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- PDB-6mzg: Structural Basis of Tubulin Recruitment and Assembly by Microtubu... -

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基本情報

登録情報
データベース: PDB / ID: 6mzg
タイトルStructural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with Tumor Overexpressed Gene (TOG) Domain Arrays
要素
  • Protein Stu2p/Alp14p
  • Truncated Darpin-D1
  • Tubulin alpha-1A chain
  • Tubulin beta chain
キーワードCELL CYCLE / Microtubule / Tubulin / Tubulin polymerization / Heat repeats / Microtubule polymerase / Protofilament / TOG arrays / and Unfurled assembly.
機能・相同性
機能・相同性情報


supramolecular complex / microtubule plus end polymerase / establishment or maintenance of microtubule cytoskeleton polarity / microtubule plus-end binding / motile cilium / spindle organization / microtubule polymerization / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration ...supramolecular complex / microtubule plus end polymerase / establishment or maintenance of microtubule cytoskeleton polarity / microtubule plus-end binding / motile cilium / spindle organization / microtubule polymerization / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / microtubule / cytoskeleton / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
類似検索 - 分子機能
XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / Helix hairpin bin / Ankyrin repeat-containing domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Leucine-rich Repeat Variant ...XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / Helix hairpin bin / Ankyrin repeat-containing domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Helix Hairpins / Alpha Horseshoe / Armadillo-type fold / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Protein Stu2p/Alp14p / Tubulin alpha-1A chain / Tubulin beta chain
類似検索 - 構成要素
生物種Lachancea kluyveri NRRL Y-12651 (菌類)
Escherichia coli (大腸菌)
Sus scrofa (ブタ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.208 Å
データ登録者Nithianantham, S. / Al-Bassam, J.
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)GM110283 米国
引用ジャーナル: Elife / 年: 2018
タイトル: Structural basis of tubulin recruitment and assembly by microtubule polymerases with Tumor Overexpressed Gene (TOG) domain arrays.
著者: Nithianantham, S. / Cook, B.D. / Beans, M. / Guo, F. / Chang, F. / Al-Bassam, J.
履歴
登録2018年11月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年11月28日Provider: repository / タイプ: Initial release
改定 1.12020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22024年3月13日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.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_label_asym_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: Tubulin alpha-1A chain
B: Tubulin beta chain
C: Tubulin alpha-1A chain
D: Tubulin beta chain
E: Protein Stu2p/Alp14p
F: Truncated Darpin-D1
G: Tubulin alpha-1A chain
H: Tubulin beta chain
I: Tubulin alpha-1A chain
J: Tubulin beta chain
K: Protein Stu2p/Alp14p
L: Truncated Darpin-D1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)560,37328
ポリマ－556,31312
非ポリマー4,06016
水00
1
A: Tubulin alpha-1A chain
B: Tubulin beta chain
C: Tubulin alpha-1A chain
D: Tubulin beta chain
E: Protein Stu2p/Alp14p
F: Truncated Darpin-D1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)280,18614
ポリマ－278,1566
非ポリマー2,0308
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
G: Tubulin alpha-1A chain
H: Tubulin beta chain
I: Tubulin alpha-1A chain
J: Tubulin beta chain
K: Protein Stu2p/Alp14p
L: Truncated Darpin-D1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)280,18614
ポリマ－278,1566
非ポリマー2,0308
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)115.130, 194.990, 149.570
Angle α, β, γ (deg.)90.000, 90.190, 90.000
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 4種, 12分子 ACGIBDHJEKFL

#1: タンパク質
Tubulin alpha-1A chain / Alpha-tubulin 1 / Tubulin alpha-1 chain


分子量: 50121.266 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 器官: Brain / 参照: UniProt: P02550
#2: タンパク質
Tubulin beta chain / Beta-tubulin


分子量: 49907.770 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 器官: Brain / 参照: UniProt: P02554
#3: タンパク質 Protein Stu2p/Alp14p


分子量: 63099.242 Da / 分子数: 2 / 由来タイプ: 組換発現
詳細: Protein was obtained from cDNA (Lachancea kluyveri NRRL Y-12651 chromosome)
由来: (組換発現) Lachancea kluyveri NRRL Y-12651 (菌類)
遺伝子: SKLU-Cont10078 / プラスミド: pLIC / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: A0A493R6X8*PLUS
#4: タンパク質 Truncated Darpin-D1


分子量: 14998.981 Da / 分子数: 2 / Mutation: N-terminal truncation (residues 1-40) / 由来タイプ: 組換発現
詳細: N-terminal residues (1-40) of Darpin-D1 were truncated.
由来: (組換発現) Escherichia coli (大腸菌) / プラスミド: pLIC / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21

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非ポリマー , 3種, 16分子

#5: 化合物
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#6: 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: 8 / 由来タイプ: 合成 / 式: Mg
#7: 化合物
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / コメント: GDP, エネルギー貯蔵分子*YM

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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: 3.02 Å3/Da / 溶媒含有率: 59.24 % / 解説: Rectangular crystal
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: 50 mM PIPES, 100 mM MgCl2 [pH 7.0], and 10-15% PEG-8000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年7月25日
放射モノクロメーター: Cryo-Cooled double crystal / 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: 0.9792 Å / 相対比: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
反射解像度: 3.2→149.571 Å / Num. obs: 104265 / % possible obs: 96.2 % / 冗長度: 2.9 % / Biso Wilson estimate: 46.6 Å2 / Rpim(I) all: 0.105 / Rrim(I) all: 0.186 / Rsym value: 0.133 / Net I/av σ(I): 5.2 / Net I/σ(I): 5.8
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3.2-3.372.90.6541.1154350.5470.9610.65497.9
3.37-3.582.70.4081.8140720.3390.5930.40894
3.58-3.822.90.2612.8137350.2070.3640.26197.6
3.82-4.132.90.1674.3127760.1330.2360.16797.9
4.13-4.532.70.1126.3112390.0860.1510.11293.1
4.53-5.0630.0868.2107240.0650.1170.08698.8
5.06-5.842.80.0927.690870.0720.1280.09294.3
5.84-7.1630.1095.979470.0750.1370.10997.2
7.16-10.122.90.0415.359250.0290.0520.0494.1
10.12-57.56530.02920.133250.0190.0350.02994.7

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解析

ソフトウェア
名称バージョン分類
MOSFLMデータ削減
SCALA3.3.21データスケーリング
PHENIX精密化
PDB_EXTRACT3.24データ抽出
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換 / 解像度: 3.208→57.565 Å / 交差検証法: THROUGHOUT / σ(F): 1.21 / 位相誤差: 22.19 / 詳細: The twin fractions were adjusted during refinement
Rfactor反射数%反射
Rfree0.2341 4535 5.13 %
Rwork0.1753 --
obs0.1802 88337 81.93 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / Bsol: 76.2 Å2 / ksol: 0.34 e/Å3
原子変位パラメータBiso max: 152.59 Å2 / Biso mean: 48.5489 Å2 / Biso min: 0.63 Å2
精密化ステップサイクル: final / 解像度: 3.208→57.565 Å
タンパク質核酸リガンド溶媒全体
原子数36617 0 248 0 36865
Biso mean--36.43 --
残基数----4660
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.501
X-RAY DIFFRACTIONf_chiral_restr0.039
X-RAY DIFFRACTIONf_plane_restr0.004
X-RAY DIFFRACTIONf_dihedral_angle_d5.783
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.218-3.27350.3176260.2412421X-RAY DIFFRACTION8
3.2735-3.3330.2352510.21311014X-RAY DIFFRACTION19
3.333-3.39710.3437910.20741760X-RAY DIFFRACTION33
3.3971-3.46640.30341580.20633007X-RAY DIFFRACTION57
3.4664-3.54170.32122570.20184662X-RAY DIFFRACTION88
3.5417-3.62410.27332300.18984652X-RAY DIFFRACTION87
3.6241-3.71470.27012560.18785017X-RAY DIFFRACTION94
3.7147-3.81510.23892680.18054949X-RAY DIFFRACTION94
3.8151-3.92730.27472560.1744991X-RAY DIFFRACTION94
3.9273-4.0540.23052940.17064938X-RAY DIFFRACTION92
4.054-4.19890.23542360.16684875X-RAY DIFFRACTION92
4.1989-4.36690.23062280.16244725X-RAY DIFFRACTION88
4.3669-4.56550.21072490.1574689X-RAY DIFFRACTION88
4.5655-4.8060.18012700.15355017X-RAY DIFFRACTION94
4.806-5.10690.21172570.16074970X-RAY DIFFRACTION93
5.1069-5.50070.23842840.1764894X-RAY DIFFRACTION91
5.5007-6.05340.26342240.20144607X-RAY DIFFRACTION86
6.0534-6.92730.25932530.20175012X-RAY DIFFRACTION94
6.9273-8.72010.20232200.18014840X-RAY DIFFRACTION90
8.7201-49.86240.18192620.17854894X-RAY DIFFRACTION90
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)
11.4486-0.24510.21410.78690.15231.8871-0.00290.1730.3714-0.3559-0.0895-0.2194-0.74190.3465-0.07980.3632-0.12650.0790.40750.02190.13459.56135.1653-9.7158
20.7404-0.0219-0.76020.9153-0.19691.7958-0.0226-0.1027-0.00210.09160.0018-0.1462-0.13310.4576-0.09020.22960.09040.01440.3909-0.05880.111511.212920.98930.5403
30.8838-0.3995-0.4970.51110.130.58350.10040.2036-0.0234-0.2706-0.11360.0807-0.1222-0.15490.17550.47880.22530.02810.3216-0.08640.2198-7.391631.1736-1.032
41.2958-0.5860.31881.03240.35990.92060.0386-0.05490.10670.0333-0.03390.0778-0.3499-0.1998-0.01220.52270.11370.23190.4586-0.0940.3525-5.834637.627612.8083
50.14420.0234-0.5190.04550.08812.54250.15-0.10860.0416-0.1159-0.09960.0790.0331-0.1279-0.02310.7386-0.090.10260.46260.05010.5787-6.006240.37811.6582
60.1241-0.0543-0.04510.39950.13710.2285-0.0242-0.17540.02560.0723-0.0470.015-0.013-0.0783-0.11420.3920.14230.20290.29950.02870.1075-0.194612.70389.8486
72.1559-0.5864-0.31964.1017-1.14491.5658-0.00730.18840.3246-0.229-0.0006-0.1137-0.2324-0.03680.00290.60040.22720.11980.44320.05520.267-2.74529.6828-33.3477
81.13460.3329-0.23360.90960.42770.5411-0.05280.16080.0676-0.1882-0.0630.0948-0.0796-0.0093-0.17690.22720.12020.10320.3612-0.02420.1243-2.1655-6.8539-28.3641
91.51790.2094-0.12222.62550.19521.07860.00180.30610.0923-0.5997-0.07740.6175-0.3564-0.39570.07160.35980.1295-0.0210.4061-0.05060.2519-15.9373.9576-16.4982
100.28980.0114-0.24940.86240.74450.89230.1068-0.01890.13590.1106-0.0570.2289-0.1005-0.08960.01490.3050.01460.10350.3812-0.09430.1279-11.0499-7.8477-12.3076
110.689-0.320.13030.5346-0.10660.6983-0.04850.02360.2756-0.0185-0.0728-0.18410.06970.13030.08180.1582-0.08920.1150.16620.02170.2116-0.6823-38.6096-53.571
121.1884-0.13560.89790.1787-0.41951.7879-0.04480.12370.3420.1624-0.08210.0832-0.1735-0.1858-0.18620.2457-0.07720.19110.19-0.03790.3649-19.2944-32.1987-41.3924
130.27430.33240.11780.47560.23050.2135-0.0483-0.01070.0823-0.0043-0.05780.1456-0.06590.072-0.47770.2149-0.06480.1230.24860.0980.2064-9.5214-45.1638-38.3254
141.34430.5264-0.15611.8409-1.22222.5794-0.02180.3310.2535-0.1280.06060.1963-0.5257-0.2939-0.16060.8361-0.00610.16430.63220.1350.30254.1975-66.0032-76.8988
150.7285-0.1169-0.15271.00510.15110.9970.00630.3978-0.2664-0.4113-0.0594-0.03850.0085-0.16610.05760.3620.04990.09690.4358-0.08010.20489.2256-79.511-67.8761
161.35920.1888-0.27681.1407-0.24630.92430.17820.7068-0.142-0.42010.02130.4318-0.2058-0.4195-0.00930.33380.1621-0.07760.4978-0.12870.3957-11.6839-70.6478-60.2389
171.1466-0.4982-0.43870.88890.39680.8358-0.0199-0.0564-0.0920.14120.05990.10490.00880.09750.05350.39990.16020.23710.39230.03760.33165.6009-88.4757-51.2804
183.96942.06214.02981.40052.16684.57170.05360.8913-0.5198-0.18420.2304-1.09750.33331.3668-0.29130.52320.06350.13770.3662-0.08270.52419.8021-115.1397-52.3022
191.53120.3548-1.55470.2986-0.03842.0566-0.0601-0.0116-0.1045-0.01310.0077-0.13380.21790.14340.03570.17110.1474-0.01570.2679-0.08120.135414.1604-112.2129-61.8318
208.6505-5.4630.84915.4091-1.44262.8399-0.1470.1117-0.71540.0701-0.02810.87130.3045-0.52170.16680.23050.03860.13690.412-0.14750.56212.4235-120.0535-68.0832
214.0153-2.5987-4.95861.72973.08826.435-0.01590.1595-0.18850.1021-0.11340.25470.0465-0.26150.17650.49540.1022-0.14230.38390.0840.221511.6657-118.4142-53.5613
220.86040.18240.05662.3860.21520.02140.0096-0.3134-0.31350.20290.20280.23730.3654-0.1931-0.24770.44460.2068-0.01240.34870.08990.24556.3896-109.7452-59.2596
231.1370.1430.60890.43870.18630.5193-0.0165-0.1416-0.10370.0031-0.09580.10820.0183-0.18930.06140.15030.07780.10080.4469-0.04870.54483.0949-115.2024-57.0476
240.3784-0.12570.17952.46391.11220.6521-0.09290.0976-0.3081-0.1544-0.0896-0.04960.39360.13890.20.43670.19890.22710.4994-0.09280.5892-0.4539-105.0611-56.491
250.06550.6151-0.15426.3665-2.11371.12370.04740.03040.27950.11080.20580.5849-0.0796-0.4196-0.2810.3017-0.03870.24020.3065-0.01860.6239-5.5857-111.5797-62.2603
261.36252.12.28883.25173.53163.84580.03780.03420.0624-0.1086-0.01820.0584-0.04040.0197-0.01160.71160.0176-0.14210.9380.10010.6926-4.9226-108.0926-46.06
275.3379-2.9535-1.17566.36-1.48831.2292-0.0206-0.191-0.18430.13840.03350.05260.2473-0.1444-0.0180.74980.16820.04350.8403-0.07930.8345-8.5095-99.5451-51.7988
280.68351.30320.36242.48510.69130.19340.0686-0.22310.25410.3316-0.01950.3469-0.1597-0.1505-0.05510.88930.2917-0.05330.9722-0.28120.9447-13.3615-103.4718-59.2634
291.02550.01130.12071.01730.14110.8913-0.21810.0101-0.35090.0862-0.0195-0.23690.37810.2160.01330.19210.03430.19440.2596-0.02210.209629.2613-15.553-10.113
300.2871-0.09350.05450.88860.37610.3726-0.14350.0428-0.29670.09910.2524-0.57280.33660.5203-0.12460.57850.08970.2780.5201-0.01030.79444.6691-82.6608-49.691
312.0411-1.0031-0.91591.24190.24721.3144-0.1161-0.45030.21910.08410.0051-0.093-0.04010.2838-0.02140.25730.09980.06220.2229-0.00670.27131.9591-65.7179-39.9058
321.39290.2753-0.1520.4514-0.59280.9926-0.1393-0.4225-0.59870.4250.08420.21730.29350.19580.01220.48040.0812-0.03630.32880.06320.3629-48.6861-66.8734-65.1224
331.3847-0.61380.07921.8624-0.02441.9053-0.1447-0.3073-0.15110.3820.1392-0.15540.2470.018-0.03890.26320.141-0.07540.2760.05190.1537-41.6369-49.8163-66.5466
341.03940.4005-0.67922.14041.20313.36180.12570.1317-0.01-0.01820.0676-0.10910.04830.0733-0.01180.23760.04520.02390.2374-0.03550.0712-44.143-53.6362-75.7666
350.76160.23140.35310.9818-0.03680.7489-0.0383-0.077-0.09050.06660.0195-0.01120.08140.02550.0830.18220.08010.14470.2867-0.05480.216-52.5288-48.8097-78.8595
365.8791.4935-1.6472.246-1.68062.69010.0325-0.13150.09570.27340.11060.4253-0.1551-0.5222-0.13140.2575-0.00640.00730.3599-0.00380.1343-69.117-57.2154-74.3318
370.9525-0.12490.5151.18190.37311.14840.07370.216-0.0376-0.11440.035-0.15080.45130.34580.07730.36810.01490.16370.2494-0.01250.2872-54.9824-64.1501-82.2432
380.36340.9988-0.30262.9575-0.8780.2903-0.07810.2835-0.2613-0.03590.19130.20510.5006-0.397-0.10060.3699-0.06730.11010.4775-0.02160.4109-70.9761-65.2424-84.8408
390.4896-0.0332-0.30850.35960.1130.9493-0.14560.108-0.3240.0687-0.25810.26030.3735-0.22620.13720.5106-0.01290.12720.3926-0.11240.2485-63.7508-71.4385-88.764
400.1390.0352-0.09350.6250.06310.4007-0.11830.1942-0.1738-0.25150.02530.01720.0774-0.0356-0.03150.2539-0.00430.04360.3979-0.170.0708-57.135-42.2878-84.7786
411.62950.2325-0.42641.7188-0.18612.0619-0.0971-0.1527-0.23190.12810.01440.05290.4081-0.07970.24960.30660.00890.16650.3439-0.01340.1182-60.6949-39.1142-41.6045
421.0566-0.061-0.1870.40970.03790.7158-0.0872-0.062-0.22550.30230.00380.18060.1224-0.20810.09670.24780.06550.12580.3408-0.10810.1033-62.7277-25.3025-48.7699
431.04680.4554-0.10121.11170.32621.1071-0.23690.182-0.1146-0.0494-0.00840.45850.2076-0.15150.10830.18910.04150.13060.3944-0.05930.2754-69.8492-23.4025-62.3194
442.39480.9354-0.61790.66370.5623.2110.1157-0.2221-0.78260.20980.0519-0.20260.79520.21180.00240.3183-0.0578-0.11050.35930.11220.3576-60.6533-1.3641-15.2369
451.58870.1841-0.06992.25290.21661.58830.0428-0.2983-0.20950.40240.0503-0.10240.24910.2553-0.09570.1759-0.0073-0.01140.20.01510.1883-51.5529.324-19.0306
460.72490.2981-0.29340.5164-0.280.5503-0.0236-0.1613-0.13230.071-0.06230.09420.2151-0.0891-0.06710.2749-0.20170.12360.25350.0280.264-66.502610.7641-28.7916
471.60630.1999-0.80370.51420.14471.39220.00860.27520.1224-0.0613-0.028-0.02710.0031-0.0662-0.3470.2189-0.07120.21360.2434-0.07610.3792-82.93637.7502-29.84
480.40650.54870.05130.9211-0.04020.1453-0.12140.1697-0.1419-0.23440.10480.06630.0430.0027-0.05910.1271-0.09250.08010.1774-0.07860.2698-69.746911.9243-36.4526
491.14910.2817-0.95981.1398-1.11551.5279-0.1214-0.45660.03920.31490.0177-0.02520.01990.01970.13840.8097-0.24930.00830.6614-0.12240.3039-47.620743.24860.9755
501.51180.5685-0.36020.3985-0.32561.15530.0398-0.22370.02950.2809-0.1990.20560.2366-0.17660.10.3994-0.1330.01790.303-0.05520.3604-53.513750.7295-10.2631
511.979-0.4247-0.29511.7680.24961.0283-0.0597-0.48280.06150.3902-0.10410.37010.2015-0.25130.06340.5851-0.15670.00940.4916-0.05730.3029-67.90843.5369-13.7426
521.6973-0.3022-0.1540.78590.28092.34150.0397-0.2788-0.10560.365-0.10310.50390.1743-0.6389-0.02120.5345-0.2406-0.05110.58150.05760.4174-73.522237.9002-17.6337
532.241.26240.57432.07650.30960.7669-0.02160.19690.119-0.2032-0.03910.2567-0.18330.24280.02180.24220.01080.07170.2633-0.09950.2923-52.00158.9527-23.6762
540.8841.1540.46953.76291.46182.3918-0.06590.1759-0.1971-0.23450.1668-0.15840.08030.0314-0.27340.3813-0.0362-0.26540.3133-0.12890.6789-43.178186.2192-12.7511
550.38710.0496-0.1931.2061-0.15990.25470.00460.00590.03280.1284-0.02690.0211-0.045-0.0033-0.07360.37890.1339-0.2420.2389-0.16190.4487-48.715885.031-18.386
562.64580.91890.08769.76931.02350.34470.0046-0.4587-0.07230.6817-0.03380.0782-0.2129-0.02340.01210.382-0.031-0.10330.4112-0.22210.6815-54.856286.875-8.5689
570.474-0.0361-0.5750.00490.03810.7114-0.12090.06610.03160.05620.01970.0602-0.0704-0.19690.0770.44850.0198-0.07840.33680.140.4667-55.075984.3401-23.0943
583.4954-1.7977-1.03682.59631.9531.69990.0202-0.0014-0.1907-0.02080.05860.24790.0241-0.1614-0.03010.4475-0.01870.10390.2493-0.15350.5169-58.341775.1814-17.4056
593.2902-3.03761.17974.03111.89087.73060.0074-0.2306-0.19980.3022-0.069-0.02640.1912-0.01480.03160.3513-0.0705-0.03790.5618-0.01770.6532-63.503581.7534-11.4897
600.0002-0.0018-0.00190.09320.09330.0927-0.03840.121-0.2414-0.1067-0.06230.09910.2071-0.06380.04210.6064-0.094-0.26760.869-0.08470.7418-64.864574.2258-24.8044
611.13542.29221.34535.50253.94843.3301-0.0128-0.063-0.39380.2068-0.0186-0.68270.37950.51590.02961.2934-0.0659-0.14141.24680.11981.2127-71.052573.3006-13.8314
620.8933-0.0271-0.28590.81850.16051.4624-0.1435-0.05240.07850.0083-0.0259-0.21240.01850.03360.09040.19930.02490.03530.08050.09710.4201-28.4793-13.8744-64.1591
630.388-0.1312-0.14891.6930.80580.82660.0406-0.12950.1806-0.04620.095-0.618-0.29080.4443-0.24370.3586-0.0882-0.08630.50080.19450.6673-13.679853.6338-23.9779
640.94990.4169-0.07361.87760.65141.71250.07850.0877-0.1448-0.07590.1795-0.20840.17540.4128-0.16660.34130.21670.0540.75380.07080.4617-24.860236.8525-34.1527
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 102 )A2 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 199 )A103 - 199
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 243 )A200 - 243
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 337 )A244 - 337
5X-RAY DIFFRACTION5chain 'A' and (resid 338 through 372 )A338 - 372
6X-RAY DIFFRACTION6chain 'A' and (resid 373 through 437 )A373 - 437
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 63 )B1 - 63
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 243 )B64 - 243
9X-RAY DIFFRACTION9chain 'B' and (resid 244 through 324 )B244 - 324
10X-RAY DIFFRACTION10chain 'B' and (resid 325 through 441 )B325 - 441
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 243 )C2 - 243
12X-RAY DIFFRACTION12chain 'C' and (resid 244 through 337 )C244 - 337
13X-RAY DIFFRACTION13chain 'C' and (resid 338 through 439 )C338 - 439
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 64 )D1 - 64
15X-RAY DIFFRACTION15chain 'D' and (resid 65 through 243 )D65 - 243
16X-RAY DIFFRACTION16chain 'D' and (resid 244 through 373 )D244 - 373
17X-RAY DIFFRACTION17chain 'D' and (resid 374 through 441 )D374 - 441
18X-RAY DIFFRACTION18chain 'F' and (resid 43 through 49 )F43 - 49
19X-RAY DIFFRACTION19chain 'F' and (resid 50 through 59 )F50 - 59
20X-RAY DIFFRACTION20chain 'F' and (resid 60 through 68 )F60 - 68
21X-RAY DIFFRACTION21chain 'F' and (resid 69 through 82 )F69 - 82
22X-RAY DIFFRACTION22chain 'F' and (resid 83 through 92 )F83 - 92
23X-RAY DIFFRACTION23chain 'F' and (resid 93 through 115 )F93 - 115
24X-RAY DIFFRACTION24chain 'F' and (resid 116 through 125 )F116 - 125
25X-RAY DIFFRACTION25chain 'F' and (resid 126 through 135 )F126 - 135
26X-RAY DIFFRACTION26chain 'F' and (resid 136 through 148 )F136 - 148
27X-RAY DIFFRACTION27chain 'F' and (resid 149 through 158 )F149 - 158
28X-RAY DIFFRACTION28chain 'F' and (resid 159 through 167 )F159 - 167
29X-RAY DIFFRACTION29chain 'E' and (resid 14 through 253 )E14 - 253
30X-RAY DIFFRACTION30chain 'E' and (resid 254 through 395 )E254 - 395
31X-RAY DIFFRACTION31chain 'E' and (resid 396 through 543 )E396 - 543
32X-RAY DIFFRACTION32chain 'G' and (resid 2 through 88 )G2 - 88
33X-RAY DIFFRACTION33chain 'G' and (resid 89 through 128 )G89 - 128
34X-RAY DIFFRACTION34chain 'G' and (resid 129 through 160 )G129 - 160
35X-RAY DIFFRACTION35chain 'G' and (resid 161 through 199 )G161 - 199
36X-RAY DIFFRACTION36chain 'G' and (resid 200 through 223 )G200 - 223
37X-RAY DIFFRACTION37chain 'G' and (resid 224 through 273 )G224 - 273
38X-RAY DIFFRACTION38chain 'G' and (resid 274 through 311 )G274 - 311
39X-RAY DIFFRACTION39chain 'G' and (resid 312 through 372 )G312 - 372
40X-RAY DIFFRACTION40chain 'G' and (resid 373 through 437 )G373 - 437
41X-RAY DIFFRACTION41chain 'H' and (resid 1 through 64 )H1 - 64
42X-RAY DIFFRACTION42chain 'H' and (resid 65 through 295 )H65 - 295
43X-RAY DIFFRACTION43chain 'H' and (resid 296 through 441 )H296 - 441
44X-RAY DIFFRACTION44chain 'I' and (resid 2 through 47 )I2 - 47
45X-RAY DIFFRACTION45chain 'I' and (resid 48 through 160 )I48 - 160
46X-RAY DIFFRACTION46chain 'I' and (resid 161 through 273 )I161 - 273
47X-RAY DIFFRACTION47chain 'I' and (resid 274 through 311 )I274 - 311
48X-RAY DIFFRACTION48chain 'I' and (resid 312 through 439 )I312 - 439
49X-RAY DIFFRACTION49chain 'J' and (resid 1 through 127 )J1 - 127
50X-RAY DIFFRACTION50chain 'J' and (resid 128 through 243 )J128 - 243
51X-RAY DIFFRACTION51chain 'J' and (resid 244 through 324 )J244 - 324
52X-RAY DIFFRACTION52chain 'J' and (resid 325 through 373 )J325 - 373
53X-RAY DIFFRACTION53chain 'J' and (resid 374 through 441 )J374 - 441
54X-RAY DIFFRACTION54chain 'L' and (resid 43 through 68 )L43 - 68
55X-RAY DIFFRACTION55chain 'L' and (resid 69 through 92 )L69 - 92
56X-RAY DIFFRACTION56chain 'L' and (resid 93 through 101 )L93 - 101
57X-RAY DIFFRACTION57chain 'L' and (resid 102 through 115 )L102 - 115
58X-RAY DIFFRACTION58chain 'L' and (resid 116 through 125 )L116 - 125
59X-RAY DIFFRACTION59chain 'L' and (resid 126 through 135 )L126 - 135
60X-RAY DIFFRACTION60chain 'L' and (resid 136 through 158 )L136 - 158
61X-RAY DIFFRACTION61chain 'L' and (resid 159 through 167 )L159 - 167
62X-RAY DIFFRACTION62chain 'K' and (resid 14 through 253 )K14 - 253
63X-RAY DIFFRACTION63chain 'K' and (resid 254 through 388 )K254 - 388
64X-RAY DIFFRACTION64chain 'K' and (resid 389 through 543 )K389 - 543

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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