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- PDB-4kod: Structure of p97 N-D1 R155H mutant in complex with ADP -

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基本情報

登録情報
データベース: PDB / ID: 4kod
タイトルStructure of p97 N-D1 R155H mutant in complex with ADP
要素Transitional endoplasmic reticulum ATPase
キーワードHYDROLASE (加水分解酵素) / AAA ATPase / Transport protein (運搬体タンパク質)
機能・相同性
機能・相同性情報


flavin adenine dinucleotide catabolic process / positive regulation of Lys63-specific deubiquitinase activity / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / VCP-NSFL1C complex / deubiquitinase activator activity / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / endoplasmic reticulum stress-induced pre-emptive quality control / positive regulation of oxidative phosphorylation ...flavin adenine dinucleotide catabolic process / positive regulation of Lys63-specific deubiquitinase activity / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / VCP-NSFL1C complex / deubiquitinase activator activity / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / endoplasmic reticulum stress-induced pre-emptive quality control / positive regulation of oxidative phosphorylation / BAT3 complex binding / Derlin-1 retrotranslocation complex / ERAD pathway / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / aggresome assembly / vesicle-fusing ATPase / regulation of protein localization to chromatin / ER-associated misfolded protein catabolic process / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of mitochondrial membrane potential / ATPase complex / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / ubiquitin-specific protease binding / negative regulation of smoothened signaling pathway / autophagosome maturation / ATP metabolic process / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / Attachment and Entry / endoplasmic reticulum to Golgi vesicle-mediated transport / Protein methylation / MHC class I protein binding / HSF1 activation / DNA修復 / interstrand cross-link repair / endoplasmic reticulum unfolded protein response / lipid droplet / viral genome replication / ubiquitin-dependent ERAD pathway / Josephin domain DUBs / proteasome complex / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / オートファジー / proteasomal protein catabolic process / ADP binding / Hh mutants are degraded by ERAD / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / positive regulation of protein catabolic process / double-strand break repair / establishment of protein localization / Aggrephagy / cytoplasmic stress granule / オートファジー / azurophil granule lumen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of canonical Wnt signaling pathway / site of double-strand break / Ovarian tumor domain proteases / E3 ubiquitin ligases ubiquitinate target proteins / proteasome-mediated ubiquitin-dependent protein catabolic process / cellular response to heat / Attachment and Entry / secretory granule lumen / protein phosphatase binding / protein ubiquitination / ficolin-1-rich granule lumen / regulation of apoptotic process / lipid binding / glutamatergic synapse / DNA修復 / intracellular membrane-bounded organelle / protein domain specific binding / cellular response to DNA damage stimulus / ubiquitin protein ligase binding / endoplasmic reticulum membrane / Neutrophil degranulation / ATP hydrolysis activity / perinuclear region of cytoplasm / 小胞体 / protein-containing complex / RNA binding / extracellular exosome / extracellular region / 核質 / ATP binding / identical protein binding / 細胞核 / 細胞質基質
類似検索 - 分子機能
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / AAA ATPase, CDC48 family / Barwin-like endoglucanases - #20 / Cell division protein 48 (CDC48), N-terminal domain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, N-terminal subdomain / CDC48, domain 2 / Cell division protein 48 (CDC48) domain 2 / Cell division protein 48 (CDC48), domain 2 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / AAA ATPase, CDC48 family / Barwin-like endoglucanases - #20 / Cell division protein 48 (CDC48), N-terminal domain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, N-terminal subdomain / CDC48, domain 2 / Cell division protein 48 (CDC48) domain 2 / Cell division protein 48 (CDC48), domain 2 / Helicase, Ruva Protein; domain 3 - #60 / CDC48 domain 2-like superfamily / Vps4 C terminal oligomerisation domain / Vps4 oligomerisation, C-terminal / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Βバレル / P-loop containing nucleoside triphosphate hydrolase / ロスマンフォールド / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / Transitional endoplasmic reticulum ATPase
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: 2.96 Å
データ登録者Xia, D. / Tang, W.K.
引用ジャーナル: J.Biol.Chem. / : 2013
タイトル: Altered Intersubunit Communication Is the Molecular Basis for Functional Defects of Pathogenic p97 Mutants.
著者: Tang, W.K. / Xia, D.
履歴
登録2013年5月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年11月13日Provider: repository / タイプ: Initial release
改定 1.12014年1月8日Group: Database references

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)659,87424
ポリマ-654,74712
非ポリマー5,12612
3,027168
1
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)329,93712
ポリマ-327,3746
非ポリマー2,5636
1086
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-74 kcal/mol
Surface area108570 Å2
手法PISA
2
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)329,93712
ポリマ-327,3746
非ポリマー2,5636
1086
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area18370 Å2
ΔGint-73 kcal/mol
Surface area111510 Å2
手法PISA
単位格子
Length a, b, c (Å)146.520, 170.737, 256.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111L
12A
22C
32D
42E
52G
62I
72J
82K
13A
23K
14A
24L
15A
25F
16A
26H
17A
27B

NCSドメイン領域:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A201 - 431
2111B201 - 431
3111C201 - 431
4111D201 - 431
5111E201 - 431
6111F201 - 431
7111G201 - 431
8111H201 - 431
9111I201 - 431
10111J201 - 431
11111L201 - 431
1211A435 - 459
2211B435 - 459
3211C435 - 459
4211D435 - 459
5211E435 - 459
6211F435 - 459
7211G435 - 459
8211H435 - 459
9211I435 - 459
10211J435 - 459
11211L435 - 459
1311A800
2311B800
3311C800
4311D800
5311E800
6311F800
7311G800
8311H800
9311I800
10311J800
11311L800
1121A24 - 107
2121C24 - 107
3121D24 - 107
4121E24 - 107
5121G24 - 107
6121I24 - 107
7121J24 - 107
8121K24 - 107
1221A108 - 195
2221C108 - 195
3221D108 - 195
4221E108 - 195
5221G108 - 195
6221I108 - 195
7221J108 - 195
8221K108 - 195
1131A368 - 431
2131K368 - 431
1231A435 - 459
2231K435 - 459
1331A800
2331K800
1431A200 - 236
2431K200 - 236
1531A246 - 264
2531K246 - 264
1141A24 - 107
2141L24 - 107
1241A108 - 195
2241L108 - 195
1151A24 - 51
2151F24 - 51
1251A53 - 107
2251F53 - 107
1351A116 - 195
2351F116 - 195
1161A24 - 51
2161H24 - 51
1261A53 - 107
2261H53 - 107
1361A108 - 195
2361H108 - 195
1171A24 - 107
2171B24 - 107
1271A108 - 195
2271B108 - 195

NCSアンサンブル:
ID
1
2
3
4
5
6
7

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要素

#1: タンパク質
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


分子量: 54562.266 Da / 分子数: 12 / 断片: UNP residue 1-481 / 変異: R155HH / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: p97, VCP / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P55072, vesicle-fusing ATPase
#2: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP / アデノシン二リン酸


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


分子量: 18.015 Da / 分子数: 168 / 由来タイプ: 天然 / : 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: 2.45 Å3/Da / 溶媒含有率: 49.82 %
結晶化温度: 288 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.8
詳細: 0.1M citrate, pH 5.8, 0.3M NaCl, 13.6% EPG 3350, 20% glycerol, 0.625% benzamidine, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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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: 22-BM / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2008年1月1日
放射モノクロメーター: Si / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.69→21.99 Å / Num. obs: 118808 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
反射 シェル解像度: 2.95→3.06 Å / % possible all: 51.3

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
MOLREP位相決定
REFMAC5.5.0102精密化
DENZOデータ削減
SCALEPACKデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 2.96→21.99 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / SU B: 71.101 / SU ML: 0.534 / 交差検証法: THROUGHOUT / ESU R Free: 0.558 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.29094 5937 5 %RANDOM
Rwork0.26841 ---
obs0.26956 112289 88.01 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 120.557 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å20 Å2
2---9.12 Å20 Å2
3---5.45 Å2
精密化ステップサイクル: LAST / 解像度: 2.96→21.99 Å
タンパク質核酸リガンド溶媒全体
原子数41268 0 324 168 41760
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01942265
X-RAY DIFFRACTIONr_bond_other_d0.0020.0241544
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.99357179
X-RAY DIFFRACTIONr_angle_other_deg0.807395722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18255258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59524.2441963
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.914157724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.42215379
X-RAY DIFFRACTIONr_chiral_restr0.0640.26519
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02147290
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028949
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5251.526285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.978242563
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.948315975
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7684.514611
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDタイプRms dev position (Å)Weight position
11A2001TIGHT POSITIONAL0.050.05
12B2001TIGHT POSITIONAL0.050.05
13C2001TIGHT POSITIONAL0.040.05
14D2001TIGHT POSITIONAL0.050.05
15E2001TIGHT POSITIONAL0.050.05
16F2001TIGHT POSITIONAL0.050.05
17G2001TIGHT POSITIONAL0.050.05
18H2001TIGHT POSITIONAL0.050.05
19I2001TIGHT POSITIONAL0.040.05
110J2001TIGHT POSITIONAL0.050.05
111L2001TIGHT POSITIONAL0.040.05
11A2001TIGHT THERMAL0.070.5
12B2001TIGHT THERMAL0.080.5
13C2001TIGHT THERMAL0.070.5
14D2001TIGHT THERMAL0.070.5
15E2001TIGHT THERMAL0.070.5
16F2001TIGHT THERMAL0.070.5
17G2001TIGHT THERMAL0.070.5
18H2001TIGHT THERMAL0.080.5
19I2001TIGHT THERMAL0.070.5
110J2001TIGHT THERMAL0.090.5
111L2001TIGHT THERMAL0.060.5
21A1373TIGHT POSITIONAL0.050.05
22C1373TIGHT POSITIONAL0.040.05
23D1373TIGHT POSITIONAL0.040.05
24E1373TIGHT POSITIONAL0.030.05
25G1373TIGHT POSITIONAL0.040.05
26I1373TIGHT POSITIONAL0.040.05
27J1373TIGHT POSITIONAL0.050.05
28K1373TIGHT POSITIONAL0.040.05
21A1373TIGHT THERMAL0.720.5
22C1373TIGHT THERMAL0.120.5
23D1373TIGHT THERMAL0.110.5
24E1373TIGHT THERMAL0.10.5
25G1373TIGHT THERMAL0.120.5
26I1373TIGHT THERMAL0.110.5
27J1373TIGHT THERMAL0.130.5
28K1373TIGHT THERMAL0.110.5
31A1119TIGHT POSITIONAL0.070.05
31A1119TIGHT THERMAL0.110.5
41A1373TIGHT POSITIONAL0.040.05
41A1373TIGHT THERMAL0.140.5
51A1292TIGHT POSITIONAL0.070.05
51A1292TIGHT THERMAL0.320.5
61A1362TIGHT POSITIONAL0.050.05
61A1362TIGHT THERMAL0.120.5
71A1373TIGHT POSITIONAL0.060.05
71A1373TIGHT THERMAL0.110.5
LS精密化 シェル解像度: 2.96→3.035 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.525 244 -
Rwork0.521 4575 -
obs--49.93 %
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.69082.77680.22448.0593-0.21138.2499-0.54841.10380.1585-0.50920.4168-0.49010.25070.8840.13150.2437-0.21030.04611.02240.1530.4618103.869232.79642.4663
211.11851.6375-4.72024.73641.08988.1398-0.2887-0.59830.84110.18430.4117-0.245-0.46670.2665-0.12310.4139-0.167-0.08910.94420.12210.7701104.727643.958259.9426
38.6353-0.97591.5151.0860.19185.3904-0.22730.60190.30170.0994-0.0722-0.1509-0.1247-0.34180.29950.3364-0.1544-0.06480.83640.1430.102470.508630.029747.0979
47.7591.48190.4726.26424.14889.02640.1859-0.5895-0.00860.6129-0.0573-0.40791.11120.5656-0.12860.46480.0626-0.20611.00860.2430.272991.919124.089373.2841
527.518311.492728.181131.785216.993629.87340.75970.76690.06370.6526-0.712-0.39350.85360.5574-0.04770.9401-0.097-0.03690.56310.24630.531881.272225.465460.2869
69.44970.54732.32525.8961.23048.6047-0.16130.2358-0.52580.3793-0.0420.6930.6601-0.54060.20340.2724-0.13750.06580.91340.16770.2246-2.730517.978716.498
75.6532-0.26461.90946.14860.0157.31620.24990.1986-0.1416-0.20950.0109-0.2317-0.1664-0.0939-0.26080.3017-0.0042-0.04820.96870.17060.105510.315429.7284.9136
83.8206-0.37851.34871.54120.14848.29130.0579-0.52210.4788-0.03610.0535-0.028-0.1390.1839-0.11140.4083-0.02040.07560.86090.15760.171117.531622.473842.7203
95.74730.9499-1.45597.0709-2.0246.6801-0.12090.8732-0.8108-0.2431-0.0123-0.42990.4680.54290.13320.42230.0821-0.0070.8913-0.06890.174431.074114.62112.1479
1023.92966.577323.018916.40559.721241.4933-0.35730.26950.60120.2558-0.73850.71270.53350.04331.09590.7999-0.01440.02670.538-0.0120.751424.658516.976127.5343
1111.63790.1016-2.6726.93361.106310.5161-0.0138-1.6011-0.55440.6062-0.2191-0.48440.25660.23080.23290.70430.02370.16821.15090.19140.263827.4921.6098122.1901
1210.55490.61091.70586.2853-3.49729.4520.0275-0.93340.90140.12870.2150.6889-0.5331-0.968-0.24250.72560.14410.24941.1764-0.09810.30278.738326.3039114.605
136.80610.69870.94522.2310.06565.843-0.61810.85440.115-0.03460.12410.0864-0.34280.9990.4940.7399-0.13630.16721.2414-0.0220.124740.17126.096291.3506
1411.5923-2.23344.35554.6796-1.09035.7813-0.05440.1668-0.8066-0.26250.1277-0.090.4746-0.0717-0.07330.6554-0.20090.27380.514-0.07620.295711.47937.802395.2251
156.57611.4048-10.104316.8053-2.932815.65580.3124-0.2794-0.41891.2172-0.8207-0.2572-0.77780.52190.50830.8749-0.04330.06670.8150.01760.871826.230815.434493.217
168.55980.0672-0.1738.058-0.45877.2212-0.0115-0.1687-0.07570.72730.50540.5557-0.5956-1.2458-0.49390.35890.10150.29631.09950.15940.3944-17.225511.380778.1048
178.2310.6102-0.73554.3328-1.96610.62540.07760.13820.64070.11560.1870.6271-0.7369-1.0189-0.26460.34360.340.21891.01830.260.5614-21.727222.226160.7999
186.03622.9240.93032.6992-0.10254.24850.3343-0.5552-0.0970.5149-0.21090.132-0.67630.7773-0.12340.6368-0.17580.11591.082-0.02790.092915.29320.112373.4235
199.1088-2.58373.69624.0705-3.31679.4166-0.03210.74640.165-0.32640.22230.04050.8352-0.5547-0.19030.4394-0.18070.08350.83580.12210.1383-2.88368.283846.9334
202.16775.82763.231815.69998.7064.860.4584-0.1375-0.12861.0834-0.3402-0.37920.5333-0.247-0.11820.9501-0.03830.02720.6490.07330.8036.577912.684460.0142
2111.2158-0.0564-0.75747.43810.64635.54430.0982-1.19940.38780.5942-0.2153-0.87070.07821.39470.11710.7742-0.193-0.36221.25950.09030.366388.138333.1049104.618
2210.6698-1.0042-4.24473.8564-1.41065.29470.6874-1.54261.2811.1653-0.37040.3591-1.19980.4156-0.3171.5508-0.3609-0.13831.6075-0.53440.650172.333740.7972115.6675
233.6369-0.17111.51322.0835-0.30116.5261-0.13970.6550.24680.11940.0124-0.0666-0.09340.15990.12730.334-0.1072-0.02640.79210.06770.073767.880431.006578.0153
248.9205-3.4019-4.2274.60762.90338.409-0.2084-0.8838-0.80090.2804-0.2460.2452-0.0172-0.14570.45440.6215-0.04260.07220.97950.1280.150357.330619.6889108.4618
2533.210512.02115.997411.70120.195311.96790.97890.3180.3322-0.3879-1.437-0.23051.00871.32830.45820.91060.04440.07070.558-0.02250.653262.829723.837293.3316
265.8412.2234-0.99797.49870.766511.4693-0.44640.6324-0.3111-0.1480.25990.27890.27630.27150.18650.3059-0.03290.20180.85870.09720.381857.942626.0128-1.6705
276.26040.542-2.13365.6030.44737.9010.0236-0.13060.05470.2350.0298-0.2201-0.14580.4678-0.05340.33570.02040.13210.93090.11480.136374.258436.95344.9515
286.53441.11091.83282.04340.08987.569-0.1738-1.07880.4436-0.016-0.2316-0.05760.1917-1.28870.40540.33380.05640.15361.13580.01260.153745.177126.959829.3102
2910.29693.03080.19236.3659-0.32676.0720.21820.3346-0.53190.1875-0.1007-0.8181-0.07140.5514-0.11750.46290.26080.03410.91630.21230.292678.373819.5225.3895
309.4622-5.13018.64243.5927-5.30458.37350.0420.32950.120.0939-0.4591-0.51740.01890.54950.41710.78130.0897-0.11130.7170.10020.864461.919921.688527.4854
3110.2618-1.10861.87616.64430.145910.4718-0.501-1.61760.54080.55280.24050.0226-0.5440.77880.26040.24140.0543-0.14221.37430.06450.448192.529974.0985109.1743
3210.8805-1.3823-0.2726.3743.052612.4387-0.43790.4617-0.7778-0.14410.3354-0.36060.24970.50540.10260.15140.0773-0.02561.00140.16170.4894102.340164.77393.4186
3310.36712.77650.54273.3763-1.04034.505-0.3781-0.15920.0024-0.1004-0.08860.03450.1203-0.5680.46670.14250.097-0.02420.7826-0.06610.312363.699169.22892.0676
349.3955-3.272-3.12472.66530.82575.36250.03480.66540.5909-0.3274-0.3338-0.437-0.58030.77220.29890.3247-0.23-0.10121.05690.2240.369491.088482.791276.4238
3523.6476-3.4507-12.34229.715313.635911.23660.92060.60351.13240.0801-0.3015-0.265-0.377-0.4105-0.61910.7998-0.0618-0.05860.60360.16080.644577.057577.590784.1401
3611.20040.4831-1.2464.5785-0.62699.6297-0.0773-0.3263-0.5115-0.4249-0.0322-0.0686-0.2867-1.24550.10960.22430.09750.10261.16840.07830.321-15.361657.372290.3794
3711.7301-0.81191.19687.1607-0.06078.4732-0.1903-1.2388-0.94820.7310.20830.27650.8378-0.4033-0.01790.31710.01120.14481.10620.35850.4106-5.232849.3088106.8351
386.59080.5489-1.56511.71520.33056.42930.0850.2676-0.39220.11180.1725-0.1493-0.20940.2053-0.25750.16060.0070.0910.67220.06390.280914.085459.991174.5272
397.7666-1.32111.11896.31-1.253910.35950.0697-1.11010.36460.14770.0571-0.0065-0.82840.4431-0.12680.44550.00590.16991.1394-0.19570.149511.386370.5506107.102
4037.0872-6.5106-38.61369.832710.292541.6291.42620.5078-0.2060.2312-1.3879-0.5234-1.2878-1.0005-0.03830.6860.0031-0.02610.7652-0.06960.706812.657366.881390.7233
419.90852.80842.10055.213-0.544511.89850.21761.56720.9475-0.2935-0.0969-0.59850.0488-0.1638-0.12070.28490.10660.21331.07680.10050.516953.886771.53865.7345
427.75260.5888-2.69396.8155-1.95017.83440.04421.5497-0.845-0.5694-0.09040.66270.8867-0.9130.04610.4399-0.1742-0.0221.7509-0.42540.238236.310459.99473.9252
437.66831.1051-0.81662.9582-3.047.785-0.1247-1.8356-0.48870.0475-0.1264-0.12270.01870.90320.25110.13320.05720.02791.3664-0.09990.188653.723165.394838.6865
447.65772.93822.31356.88422.12239.68720.06540.61541.34880.01590.08110.4395-0.2269-1.1449-0.14650.21660.11460.15141.1670.16190.458224.590874.828423.1473
458.809613.475-2.202530.5311-9.35274.8199-0.72060.3152-0.3884-0.78360.0885-0.57410.4193-0.25430.63210.7804-0.0430.15630.7541-0.21150.873939.002571.664931.3052
468.12491.39151.5457.74690.86948.4461-0.11070.31560.0606-0.63560.26810.1442-0.1983-0.701-0.15740.17680.0575-0.01020.833-0.17520.1747-5.189462.82527.8107
4710.60372.52881.85586.7864-0.43617.7295-0.4603-0.3942-0.54840.40250.07850.47910.8561-0.66820.38180.394-0.26090.13370.9082-0.15240.5799-13.363450.318742.6716
487.15870.0749-0.5821.56590.01463.3725-0.12230.0747-0.18830.0189-0.0816-0.04810.15260.50660.20390.12420.01930.03770.7624-0.10220.17923.744862.040745.1112
4910.99985.2374-3.93478.272-3.57557.22340.0742-0.20410.01630.39770.08020.2256-0.2083-0.6658-0.15440.26010.11840.04340.7047-0.12450.2023-5.430668.395761.4614
508.03688.91699.977427.529711.818625.60750.9244-0.04811.21870.0183-1.3849-0.38270.9872-1.07180.46050.63790.12130.11980.4746-0.03270.61758.914866.706253.4582
5117.68932.24024.28034.63932.70269.01160.20630.1178-0.98450.10950.3199-1.0180.00360.6646-0.52620.08630.06660.06440.9620.28180.4336102.725775.928246.2328
5211.15040.48035.00379.4816-1.23187.07021.74121.083-2.9068-1.5077-0.1069-0.53851.42791.1435-1.63430.81650.2789-0.05791.4127-0.32371.341895.830565.442129.6894
534.2933-2.942710.036510.3894-5.499823.835-0.6182-0.61080.16440.66470.4413-1.0373-1.5468-1.08480.17690.2113-0.13440.03061.88370.22220.287286.54973.868461.1673
542.5294-0.4464-0.40154.56711.86250.85820.2091-0.0934-0.080.4976-0.50960.39920.2354-0.16570.30060.1132-0.03580.11841.67120.23830.233970.68966.386562.396
556.1640.5005-1.57855.87213.579811.5961-0.2342-0.3642-0.1165-0.30540.24260.1644-0.21280.0487-0.00840.0567-0.11520.00140.47390.01410.018772.77979.666930.5207
560.0630.5902-0.73310.5163-3.239912.01840.03850.0193-0.03071.49020.844-1.8442-0.0458-0.1251-0.88260.81590.0016-0.04720.9838-0.0821.108573.064275.396246.3851
578.66171.09740.98674.6743-4.897211.54650.3407-1.2246-0.03160.4883-0.37230.37590.3165-0.40880.03160.6205-0.1580.11271.94540.03860.160833.065865.1338131.7761
585.8652-0.674-0.48269.3891-0.79864.46060.1747-0.9854-0.72040.4741-0.3417-1.31740.69681.20750.1670.72680.0396-0.15192.19490.32760.331552.983959.3494131.9058
595.86831.29891.05221.2921.49116.7375-0.1409-0.193-0.2104-0.0230.0851-0.04020.0674-0.60370.05580.11620.00150.07221.12120.04150.161233.863363.884698.0798
609.9301-2.2229-0.2445.96620.47236.25640.3272-1.16920.78230.6375-0.5135-0.1878-0.62361.12260.18630.3596-0.1991-0.08551.3669-0.22030.207959.368579.3851115.0713
617.94138.475712.52089.287814.256623.14-0.5228-0.53160.6202-0.5293-0.54030.7024-0.7229-0.45231.06310.74820.0180.01950.8788-0.09370.861746.328473.198106.3945
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 107
2X-RAY DIFFRACTION2A108 - 200
3X-RAY DIFFRACTION3A201 - 371
4X-RAY DIFFRACTION4A372 - 459
5X-RAY DIFFRACTION5A800
6X-RAY DIFFRACTION6B21 - 107
7X-RAY DIFFRACTION7B108 - 200
8X-RAY DIFFRACTION8B201 - 371
9X-RAY DIFFRACTION9B372 - 459
10X-RAY DIFFRACTION10B800
11X-RAY DIFFRACTION11C23 - 107
12X-RAY DIFFRACTION12C108 - 200
13X-RAY DIFFRACTION13C201 - 371
14X-RAY DIFFRACTION14C372 - 460
15X-RAY DIFFRACTION15C800
16X-RAY DIFFRACTION16D22 - 107
17X-RAY DIFFRACTION17D108 - 200
18X-RAY DIFFRACTION18D201 - 371
19X-RAY DIFFRACTION19D372 - 460
20X-RAY DIFFRACTION20D800
21X-RAY DIFFRACTION21E23 - 107
22X-RAY DIFFRACTION22E108 - 200
23X-RAY DIFFRACTION23E201 - 371
24X-RAY DIFFRACTION24E372 - 461
25X-RAY DIFFRACTION25E800
26X-RAY DIFFRACTION26F23 - 107
27X-RAY DIFFRACTION27F108 - 200
28X-RAY DIFFRACTION28F201 - 371
29X-RAY DIFFRACTION29F372 - 460
30X-RAY DIFFRACTION30F800
31X-RAY DIFFRACTION31G23 - 107
32X-RAY DIFFRACTION32G108 - 200
33X-RAY DIFFRACTION33G201 - 371
34X-RAY DIFFRACTION34G372 - 459
35X-RAY DIFFRACTION35G800
36X-RAY DIFFRACTION36H22 - 107
37X-RAY DIFFRACTION37H108 - 200
38X-RAY DIFFRACTION38H201 - 371
39X-RAY DIFFRACTION39H372 - 459
40X-RAY DIFFRACTION40H800
41X-RAY DIFFRACTION41I21 - 107
42X-RAY DIFFRACTION42I108 - 200
43X-RAY DIFFRACTION43I201 - 371
44X-RAY DIFFRACTION44I372 - 459
45X-RAY DIFFRACTION45I800
46X-RAY DIFFRACTION46J21 - 107
47X-RAY DIFFRACTION47J108 - 200
48X-RAY DIFFRACTION48J201 - 371
49X-RAY DIFFRACTION49J372 - 462
50X-RAY DIFFRACTION50J800
51X-RAY DIFFRACTION51K23 - 107
52X-RAY DIFFRACTION52K108 - 200
53X-RAY DIFFRACTION53K201 - 238
54X-RAY DIFFRACTION54K239 - 369
55X-RAY DIFFRACTION55K370 - 459
56X-RAY DIFFRACTION56K800
57X-RAY DIFFRACTION57L23 - 107
58X-RAY DIFFRACTION58L108 - 200
59X-RAY DIFFRACTION59L201 - 371
60X-RAY DIFFRACTION60L372 - 459
61X-RAY DIFFRACTION61L800

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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