893-0.19230.0844-0.08110.2777-0.17320.16660.4707-0.06650.15110.2884-0.00620.10641.1921-53.788-4.0227
196.5909-1.65050.62716.0218-0.33155.1524-0.0640.1313-0.3254-0.1869-0.06470.20230.424-0.28650.08160.1986-0.08020.06240.3892-0.07880.269530.1597-56.9161-0.9269
200.8197-0.4608-0.26850.92370.0111.3517-0.0453-0.04450.14910.032-0.0286-0.057-0.0760.20210.04780.2105-0.0258-0.03920.29620.13661.040525.507-3.3201-0.0202
215.9538-3.056-3.44367.79262.74057.92980.0238-0.00130.16980.0922-0.08450.2434-0.5088-0.38740.11590.54910.1450.1960.33470.02431.13483.9342-10.62651.8236
220.9348-0.2124-0.07390.51950.36850.2684-0.3111-0.2094-0.75050.46460.21380.3250.2949-0.06380.04880.53320.03840.30380.3749-0.02961.47046.9139-0.361110.8928
230.18370.4585-0.09891.2828-0.42010.27820.00490.06830.0447-0.1149-0.09950.0250.01550.01070.01730.34410.0376-0.08880.33160.02171.436313.26011.943-2.2992
240.85680.9415-0.25322.3878-0.60430.5615-0.0108-0.07060.44410.1738-0.12030.3275-0.0783-0.0622-0.0360.2732-0.0960.11660.3023-0.06641.193221.9633-3.68175.4709
252.41742.0584-0.51442.0772-0.77422.645-0.1225-0.25280.09250.5221-0.33560.0728-0.1189-0.0590.30750.6238-0.15350.18060.4637-0.26191.284922.0225-3.104617.8364
262.81571.5833-0.82992.3273-0.54691.468-0.06280.15960.3473-0.1522-0.1844-0.10910.00030.20550.09860.1677-0.0261-0.07310.32640.24470.567838.255-6.4281-6.6584
275.0136-3.66653.47463.3726-1.22734.90240.03220.10850.3158-0.0205-0.1988-0.7507-0.00320.80560.17050.28180.08390.07150.54580.32980.965654.2554-14.105-8.9928
283.4305-0.2051.59383.27191.98764.5451-0.270.9201-0.0872-0.68790.15760.1915-0.02610.00590.07070.8566-0.13850.17791.14860.25950.606946.8766-13.8205-22.1249
297.41051.75931.77381.06460.66141.9162-0.08440.25470.1037-0.48110.0174-0.09220.1151-0.2077-0.06510.4610.0231-0.05730.57880.37490.585636.485-8.5368-16.9971
303.1477-0.29650.52161.0320.54971.7875-0.18140.1748-0.3085-0.1505-0.10110.0860.1546-0.0417-0.24780.219-0.0645-0.07620.38370.32090.644734.6857-15.1003-10.217
312.8323-0.3196-2.50973.65910.97682.7560.2482-0.2340.25850.3966-0.18770.2176-0.22770.1246-0.07830.3877-0.1813-0.19610.4530.32480.857248.84741.16193.2183
325.4555-1.47220.69711.8725-0.45371.5305-0.0364-0.1676-0.10290.0486-0.0428-0.05130.0221-0.0245-0.01430.14930.0293-0.01630.22510.19670.591237.8638-14.58031.8167
333.3274-2.08430.79422.77810.20744.6935-0.1043-0.0577-0.30930.13860.02690.13810.19090.1270.04270.240.12560.01080.41810.19370.749647.0168-19.63792.0191
341.9973-0.0515-0.15421.9167-0.54131.5364-0.11640.41810.4439-0.4937-0.05820.2461-0.1185-0.38440.02860.55770.1182-0.14290.4710.06040.25880.5205-37.6933-10.8829
356.4585-4.68520.454.7324-0.46625.0978-0.08580.21540.5161-0.48540.06620.7073-0.8866-0.70570.010.77390.1254-0.20460.4440.29350.9188-0.0319-19.9664-12.7367
361.7569-1.29590.13781.09070.15970.60140.15120.39810.7157-0.1974-0.0041-0.052-0.8036-0.1648-0.07931.14810.0813-0.1250.73340.4320.93375.159-26.5701-25.4313
370.60810.576-0.82331.00280.1292.9231-0.0080.34190.1407-0.3748-0.06480.0469-0.0177-0.05560.05350.87050.1549-0.07870.75120.21860.30862.3114-35.4541-20.4
381.6988-1.22081.54840.9776-1.31891.83410.00890.157-0.2001-0.2397-0.0664-0.03990.44450.29580.04230.93790.04540.28080.94690.01440.357214.7156-48.7426-19.2913
392.8639-0.45090.7146.2455-1.14113.8552-0.02990.1135-0.1369-0.56620.0192-1.7262-0.03880.91330.02940.73840.06730.44480.91860.09850.828921.8003-45.1451-17.6527
400.6630.5679-0.48890.94790.4111.84150.00890.33030.5847-0.5811-0.1335-0.072-0.16510.12650.03710.59890.0991-0.03720.39540.24120.41995.7785-31.1487-10.9773
411.53880.0577-1.71581.10110.87625.11840.03450.0522-0.17450.17330.06050.34220.0063-0.2158-0.09120.42110.1745-0.06590.40420.07831.0502-12.7183-31.7036-2.6333
425.9441.1485-0.00134.4905-0.26734.07840.066-0.1460.3756-0.0902-0.2526-0.0929-0.25190.10020.09750.31810.08070.01410.17080.08640.38536.532-34.5971-1.2988
431.92590.99332.33427.7548-0.77716.711-0.02780.12840.634-0.1291-0.1467-0.1318-0.93890.60350.13670.5497-0.15870.21750.26860.03520.8316.7215-23.7188-0.6495
441.0027-0.1436-0.2021.9728-0.56061.18370.0095-0.2656-0.12550.5936-0.12110.1075-0.06910.0850.09650.33170.0538-0.0090.3463-0.01230.15359.8758-67.492916.0631
450.5993-0.986-0.56773.31413.2153.6144-0.1708-0.43060.20650.52210.3231-0.32230.03570.5754-0.15520.6017-0.1153-0.0690.5512-0.10590.167217.4135-51.730915.2501
463.06141.17741.11290.84020.06321.77350.0635-0.64370.6960.3252-0.1736-0.233-0.347-0.19790.01420.39250.00680.03140.49510.05480.295460.4545-33.200220.2357
472.5518-0.6185-1.79427.431-1.4121.73540.0731-0.68390.46930.3821-0.08190.3824-0.2713-0.39020.02940.52350.2620.0630.6270.0140.34642.4943-32.73918.6311
482.9089-2.07653.47951.4973-2.49654.18460.0756-0.2518-0.389-0.07570.32640.40790.1717-0.7798-0.41970.5729-0.02030.13780.799-0.14160.606229.3438-65.2835-9.8402
495.11931.93434.24862.30750.99483.76290.1733-0.9713-0.03021.0573-0.05670.60010.1531-0.547-0.11630.68180.06890.19550.6260.00020.72735.3232-66.40557.2967
505.4686-3.3176-4.61282.01412.80453.914-0.2566-0.3109-0.05721.22020.12760.66460.36180.02450.11660.83830.07150.16520.7714-0.2240.935210.2746-4.022918.5075
511.2138-0.25971.67183.6507-0.31462.30320.0532-0.21980.7460.165-0.0242-0.1-0.65740.1878-0.04641.14980.01540.16960.75150.02720.977118.9103-18.782618.3361
525.1649-1.2522-0.02593.06321.32992.1276-0.15-0.0723-0.01630.19540.1309-0.14860.02960.4301-0.01610.3880.15740.01470.80490.43090.643754.237-13.9849-2.9674
533.73844.6840.74466.60441.46310.53060.0186-0.29870.50930.3711-0.0183-0.5708-0.24490.3836-0.01160.74810.015-0.18210.68110.1110.948251.7854-9.177510.9301
540.2123-0.3510.11610.92360.08930.34670.18730.03680.36050.2223-0.1750.1791-0.4699-0.0364-0.08570.5804-0.0192-0.03860.75810.01581.3464-1.5064-20.9959-2.9683
550.72891.2797-0.14023.6638-2.89085.28910.12440.30860.3817-0.16840.24620.8997-0.3829-0.718-0.3160.65540.1127-0.04440.7782-0.02940.4485-4.7597-43.2155-17.1684
562.4689-0.79731.61053.625-3.71814.72170.25440.5496-0.0446-0.9702-0.1494-0.00850.1520.0826-0.04280.48180.126-0.03720.6429-0.08790.168811.3319-57.1213-11.2373
578.35267.19046.44876.40766.33617.8064-0.26780.3428-0.1494-0.59240.27480.4260.1203-0.150.00480.74050.21480.04020.7709-0.1340.596314.2121-57.4412-14.0783
580.3098-0.0746-0.13140.7078-0.10271.3904-0.05230.1249-0.0095-0.1417-0.003-0.065-0.01240.0253-0.02910.5688-0.060.18510.59780.1080.201258.173-41.7213-6.8318
591.6653-1.318-0.94841.11290.57260.9936-0.02270.1277-0.3163-0.09030.0313-0.07310.1257-0.0409-0.00750.57660.041-0.11340.34640.2430.988123.1845-3.7506-8.6407
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 94 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 110 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 143 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 175 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 192 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 193 through 211 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 52 through 85 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 100 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 110 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 111 through 143 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 144 through 212 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 52 through 75 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 76 through 95 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 96 through 105 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 106 through 110 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 111 through 126 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 127 through 136 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 137 through 197 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 198 through 211 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 52 through 75 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 76 through 85 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 86 through 110 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 111 through 126 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 127 through 193 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 194 through 211 )D0
26X-RAY DIFFRACTION26chain 'E' and (resid 52 through 85 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 86 through 95 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 96 through 110 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 111 through 131 )E0
30X-RAY DIFFRACTION30chain 'E' and (resid 132 through 165 )E0
31X-RAY DIFFRACTION31chain 'E' and (resid 166 through 175 )E0
32X-RAY DIFFRACTION32chain 'E' and (resid 176 through 197 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 198 through 211 )E0
34X-RAY DIFFRACTION34chain 'F' and (resid 52 through 85 )F0
35X-RAY DIFFRACTION35chain 'F' and (resid 86 through 95 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 96 through 110 )F0
37X-RAY DIFFRACTION37chain 'F' and (resid 111 through 126 )F0
38X-RAY DIFFRACTION38chain 'F' and (resid 127 through 136 )F0
39X-RAY DIFFRACTION39chain 'F' and (resid 137 through 143 )F0
40X-RAY DIFFRACTION40chain 'F' and (resid 144 through 165 )F0
41X-RAY DIFFRACTION41chain 'F' and (resid 166 through 175 )F0
42X-RAY DIFFRACTION42chain 'F' and (resid 176 through 197 )F0
43X-RAY DIFFRACTION43chain 'F' and (resid 198 through 211 )F0
44X-RAY DIFFRACTION44chain 'G' and (resid 377 through 391 )G0
45X-RAY DIFFRACTION45chain 'G' and (resid 392 through 398 )G0
46X-RAY DIFFRACTION46chain 'H' and (resid 377 through 393 )H0
47X-RAY DIFFRACTION47chain 'H' and (resid 394 through 399 )H0
48X-RAY DIFFRACTION48chain 'I' and (resid 379 through 392 )I0
49X-RAY DIFFRACTION49chain 'I' and (resid 393 through 398 )I0
50X-RAY DIFFRACTION50chain 'J' and (resid 379 through 393 )J0
51X-RAY DIFFRACTION51chain 'J' and (resid 394 through 398 )J0
52X-RAY DIFFRACTION52chain 'K' and (resid 379 through 393 )K0
53X-RAY DIFFRACTION53chain 'K' and (resid 394 through 398 )K0
54X-RAY DIFFRACTION54chain 'L' and (resid 379 through 397 )L0
55X-RAY DIFFRACTION55chain 'M' and (resid 380 through 389 )M0
56X-RAY DIFFRACTION56chain 'M' and (resid 390 through 394 )M0
57X-RAY DIFFRACTION57chain 'M' and (resid 395 through 396 )M0
58X-RAY DIFFRACTION58chain 'N' and (resid 385 through 396 )N0
59X-RAY DIFFRACTION59chain 'O' and (resid 386 through 393 )O0

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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

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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