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- PDB-5dyi: Structure of p97 N-D1 wild-type in complex with ADP -

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基本情報

登録情報
データベース: PDB / ID: 5dyi
タイトルStructure of p97 N-D1 wild-type in complex with ADP
要素Transitional endoplasmic reticulum ATPase
キーワードHYDROLASE (加水分解酵素) / VCP / AAA ATPase
機能・相同性
機能・相同性情報


positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex ...positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / NADH metabolic process / vesicle-fusing ATPase / cellular response to misfolded protein / : / positive regulation of mitochondrial membrane potential / stress granule disassembly / ERAD pathway / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / DNA修復 / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / interstrand cross-link repair / negative regulation of smoothened signaling pathway / Attachment and Entry / ATP metabolic process / : / endoplasmic reticulum unfolded protein response / proteasome complex / lipid droplet / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ADP binding / proteasomal protein catabolic process / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / オートファジー / Translesion Synthesis by POLH / ABC-family proteins mediated transport / establishment of protein localization / オートファジー / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / double-strand break repair / KEAP1-NFE2L2 pathway / azurophil granule lumen / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / cellular response to heat / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / DNA修復 / intracellular membrane-bounded organelle / lipid binding / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / 小胞体 / ATP hydrolysis activity / protein-containing complex / RNA binding
類似検索 - 分子機能
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / 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 / 解像度: 3.71 Å
データ登録者Tang, W.K. / Xia, D.
引用ジャーナル: Sci Rep / 年: 2016
タイトル: Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain.
著者: Tang, W.K. / Xia, D.
履歴
登録2015年9月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年2月10日Provider: repository / タイプ: Initial release
改定 1.12024年3月6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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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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)660,10224
ポリマ－654,97612
非ポリマー5,12612
水0
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)330,05112
ポリマ－327,4886
非ポリマー2,5636
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area23910 Å2
ΔGint-113 kcal/mol
Surface area110050 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)330,05112
ポリマ－327,4886
非ポリマー2,5636
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area24030 Å2
ΔGint-110 kcal/mol
Surface area110040 Å2
手法PISA
単位格子
Length a, b, c (Å)146.440, 176.210, 256.870
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
121K
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
13A
23B
33C
43D
53E
63F
73G
83H
93I
103J
113K
123L

NCSドメイン領域:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLYSLYSAA21 - 6321 - 63
211ASNASNLYSLYSBB21 - 6321 - 63
311ASNASNLYSLYSCC21 - 6321 - 63
411ASNASNLYSLYSDD21 - 6321 - 63
511ASNASNLYSLYSEE21 - 6321 - 63
611ASNASNLYSLYSFF21 - 6321 - 63
711ASNASNLYSLYSGG21 - 6321 - 63
811ASNASNLYSLYSHH21 - 6321 - 63
911ASNASNLYSLYSII21 - 6321 - 63
1011ASNASNLYSLYSJJ21 - 6321 - 63
1111ASNASNLYSLYSLL21 - 6321 - 63
1211ASNASNLYSLYSKK21 - 6321 - 63
121ILEILEARGARGAA114 - 147114 - 147
221ILEILEARGARGBB114 - 147114 - 147
321ILEILEARGARGCC114 - 147114 - 147
421ILEILEARGARGDD114 - 147114 - 147
521ILEILEARGARGEE114 - 147114 - 147
621ILEILEARGARGFF114 - 147114 - 147
721ILEILEARGARGGG114 - 147114 - 147
821ILEILEARGARGHH114 - 147114 - 147
921ILEILEARGARGII114 - 147114 - 147
1021ILEILEARGARGJJ114 - 147114 - 147
1121ILEILEARGARGLL114 - 147114 - 147
1221ILEILEARGARGKK114 - 147114 - 147
131GLYGLYASNASNAA149 - 199149 - 199
231GLYGLYASNASNBB149 - 199149 - 199
331GLYGLYASNASNCC149 - 199149 - 199
431GLYGLYASNASNDD149 - 199149 - 199
531GLYGLYASNASNEE149 - 199149 - 199
631GLYGLYASNASNFF149 - 199149 - 199
731GLYGLYASNASNGG149 - 199149 - 199
831GLYGLYASNASNHH149 - 199149 - 199
931GLYGLYASNASNII149 - 199149 - 199
1031GLYGLYASNASNJJ149 - 199149 - 199
1131GLYGLYASNASNLL149 - 199149 - 199
1231GLYGLYASNASNKK149 - 199149 - 199
141ARGARGLYSLYSAA65 - 11265 - 112
241ARGARGLYSLYSBB65 - 11265 - 112
341ARGARGLYSLYSCC65 - 11265 - 112
441ARGARGLYSLYSDD65 - 11265 - 112
541ARGARGLYSLYSEE65 - 11265 - 112
641ARGARGLYSLYSFF65 - 11265 - 112
741ARGARGLYSLYSGG65 - 11265 - 112
841ARGARGLYSLYSHH65 - 11265 - 112
941ARGARGLYSLYSII65 - 11265 - 112
1041ARGARGLYSLYSJJ65 - 11265 - 112
1141ARGARGLYSLYSLL65 - 11265 - 112
1241ARGARGLYSLYSKK65 - 11265 - 112
112GLUGLUCYSCYSAA200 - 209200 - 209
212GLUGLUCYSCYSBB200 - 209200 - 209
312GLUGLUCYSCYSCC200 - 209200 - 209
412GLUGLUCYSCYSDD200 - 209200 - 209
512GLUGLUCYSCYSEE200 - 209200 - 209
612GLUGLUCYSCYSFF200 - 209200 - 209
712GLUGLUCYSCYSGG200 - 209200 - 209
812GLUGLUCYSCYSHH200 - 209200 - 209
912GLUGLUCYSCYSII200 - 209200 - 209
1012GLUGLUCYSCYSJJ200 - 209200 - 209
1112GLUGLUCYSCYSKK200 - 209200 - 209
1212GLUGLUCYSCYSLL200 - 209200 - 209
122GLNGLNGLYGLYAA212 - 370212 - 370
222GLNGLNGLYGLYBB212 - 370212 - 370
322GLNGLNGLYGLYCC212 - 370212 - 370
422GLNGLNGLYGLYDD212 - 370212 - 370
522GLNGLNGLYGLYEE212 - 370212 - 370
622GLNGLNGLYGLYFF212 - 370212 - 370
722GLNGLNGLYGLYGG212 - 370212 - 370
822GLNGLNGLYGLYHH212 - 370212 - 370
922GLNGLNGLYGLYII212 - 370212 - 370
1022GLNGLNGLYGLYJJ212 - 370212 - 370
1122GLNGLNGLYGLYKK212 - 370212 - 370
1222GLNGLNGLYGLYLL212 - 370212 - 370
113ILEILETHRTHRAA371 - 403371 - 403
213ILEILETHRTHRBB371 - 403371 - 403
313ILEILETHRTHRCC371 - 403371 - 403
413ILEILETHRTHRDD371 - 403371 - 403
513ILEILETHRTHREE371 - 403371 - 403
613ILEILETHRTHRFF371 - 403371 - 403
713ILEILETHRTHRGG371 - 403371 - 403
813ILEILETHRTHRHH371 - 403371 - 403
913ILEILETHRTHRII371 - 403371 - 403
1013ILEILETHRTHRJJ371 - 403371 - 403
1113ILEILETHRTHRKK371 - 403371 - 403
1213ILEILETHRTHRLL371 - 403371 - 403
123VALVALADPADPAA - M407 - 800407
223VALVALADPADPBB - N407 - 800407
323VALVALADPADPCC - O407 - 800407
423VALVALADPADPDD - P407 - 800407
523VALVALADPADPEE - Q407 - 800407
623VALVALADPADPFF - R407 - 800407
723VALVALADPADPGG - S407 - 800407
823VALVALADPADPHH - T407 - 800407
923VALVALADPADPII - U407 - 800407
1023VALVALADPADPJJ - V407 - 800407
1123VALVALADPADPKK - W407 - 800407
1223VALVALADPADPLL - X407 - 800407

NCSアンサンブル:
ID
1
2
3

NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2given(0.551987, -0.050203, 0.83234), (-0.175118, 0.968946, 0.174576), (-0.815257, -0.242121, 0.526054)-81.46857, -20.73938, -21.47482
3given(-0.439546, -0.206886, 0.874069), (-0.344894, 0.937391, 0.048436), (-0.829366, -0.280172, -0.48338)-138.511, -20.15041, 45.8543
4given(-0.980484, -0.196504, -0.00611), (-0.195622, 0.978237, -0.069165), (0.019568, -0.06662, -0.997587)-100.12651, -0.71625, 134.61647
5given(-0.491803, -0.240156, -0.836932), (-0.131331, 0.970673, -0.20136), (0.860745, 0.010886, -0.50892)-24.78069, 6.152, 141.73474
6given(0.491615, -0.157791, -0.856398), (0.048246, 0.986871, -0.154135), (0.869475, 0.034457, 0.492774)25.46204, 10.92739, 74.65029
7given(-0.92801, -0.052511, 0.368835), (0.093444, -0.991178, 0.093995), (0.360646, 0.121694, 0.92473)-108.56269, -93.65288, 30.77656
8given(-0.15097, 0.087191, 0.984686), (0.250292, -0.960274, 0.123403), (0.956327, 0.265089, 0.12315)-108.02319, -89.0003, 108.84141
9given(0.734534, 0.31259, 0.602285), (0.408954, -0.912204, -0.025313), (0.541494, 0.2649, -0.79788)-40.78196, -71.17594, 146.47615
10given(0.887192, 0.237236, -0.395738), (0.245141, -0.968982, -0.031308), (-0.390891, -0.069236, -0.917829)23.63136, -78.64913, 105.62397
11given(-0.776637, 0.076527, -0.625283), (-0.091125, -0.995802, -0.008691), (-0.623322, 0.050229, 0.78035)-38.56246, -97.86588, -5.34829
12given(0.119378, 0.16116, -0.979682), (0.063422, -0.985961, -0.154465), (-0.990821, -0.043694, -0.127923)24.0239, -81.8044, 32.02054
13given(1), (1), (1)
14given(0.513883, -0.02138, 0.857594), (-0.163624, 0.978894, 0.12245), (-0.842111, -0.203249, 0.499539)-81.90866, -15.56269, -16.461
15given(-0.459153, -0.194604, 0.86678), (-0.290206, 0.955038, 0.06069), (-0.839618, -0.223679, -0.494983)-137.57318, -18.13224, 50.84983
16given(-0.969504, -0.244669, 0.014106), (-0.245071, 0.968205, -0.050198), (-0.001376, -0.052124, -0.99864)-104.53783, -7.25985, 134.13371
17given(-0.481962, -0.18964, -0.855423), (-0.136829, 0.980609, -0.1403), (0.865442, 0.049427, -0.498565)-19.00977, 3.37332, 144.70621
18given(0.511282, -0.127779, -0.849861), (0.018501, 0.990292, -0.137763), (0.859214, 0.054712, 0.508683)28.43859, 9.19388, 75.51876
19given(-0.919818, -0.043631, 0.389911), (0.077573, -0.994403, 0.071725), (0.3846, 0.096221, 0.918055)-108.50462, -94.26031, 32.41102
20given(-0.12801, 0.059141, 0.990008), (0.23664, -0.967568, 0.088398), (0.963128, 0.245591, 0.109864)-107.79413, -87.14413, 110.24301
21given(0.758083, 0.28893, 0.584662), (0.357575, -0.933882, -0.00213), (0.54539, 0.210676, -0.811274)-38.79326, -75.6298, 147.0369
22given(0.881949, 0.267817, -0.387866), (0.270136, -0.96154, -0.049682), (-0.386254, -0.060959, -0.920376)23.88871, -77.59416, 105.80286
23given(0.101986, 0.098044, -0.989942), (0.090764, -0.991898, -0.088887), (-0.990637, -0.080785, -0.110058)22.56467, -83.26202, 30.89696
24given(-0.808769, 0.015409, -0.587924), (-0.010698, -0.999877, -0.01149), (-0.588029, -0.003003, 0.808834)-42.74069, -93.26448, -5.02406
25given(1), (1), (1)
26given(0.523312, -0.053484, 0.850461), (-0.160754, 0.973912, 0.160164), (-0.836841, -0.220531, 0.501062)-83.54804, -18.95009, -17.89763
27given(-0.465676, -0.215875, 0.858222), (-0.311685, 0.947659, 0.06925), (-0.82825, -0.235247, -0.508587)-138.64627, -20.2962, 51.90207
28given(-0.97043, -0.241153, -0.010561), (-0.240385, 0.969464, -0.04852), (0.02194, -0.044546, -0.998766)-102.27466, -7.04921, 136.4299
29given(-0.471153, -0.232787, -0.850779), (-0.146153, 0.971816, -0.184967), (0.869859, 0.037196, -0.491897)-21.75395, 4.24316, 143.56549
30given(0.512415, -0.150193, -0.845502), (0.037724, 0.987573, -0.152568), (0.857909, 0.046282, 0.511712)26.66148, 10.46104, 74.62125
31given(-0.916757, -0.034015, 0.397994), (0.067617, -0.995203, 0.070696), (0.39368, 0.091722, 0.91466)-108.55981, -94.97082, 33.18823
32given(-0.130046, 0.081024, 0.988192), (0.258532, -0.959408, 0.112687), (0.957209, 0.270133, 0.10382)-107.35251, -87.61891, 110.87753
33given(0.746291, 0.320658, 0.583291), (0.392328, -0.919818, 0.003696), (0.537706, 0.226083, -0.812255)-38.4814, -74.70379, 146.98178
34given(0.878334, 0.256913, -0.403145), (0.269248, -0.962695, -0.026887), (-0.395013, -0.084931, -0.914741)24.61031, -79.12782, 104.92518
35given(0.09921, 0.12488, -0.987199), (0.075931, -0.990151, -0.117622), (-0.992165, -0.06329, -0.107715)22.90652, -82.37713, 31.02101
36given(-0.808223, 0.059673, -0.585845), (-0.045443, -0.998206, -0.038984), (-0.58712, -0.004885, 0.809485)-41.86206, -94.25135, -5.14019

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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: 54581.312 Da / 分子数: 12 / 断片: UNP residues 1-481 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: 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 / 式: C10H15N5O10P2 / コメント: ADP, 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

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試料調製

結晶マシュー密度: 2.53 Å3/Da / 溶媒含有率: 51.38 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6
詳細: 0.1 M sodium citrate, pH 6.0, 0.3 M NaCl, 15.2 % PEG3350, 20 % glycerol, 2 % benzamidine

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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-ID / 波長: 1 Å
検出器タイプ: RAYONIX MX300HS / 検出器: CCD / 日付: 2009年3月1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: 1 Å / 相対比: 1
反射解像度: 3.71→50 Å / Num. obs: 62997 / % possible obs: 88.8 % / 冗長度: 4.9 % / Net I/σ(I): 7.12

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0124精密化
DENZOデータ削減
SCALEPACKデータスケーリング
MOLREP位相決定
精密化解像度: 3.71→50 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.833 / SU B: 172.044 / SU ML: 0.957 / 交差検証法: THROUGHOUT / ESU R Free: 1.164 / 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
Rfree0.28527 2448 5.1 %RANDOM
Rwork0.24855 ---
obs0.25037 45977 68.08 %-
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: 140.215 Å2
Baniso -1Baniso -2Baniso -3
1--3.59 Å20 Å20 Å2
2--2.14 Å20 Å2
3---1.45 Å2
精密化ステップサイクル: 1 / 解像度: 3.71→50 Å
タンパク質核酸リガンド溶媒全体
原子数41255 0 324 0 41579
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01942240
X-RAY DIFFRACTIONr_bond_other_d0.0030.0241575
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.99357118
X-RAY DIFFRACTIONr_angle_other_deg1.173395756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.92155253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87124.1521970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.582157736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7715396
X-RAY DIFFRACTIONr_chiral_restr0.0810.26513
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02147188
X-RAY DIFFRACTIONr_gen_planes_other0.0030.028964
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_it2.2987.22621048
X-RAY DIFFRACTIONr_mcbond_other2.2987.22621047
X-RAY DIFFRACTIONr_mcangle_it4.12810.83626289
X-RAY DIFFRACTIONr_mcangle_other4.12810.83626290
X-RAY DIFFRACTIONr_scbond_it1.837.41121192
X-RAY DIFFRACTIONr_scbond_other1.837.41121193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.44511.04430830
X-RAY DIFFRACTIONr_long_range_B_refined9.93967.801170732
X-RAY DIFFRACTIONr_long_range_B_other9.93967.801170733
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 / タイプ: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-ID数Rms dev position (Å)
11A27958.1
11B279510.31
11C279510.4
11D27959.18
11E279510.44
11F279510.77
11G27958.83
11H279510.48
11I27957.42
11J27958.79
11K279517.58
11L279513.72
22A26377.21
22B26376.28
22C26378.31
22D26378.39
22E263716.81
22F263710.71
22G26377.68
22H26378.6
22I26379.09
22J26377.96
22K26376.83
22L26378.6
33A13309.82
33B13308.99
33C133011.16
33D133010.39
33E13308.38
33F13309.21
33G13307.04
33H13307.76
33I13308.32
33J13309.73
33K13308.95
33L133010.24
LS精密化 シェル解像度: 3.71→3.805 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.57 33 -
Rwork0.463 681 -
obs--13.78 %
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)
14.54591.55513.8315.22091.49517.95870.06420.30130.2014-0.2989-0.1075-0.5431-0.29390.20210.04330.3133-0.11470.33740.24340.13760.80399.4683-58.846436.183
27.1485-3.3193-4.42827.35343.192410.4379-0.0634-0.07340.93640.1090.0456-0.1848-0.40960.77610.01780.1754-0.075-0.28340.5437-0.11150.67829.8619-55.442699.3618
36.935-0.4382-1.18324.79822.06853.40280.0184-1.09830.16530.44830.01520.1326-0.174-0.0931-0.03371.26860.03850.05941.1045-0.22090.5673-43.6788-64.1677132.136
45.5096-1.18052.95776.1177-3.25769.3983-0.2902-0.2440.08090.59160.35450.06840.0013-0.3986-0.06430.22480.07950.23440.7068-0.34840.6828-98.0126-71.8353101.5424
55.80641.557-3.75045.033-2.49586.87420.5287-0.43181.2921-0.3334-0.12191.0483-0.3473-0.7907-0.40670.8845-0.0024-0.39140.6788-0.19121.1625-99.157-72.45938.1499
69.22571.15970.56983.46551.09822.95840.10590.5426-0.017-0.5665-0.10.0175-0.27990.1058-0.00591.2261-0.0741-0.08890.48280.3020.3764-44.6793-67.65085.5035
75.2921.44190.25314.6565-2.02099.028-0.19630.3981-0.4915-0.25510.10880.41740.113-0.57790.08760.7448-0.14840.07720.3578-0.20861.0655-104.3289-40.038851.8029
87.6939-2.59283.02295.4235-1.26274.85780.0809-0.6144-0.92240.4606-0.18530.58820.6414-0.8470.10441.5446-0.18820.38170.62310.12460.5656-79.6733-37.9759110.4684
99.2167-0.7608-1.43846.46611.39595.5989-0.2654-0.8413-0.45950.4621-0.1076-0.05570.26640.25970.3731.02480.0369-0.50450.55680.04840.3192-17.7773-24.7605117.9484
103.0368-1.1919-0.55855.76961.34935.6974-0.0972-0.8295-0.29150.19220.3165-0.89620.46360.8971-0.21930.79870.1374-0.17910.9486-0.04071.178319.429-17.747668.719
118.8104-0.24841.42537.31810.25893.33530.09920.37740.13590.0751-0.2025-0.8763-0.21030.12030.10330.6165-0.06760.22690.4311-0.0680.2229-4.4067-25.167510.2011
127.2813.46-2.04847.9202-1.05815.7431-0.37170.06840.3306-0.21840.0629-0.08140.05760.19640.30880.60110.1949-0.30440.4814-0.15070.2069-66.749-33.09712.0351
136.7978-1.46211.92412.3410.11475.962-0.08770.05620.28430.06050.0718-0.01670.1164-0.2590.01590.2061-0.0370.14820.09080.08350.2781-13.811-67.180151.1632
143.4741-0.0150.98933.7005-1.60418.1-0.2046-0.17470.16390.02470.1427-0.0925-0.0227-0.02810.06190.04150.0786-0.10050.2515-0.11780.4175-13.3847-65.984585.8089
156.2132.0536-1.77324.2961-1.39426.82890.1303-0.29140.03620.1741-0.06880.1828-0.018-0.2439-0.06150.30510.1961-0.12560.5578-0.11520.2498-42.7691-71.1589104.0898
168.34542.49791.44783.50960.9793.5848-0.21090.0311-0.0324-0.2555-0.0363-0.00760.2991-0.09190.24710.23760.02240.22730.449-0.14450.3879-73.1113-75.785987.0306
174.4541-0.0851-1.67792.81581.84556.9172-0.0114-1.13210.8377-0.09850.104-0.1458-0.1563-0.0788-0.09260.4612-0.2089-0.17430.7748-0.11720.7166-73.7402-75.024452.2141
187.666-0.19280.09162.21821.54075.956-0.02-0.66640.2251-0.1043-0.1231-0.02450.0995-0.59070.14310.6717-0.0833-0.16080.2050.11330.2549-44.0106-71.725134.0817
196.129-0.922-1.62282.86350.9666.24070.01550.27940.20430.06950.06590.247-0.1272-0.0837-0.08150.50710.0604-0.06260.1944-0.15620.2146-77.7655-29.261656.0372
204.70840.58860.61853.34541.66626.4923-0.25180.1957-0.03480.22710.0186-0.07470.2853-0.26920.23320.71190.04650.13780.1657-0.07430.0793-64.2601-28.050488.307
216.52061.81390.40854.13510.20044.7819-0.1981-0.11250.1781-0.190.0515-0.0553-0.06810.08040.14660.92410.1012-0.26740.2215-0.05670.0913-30.4574-20.597392.3403
223.95342.3585-1.85063.5486-1.17236.65850.2389-0.4072-0.01550.11620.0157-0.10480.21950.2841-0.25460.5459-0.0057-0.20950.3576-0.15970.3648-9.4079-16.905264.2056
236.1167-0.00190.71542.9072-0.7766.11440.093-0.28430.04120.09310.05770.1097-0.41620.0138-0.15070.5269-0.0750.10790.1348-0.09680.0872-22.3248-20.856532.4127
247.2137-0.70140.0052.6782-0.75634.52130.04860.0325-0.03140.2619-0.00030.1518-0.27550.2095-0.04830.68390.0879-0.09880.182-0.07130.0472-56.6574-25.517328.1277
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 200
2X-RAY DIFFRACTION2B21 - 200
3X-RAY DIFFRACTION3C21 - 200
4X-RAY DIFFRACTION4D21 - 200
5X-RAY DIFFRACTION5E21 - 200
6X-RAY DIFFRACTION6F21 - 200
7X-RAY DIFFRACTION7G21 - 200
8X-RAY DIFFRACTION8H21 - 200
9X-RAY DIFFRACTION9I21 - 200
10X-RAY DIFFRACTION10J21 - 200
11X-RAY DIFFRACTION11K21 - 200
12X-RAY DIFFRACTION12L21 - 200
13X-RAY DIFFRACTION13A201 - 460
14X-RAY DIFFRACTION13A800
15X-RAY DIFFRACTION14B201 - 458
16X-RAY DIFFRACTION14B800
17X-RAY DIFFRACTION15C201 - 458
18X-RAY DIFFRACTION15C800
19X-RAY DIFFRACTION16D201 - 459
20X-RAY DIFFRACTION16D800
21X-RAY DIFFRACTION17E201 - 458
22X-RAY DIFFRACTION17E800
23X-RAY DIFFRACTION18F201 - 458
24X-RAY DIFFRACTION18F800
25X-RAY DIFFRACTION19G201 - 458
26X-RAY DIFFRACTION19G800
27X-RAY DIFFRACTION20H201 - 459
28X-RAY DIFFRACTION20H800
29X-RAY DIFFRACTION21I201 - 459
30X-RAY DIFFRACTION21I800
31X-RAY DIFFRACTION22J201 - 461
32X-RAY DIFFRACTION22J800
33X-RAY DIFFRACTION23K201 - 459
34X-RAY DIFFRACTION23K800
35X-RAY DIFFRACTION24L201 - 458
36X-RAY DIFFRACTION24L800

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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

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