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- PDB-5flv: Crystal structure of NKX2-5 and TBX5 bound to the Nppa promoter region -

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基本情報

登録情報
データベース: PDB / ID: 5flv
タイトルCrystal structure of NKX2-5 and TBX5 bound to the Nppa promoter region
要素
  • 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'
  • 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
  • HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
キーワードTRANSCRIPTION
機能・相同性
機能・相同性情報


Purkinje myocyte differentiation / right ventricular cardiac muscle tissue morphogenesis / septum secundum development / proepicardium development / pulmonary myocardium development / Nkx-2.5 complex / cardiac ventricle formation / apoptotic process involved in heart morphogenesis / atrioventricular node cell fate commitment / bundle of His development ...Purkinje myocyte differentiation / right ventricular cardiac muscle tissue morphogenesis / septum secundum development / proepicardium development / pulmonary myocardium development / Nkx-2.5 complex / cardiac ventricle formation / apoptotic process involved in heart morphogenesis / atrioventricular node cell fate commitment / bundle of His development / atrial cardiac muscle cell development / ventricular cardiac myofibril assembly / atrioventricular node cell development / embryonic heart tube left/right pattern formation / positive regulation of cardioblast differentiation / atrial cardiac muscle tissue development / atrioventricular node development / ventricular cardiac muscle cell development / regulation of cardiac muscle cell proliferation / atrial septum morphogenesis / positive regulation of heart contraction / cardiac ventricle morphogenesis / negative regulation of myotube differentiation / cardiac conduction system development / pharyngeal system development / positive regulation of sodium ion transport / negative regulation of epithelial cell apoptotic process / cardiac muscle cell differentiation / endoderm development / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / heart trabecula formation / adult heart development / cardiac muscle tissue morphogenesis / embryonic heart tube development / cardiac muscle tissue development / cardiac muscle cell development / epithelial cell apoptotic process / cardiac muscle cell proliferation / negative regulation of cardiac muscle cell apoptotic process / tongue development / ventricular septum morphogenesis / heart contraction / cardiac septum morphogenesis / heart looping / outflow tract morphogenesis / hemopoiesis / thyroid gland development / regulation of cardiac conduction / positive regulation of transcription initiation by RNA polymerase II / regulation of cardiac muscle contraction / vasculogenesis / heart morphogenesis / spleen development / cardiac muscle contraction / epithelial cell differentiation / positive regulation of neuron differentiation / positive regulation of epithelial cell proliferation / epithelial cell proliferation / negative regulation of canonical Wnt signaling pathway / protein-DNA complex / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / apoptotic process / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
類似検索 - 分子機能
: / Transcription factor, T-box / T-box / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain ...: / Transcription factor, T-box / T-box / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Homeobox protein Nkx-2.5
類似検索 - 構成要素
生物種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: 3.005 Å
データ登録者Stirnimann, C.U. / Glatt, S. / Mueller, C.W.
引用ジャーナル: Cell(Cambridge,Mass.) / 年: 2016
タイトル: Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.
著者: Luna-Zurita, L. / Stirnimann, C.U. / Glatt, S. / Kaynak, B.L. / Thomas, S. / Baudin, F. / Samee, M.A.H. / He, D. / Small, E.M. / Mileikovsky, M. / Nagy, A. / Holloway, A.K. / Pollard, K.S. / ...著者: Luna-Zurita, L. / Stirnimann, C.U. / Glatt, S. / Kaynak, B.L. / Thomas, S. / Baudin, F. / Samee, M.A.H. / He, D. / Small, E.M. / Mileikovsky, M. / Nagy, A. / Holloway, A.K. / Pollard, K.S. / Muller, C.W. / Bruneau, B.G.
履歴
登録2015年10月28日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年2月10日Provider: repository / タイプ: Initial release
改定 1.12016年8月17日Group: Database references
改定 1.22024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
B: 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
C: 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'
E: HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
F: 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
G: 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'
I: HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
J: 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
K: 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'
M: HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
N: 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
O: 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)186,19114
ポリマ－185,80212
非ポリマー3882
水00
1
A: HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
B: 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
C: 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,8395
ポリマ－46,4513
非ポリマー3882
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-7.8 kcal/mol
Surface area22450 Å2
手法PQS
2
E: HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
F: 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
G: 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'


分子量 (理論値)分子数
合計 (水以外)46,4513
ポリマ－46,4513
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-8.8 kcal/mol
Surface area22010 Å2
手法PQS
3
I: HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
J: 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
K: 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'


分子量 (理論値)分子数
合計 (水以外)46,4513
ポリマ－46,4513
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-6.2 kcal/mol
Surface area22160 Å2
手法PQS
4
M: HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
N: 5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'
O: 5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'


分子量 (理論値)分子数
合計 (水以外)46,4513
ポリマ－46,4513
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-11 kcal/mol
Surface area22950 Å2
手法PQS
単位格子
Length a, b, c (Å)58.080, 158.620, 87.860
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
22
33
44
/ NCSアンサンブル:
ID
1
2
3
4

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要素

#1: タンパク質
HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5 / CARDIAC-SPECIFIC HOMEOBOX / HOMEOBOX PROTEIN CSX / HOMEOBOX PROTEIN NK-2 HOMOLOG E / T-BOX PROTEIN 5


分子量: 32947.793 Da / 分子数: 4
断片: DNA BINDING DOMAINS OF TBX5 AND NKX2-5, UNP RESIDUES 134-197 AND 51-251
変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): GOLD / 参照: UniProt: P42582
#2: DNA鎖
5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'


分子量: 6693.327 Da / 分子数: 4 / 断片: SENSE STRAND - NPPA / 由来タイプ: 合成 / 由来: (合成) MUS MUSCULUS (ハツカネズミ)
#3: DNA鎖
5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'


分子量: 6809.431 Da / 分子数: 4 / 断片: ANTISENSE STRAND - NPPA / 由来タイプ: 合成 / 由来: (合成) MUS MUSCULUS (ハツカネズミ)
#4: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
配列の詳細PROTEIN FUSION OF MNKX2-5(AA134-197,UNIPROT-P42582)AND MTBX5(AA51-251, UNIPROT-P70326) USING A ...PROTEIN FUSION OF MNKX2-5(AA134-197,UNIPROT-P42582)AND MTBX5(AA51-251, UNIPROT-P70326) USING A 15SER LINKER AND ALL CYSTEINE RESIDUES MUTATED TO SERINE RESIDUES MUTATION CYS TO SER

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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: 2.18 Å3/Da / 溶媒含有率: 43.53 % / 解説: NONE
結晶化詳細: 0.1M HEPES PH7.5 0.1 M KBR, 0.2M NA-ACETATE AND 20 % PEG 3000

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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: ESRF / ビームライン: ID14-4 / 波長: 0.97488
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2010年4月11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: 0.97488 Å / 相対比: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.57
反射解像度: 3→50 Å / Num. obs: 31026 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / 冗長度: 3.7 % / Rmerge(I) obs: 0.12
反射 シェル解像度: 3→3.08 Å / 冗長度: 3.4 % / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 0.95 / % possible all: 91.3

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
XSCALEデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 2X6V

2x6v


解像度: 3.005→19.966 Å / σ(F): 1.37 / 位相誤差: 38.18 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.241 1094 3.5 %
Rwork0.1904 --
obs0.196 30939 98 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.005→19.966 Å
タンパク質核酸リガンド溶媒全体
原子数7550 3459 26 0 11035
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00411652
X-RAY DIFFRACTIONf_angle_d0.7516431
X-RAY DIFFRACTIONf_dihedral_angle_d22.2144615
X-RAY DIFFRACTIONf_chiral_restr0.0321788
X-RAY DIFFRACTIONf_plane_restr0.0041483
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0073-3.14340.34861320.34743589X-RAY DIFFRACTION92
3.1434-3.30810.29951310.24773745X-RAY DIFFRACTION95
3.3081-3.51380.28311370.22633731X-RAY DIFFRACTION95
3.5138-3.78260.2561260.21593724X-RAY DIFFRACTION95
3.7826-4.15860.23131360.19553752X-RAY DIFFRACTION95
4.1586-4.74980.22961320.17193740X-RAY DIFFRACTION95
4.7498-5.94510.22161370.16593760X-RAY DIFFRACTION96
5.9451-17.50870.20521450.16263756X-RAY DIFFRACTION94
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)
18.02380.9455-2.11321.50370.79834.8704-0.0049-0.32921.57810.35370.32630.393-0.87290.1291-0.29870.6821-0.02720.23780.5089-0.03770.81791.993433.434810.2212
25.7934-1.99652.64322.5376-0.57921.26920.50860.10670.03180.033-0.11370.0236-0.2874-0.1244-0.33620.40850.05110.1640.40050.04270.86149.71522.71337.7396
33.37570.05140.27122.2861-0.47630.826-0.0150.0740.1050.1527-0.08670.47820.0534-0.2133-0.0857-0.18120.0963-0.07111.0104-0.16480.8457-6.633121.82076.7786
40.7820.47882.0430.32781.21295.722-0.32140.33211.1514-0.0428-0.05110.9031-1.57430.89020.28130.8364-0.15190.1490.91080.40321.141813.873938.4573-7.4179
51.6241-0.13340.15321.7057-0.7122.2180.18090.79280.7306-0.1516-0.2191-0.4577-0.24040.49030.06860.1257-0.0907-0.18771.01950.05941.05165.432221.8604-10.8908
60.4594-0.1311-0.30050.4795-0.11860.56660.0419-0.0361-0.05440.41270.08270.1066-0.11110.0135-0.0889-0.17260.10790.0840.62720.0790.76250.877218.28986.6912
72.72591.0560.37620.61740.4150.42370.0341-0.1011-0.0118-0.0371-0.21540.1454-0.1031-0.38470.05570.5116-0.06180.1160.72010.1050.6359-2.969226.96844.4046
81.3069-1.2840.49461.7734-1.32521.58470.2105-0.12450.51950.0877-0.1139-0.2-0.49590.2901-0.08570.6668-0.19420.14690.59790.02170.967317.224834.23085.3797
93.48133.44771.47674.24480.08742.90380.42350.17450.9129-0.0679-0.3606-0.4569-0.57550.85280.1420.4645-0.22150.14110.946-0.11380.964618.868130.368916.9108
100.02460.0170.05340.02290.03440.1105-0.225-0.0686-0.04630.17670.1623-0.2242-0.15680.3944-0.04790.5286-0.0010.10790.79590.11660.92917.10572.66324.152
112.8519-0.8531-1.26170.8471-0.41884.3828-0.2161-0.1322-0.41620.29850.40530.3858-0.3119-0.8122-0.03350.1893-0.00210.07510.91760.09380.84470.09570.952125.3483
125.40441.54433.67432.9705-1.00384.1616-0.1128-0.5494-0.22010.1398-0.06590.5964-0.0848-0.41510.02550.39790.1297-0.07470.54910.14271.10074.8988-8.022829.5082
139.0154-0.7163-2.7485.5120.86693.0847-0.1666-1.4058-0.05661.0210.27581.0381-0.1345-0.11130.00720.40030.07390.0931.05250.06090.57775.89654.241432.3131
140.0518-0.04270.13380.0419-0.11650.2762-0.03850.2571-0.1762-0.0965-0.25480.4319-0.0086-0.2343-0.22210.1368-0.3279-0.27341.11020.00970.9523-19.8534-2.5556-6.3253
150.2954-0.22090.08730.2052-0.04190.1066-0.06440.13520.238-0.1067-0.10570.0724-0.2358-0.1730.1273-0.3193-0.0895-0.3390.99820.13660.8649-10.10256.6073-6.1744
162.7244-1.2063-2.03525.46170.25481.67670.1482-0.5384-0.1280.0939-0.1288-0.8514-0.11380.24380.05110.1562-0.35350.23471.4218-0.09781.1683-19.1061-9.92712.9225
171.6526-0.14220.32410.75630.88891.21030.1782-0.1408-0.11370.099-0.13870.43940.1316-0.85830.0113-0.01390.1128-0.00930.7665-0.01441.0527-8.85366.03770.0852
183.2111-0.90721.42431.1199-0.33950.63460.02780.44920.1104-0.2116-0.08020.2321-0.02240.07350.2039-0.0142-0.2152-0.1771.1007-0.03610.6614-7.23672.5122-8.9564
190.8679-0.42380.35420.7958-0.69681.0053-0.23810.0886-0.0963-0.0508-0.17850.2356-0.1294-0.3264-0.2781-0.1763-0.16380.02330.95690.05930.6569-6.97862.43274.7978
200.24290.0737-0.04310.3456-0.2340.16510.20240.12890.0985-0.08780.16310.0927-0.0697-0.2211-0.0202-0.1066-0.18790.12711.12310.31230.9619-17.28563.4194-0.3314
211.3103-0.6346-0.22421.9077-0.43151.72210.073-0.0931-0.09930.11330.02440.03210.0969-0.1144-0.05780.3774-0.4079-0.16431.0274-0.0811.1608-14.66-16.0055-0.6241
220.640.46810.5640.68110.69450.73160.01180.2068-0.2573-0.0708-0.0652-0.00780.0876-0.1178-0.18890.3669-0.3611-0.16710.95660.05120.8867-9.5416-15.9343-11.5443
237.4758-0.26971.43952.2702-1.42861.11090.13010.1012-0.0269-0.00270.02540.2453-0.0360.1034-0.0730.0827-0.02410.08731.0747-0.27010.885410.85668.2501-17.2908
248.4104-1.9579-4.96885.04194.26815.04880.19190.66190.4435-1.61410.4195-0.3364-1.29740.1825-0.61621.0145-0.0652-0.05220.56510.18330.74555.994315.8032-26.1698
258.67962.5843.40055.63061.45017.63070.35670.65440.3692-1.54670.22380.0266-1.10830.6024-0.60091.19620.06550.04460.5664-0.11210.56229.09778.0924-26.2132
260.3418-0.1113-0.3514.95262.3791.40.13030.17690.6027-0.36830.2769-0.5406-0.22640.3531-0.49130.53140.28410.35711.79280.64060.951-8.9925-24.591729.4694
274.2786-1.0263-2.39341.12590.15912.07650.74920.7126-0.24920.2571-0.5942-0.7856-0.12750.7612-0.04690.4998-0.0485-0.26730.96360.32660.9727-19.4929-18.743437.9415
281.9212-0.8655-0.01442.0841-0.21450.8192-0.17710.2371-0.3279-0.0395-0.1543-0.6002-0.04580.71850.11060.10110.1370.03331.27440.12890.831-15.7845-33.228737.4942
292.36590.1591-0.17620.4340.85191.8513-0.3454-0.45940.06460.3342-0.1932-0.197-0.13310.97530.15680.41820.0752-0.26841.07660.03130.9027-15.9089-21.464150.1014
302.4094-3.2717-3.91794.73645.49586.5543-0.36830.16250.2434-0.0440.4695-0.75551.1021.1719-0.13850.65650.31450.16520.84160.1170.7958-24.3495-40.379727.3467
310.97641.1255-0.90911.8559-2.06382.7379-0.26460.497-0.5282-0.3155-0.0248-0.67190.77710.72940.39170.55980.41440.10831.00840.18490.6967-20.9667-33.009726.0832
321.10980.78540.41960.75290.08730.3805-0.15850.1921-0.2408-0.0873-0.0905-0.3270.05810.3472-0.1664-0.1330.1163-0.03470.98080.21440.7599-22.4894-27.982143.4984
330.3109-0.10380.05290.35240.09560.16230.03970.3484-0.1505-0.09630.1705-0.7743-0.00180.4904-0.09530.003-0.2329-0.04751.35590.20681.2242-13.8611-21.018237.6992
340.82641.7840.14164.81550.82010.91270.150.20180.3172-0.26930.2051-0.2699-0.34410.2574-0.06060.291-0.01850.10751.17340.07170.7446-20.1363-10.829726.3928
350.2963-0.50111.01441.7697-3.24696.10070.5025-0.5058-0.7046-1.79690.6121.33551.725-0.9042-1.03941.1968-0.348-0.45931.3257-0.13711.3611-44.3157-23.490919.6048
361.99910.6509-0.11442.2358-3.88877.81680.2356-0.5983-1.36130.4736-0.0535-0.25290.9201-0.3317-0.02910.3287-0.0873-0.13340.75510.2790.8453-39.6551-37.613322.1273
372.94012.18934.87311.63193.62968.0764-0.66560.27380.2089-0.86010.3056-0.5623-0.0742-0.26680.30051.1215-0.11380.09420.5972-0.1820.9999-35.3976-42.571712.9349
383.3592-3.1745-3.44158.5233.40025.3698-0.61350.1846-1.61070.2293-1.07912.95371.6278-2.91591.66910.9955-0.5055-0.1381.3180.13781.328-48.0861-39.121114.0502
395.60360.31-6.20057.5447-3.96888.9421-0.068-0.01360.4463-0.22780.329-0.4686-0.15650.3706-0.16120.30410.0489-0.01180.6612-0.11040.8265-34.2528-32.119212.0897
408.1378-1.33451.94540.2227-0.3430.61180.55350.5293-0.9801-0.488-0.34710.76471.1089-0.3625-0.15761.5034-0.0959-0.58430.6916-0.00781.0286-25.928620.277637.5694
414.1504-1.3765-2.04225.6583-2.10062.52851.142-0.084-0.4009-0.6609-0.50750.70231.1707-0.933-0.55560.6873-0.1689-0.19770.57710.05980.6804-18.269931.090340.5849
420.0291-0.0094-0.02710.00080.00610.02740.3421-0.0772-0.22640.0204-0.12750.67270.4786-0.5676-0.12030.6969-0.0888-0.28790.942-0.01050.8584-42.108934.789631.2697
432.4437-0.85420.60510.5915-0.64072.34590.2003-0.864-0.46170.1759-0.1260.19590.50530.1058-0.17120.6929-0.2991-0.53061.06840.29460.9154-21.42722.179353.6707
446.0183-0.41481.53384.0312-1.70853.35180.0336-0.207-0.0516-0.007-0.02630.0144-0.06670.0567-0.14080.1774-0.2043-0.13180.5992-0.1050.8456-30.929237.345540.6539
457.5662-1.18372.3364.3542-2.27124.51230.29721.0397-0.355-0.53290.02690.00640.49290.3396-0.27990.6223-0.0279-0.25780.8171-0.02120.4909-25.101633.819935.1766
467.40641.34232.34913.70150.71342.13590.5014-0.4754-0.56120.378-0.1476-0.05320.6713-0.4148-0.24660.4861-0.2921-0.02060.6660.00340.5227-23.221933.497449.4077
471.4856-2.8751.90155.5769-3.74042.6303-0.4733-0.6507-0.44750.19660.2390.86890.0785-0.8020.09970.7566-0.2699-0.32490.71260.08141.2244-37.890429.66942.16
482.1921-0.25251.53890.9427-0.94975.86440.27860.3623-0.9395-0.1928-0.1292-0.17171.03081.1631-0.57550.62790.1426-0.63770.594-0.09771.0577-11.364421.920139.3249
493.81070.0502-0.78346.2369-3.72228.39450.4092-0.65360.4707-0.16260.120.4553-0.2201-0.972-0.5150.2463-0.04220.07360.6696-0.02880.5253-26.753852.50323.6401
507.19084.86115.38333.35523.41184.8548-0.88930.04422.413-0.77690.03941.2202-2.3941-1.16190.78911.05970.42220.02970.67490.16160.8914-24.475361.770218.6872
516.3443-3.5233-1.31829.55811.79226.51540.1556-0.0519-0.6840.1486-0.18530.03870.04560.3989-0.12420.49750.20870.14310.5919-0.05750.8226-23.212646.24616.5008
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1053 THROUGH 1075 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 1076 THROUGH 1088 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 1089 THROUGH 1113 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 1114 THROUGH 1123 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 1124 THROUGH 1134 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 1135 THROUGH 1187 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 1188 THROUGH 1214 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 1215 THROUGH 1227 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 1228 THROUGH 1238 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 140 THROUGH 145 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 146 THROUGH 163 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 164 THROUGH 177 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 178 THROUGH 191 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 1054 THROUGH 1075 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 1076 THROUGH 1108 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 1109 THROUGH 1120 )
17X-RAY DIFFRACTION17CHAIN 'E' AND (RESID 1121 THROUGH 1150 )
18X-RAY DIFFRACTION18CHAIN 'E' AND (RESID 1151 THROUGH 1160 )
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 1161 THROUGH 1187 )
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESID 1188 THROUGH 1214 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 1215 THROUGH 1227 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 1228 THROUGH 1237 )
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESID 142 THROUGH 156 )
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESID 157 THROUGH 163 )
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESID 164 THROUGH 197 )
26X-RAY DIFFRACTION26CHAIN 'I' AND (RESID 1056 THROUGH 1068 )
27X-RAY DIFFRACTION27CHAIN 'I' AND (RESID 1069 THROUGH 1085 )
28X-RAY DIFFRACTION28CHAIN 'I' AND (RESID 1086 THROUGH 1116 )
29X-RAY DIFFRACTION29CHAIN 'I' AND (RESID 1117 THROUGH 1136 )
30X-RAY DIFFRACTION30CHAIN 'I' AND (RESID 1137 THROUGH 1148 )
31X-RAY DIFFRACTION31CHAIN 'I' AND (RESID 1149 THROUGH 1158 )
32X-RAY DIFFRACTION32CHAIN 'I' AND (RESID 1159 THROUGH 1187 )
33X-RAY DIFFRACTION33CHAIN 'I' AND (RESID 1188 THROUGH 1227 )
34X-RAY DIFFRACTION34CHAIN 'I' AND (RESID 1228 THROUGH 1237 )
35X-RAY DIFFRACTION35CHAIN 'I' AND (RESID 140 THROUGH 145 )
36X-RAY DIFFRACTION36CHAIN 'I' AND (RESID 146 THROUGH 156 )
37X-RAY DIFFRACTION37CHAIN 'I' AND (RESID 157 THROUGH 163 )
38X-RAY DIFFRACTION38CHAIN 'I' AND (RESID 164 THROUGH 177 )
39X-RAY DIFFRACTION39CHAIN 'I' AND (RESID 178 THROUGH 196 )
40X-RAY DIFFRACTION40CHAIN 'M' AND (RESID 1053 THROUGH 1075 )
41X-RAY DIFFRACTION41CHAIN 'M' AND (RESID 1076 THROUGH 1088 )
42X-RAY DIFFRACTION42CHAIN 'M' AND (RESID 1089 THROUGH 1100 )
43X-RAY DIFFRACTION43CHAIN 'M' AND (RESID 1101 THROUGH 1126 )
44X-RAY DIFFRACTION44CHAIN 'M' AND (RESID 1127 THROUGH 1150 )
45X-RAY DIFFRACTION45CHAIN 'M' AND (RESID 1151 THROUGH 1160 )
46X-RAY DIFFRACTION46CHAIN 'M' AND (RESID 1161 THROUGH 1186 )
47X-RAY DIFFRACTION47CHAIN 'M' AND (RESID 1187 THROUGH 1209 )
48X-RAY DIFFRACTION48CHAIN 'M' AND (RESID 1210 THROUGH 1237 )
49X-RAY DIFFRACTION49CHAIN 'M' AND (RESID 142 THROUGH 163 )
50X-RAY DIFFRACTION50CHAIN 'M' AND (RESID 164 THROUGH 177 )
51X-RAY DIFFRACTION51CHAIN 'M' AND (RESID 178 THROUGH 195 )

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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://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