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- PDB-7pli: DEAD-box helicase DbpA bound to single stranded RNA and ADP/BeF3 -

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基本情報

登録情報
データベース: PDB / ID: 7pli
タイトルDEAD-box helicase DbpA bound to single stranded RNA and ADP/BeF3
要素
  • ATP-dependent RNA helicase DbpA
  • RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
キーワードRNA BINDING PROTEIN / DEAD-box helicase / RNA / ribosome biogenesis / ATPase
機能・相同性
機能・相同性情報


DNA/RNA helicase activity / 3'-5' RNA helicase activity / ADP binding / ribosomal large subunit assembly / RNA helicase activity / rRNA binding / RNA helicase / ATP hydrolysis activity / ATP binding / cytosol
類似検索 - 分子機能
ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain ...ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA / RNA (> 10) / ATP-dependent RNA helicase DbpA
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å
データ登録者Wurm, J.P.
資金援助 ドイツ, 1件
組織認可番号国
German Research Foundation (DFG)WU 988/1-1 ドイツ
引用ジャーナル: Rna / 年: 2023
タイトル: Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.
著者: Wurm, J.P.
履歴
登録2021年8月31日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年9月7日Provider: repository / タイプ: Initial release
改定 1.12023年9月20日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.22024年1月31日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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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: ATP-dependent RNA helicase DbpA
D: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
B: ATP-dependent RNA helicase DbpA
C: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
E: ATP-dependent RNA helicase DbpA
G: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
J: ATP-dependent RNA helicase DbpA
L: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
I: ATP-dependent RNA helicase DbpA
K: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
F: ATP-dependent RNA helicase DbpA
H: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)344,11530
ポリマ－341,01012
非ポリマー3,10518
水43224
1
A: ATP-dependent RNA helicase DbpA
D: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
B: ATP-dependent RNA helicase DbpA
C: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)114,70510
ポリマ－113,6704
非ポリマー1,0356
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: ATP-dependent RNA helicase DbpA
G: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
F: ATP-dependent RNA helicase DbpA
H: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)114,70510
ポリマ－113,6704
非ポリマー1,0356
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
J: ATP-dependent RNA helicase DbpA
L: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
I: ATP-dependent RNA helicase DbpA
K: RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)114,70510
ポリマ－113,6704
非ポリマー1,0356
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)58.643, 121.599, 122.417
Angle α, β, γ (deg.)97.157, 92.426, 103.438
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 3 through 272 or resid 274...
d_2ens_1(chain "B" and (resid 3 through 272 or resid 274...
d_3ens_1(chain "E" and (resid 3 through 272 or resid 274...
d_4ens_1(chain "F" and resid 3 through 502)
d_5ens_1(chain "I" and (resid 3 through 272 or resid 274 through 502))
d_6ens_1(chain "J" and (resid 3 through 272 or resid 274 through 369 or resid 373 through 502))
d_1ens_2(chain "C" and (resid 0 through 4 or resid 7...
d_2ens_2(chain "D" and (resid 0 through 4 or resid 7...
d_3ens_2(chain "G" and (resid 0 through 4 or resid 7...
d_4ens_2(chain "H" and (resid 0 through 4 or resid 7 through 21))
d_5ens_2(chain "K" and (resid 0 through 4 or resid 7...
d_6ens_2(chain "L" and (resid 0 through 4 or resid 7...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAHISHISAA3 - 2725 - 274
d_12ens_1ASPASPPROPROAA274 - 369276 - 371
d_13ens_1SERSERLEULEUAA373 - 456375 - 458
d_14ens_1ADPADPADPADPAM500
d_15ens_1BEFBEFBEFBEFAN501
d_21ens_1ALAALAHISHISBC3 - 2725 - 274
d_22ens_1ASPASPPROPROBC274 - 369276 - 371
d_23ens_1SERSERLEULEUBC373 - 456375 - 458
d_24ens_1ADPADPADPADPBP500
d_25ens_1BEFBEFBEFBEFBQ501
d_31ens_1ALAALAHISHISEE3 - 2725 - 274
d_32ens_1ASPASPPROPROEE274 - 369276 - 371
d_33ens_1SERSERLEULEUEE373 - 456375 - 458
d_34ens_1ADPADPADPADPES500
d_35ens_1BEFBEFBEFBEFET501
d_41ens_1ALAALALEULEUFK3 - 4565 - 458
d_42ens_1ADPADPADPADPFBA500
d_43ens_1BEFBEFBEFBEFFCA501
d_51ens_1ALAALAHISHISII3 - 2725 - 274
d_52ens_1ASPASPLEULEUII274 - 456276 - 458
d_53ens_1ADPADPADPADPIY500
d_54ens_1BEFBEFBEFBEFIZ501
d_61ens_1ALAALAHISHISJG3 - 2725 - 274
d_62ens_1ASPASPPROPROJG274 - 369276 - 371
d_63ens_1SERSERLEULEUJG373 - 456375 - 458
d_64ens_1ADPADPADPADPJV500
d_65ens_1BEFBEFBEFBEFJW501
d_11ens_2POPPOPUUDB0 - 221 - 23
d_21ens_2POPPOPUUCD0 - 221 - 23
d_31ens_2POPPOPUUGF0 - 211 - 22
d_41ens_2POPPOPUULH0 - 221 - 23
d_51ens_2POPPOPUUKJ0 - 221 - 23
d_61ens_2POPPOPUUHL0 - 221 - 23

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.993931689136, -0.0734803316032, 0.0818562043958), (-0.075800501009, -0.996794251992, 0.0256027975426), (0.0797124919782, -0.031652173112, -0.996315240554)0.0298296219097, 66.0051818645, 63.5435859494
2given(-0.168639234508, 0.474729592579, 0.863824416484), (-0.647126799806, 0.607726364718, -0.460321160277), (-0.743496949258, -0.636632138331, 0.204723733083)-35.8504507357, 55.5694274787, 77.5006105826
3given(-0.175046275283, -0.556764749942, -0.812017127117), (-0.557651530751, -0.623638031967, 0.547814179568), (-0.811408387781, 0.548715425613, -0.201315200452)47.7516679401, 71.3961560291, 49.44389138
4given(-0.15794774334, -0.50296784935, -0.849750465074), (0.56024625021, 0.66298808663, -0.496559096294), (0.813127695691, -0.554499900367, 0.17706837943)53.1326881522, -4.97110300715, 13.9603242151
5given(-0.207357578363, 0.449904867867, 0.868670504026), (0.604847251978, -0.638941320811, 0.475303892615), (0.768871014196, 0.623970831393, -0.139634397982)-32.0029534513, 11.2752646337, -16.9655620476
6given(0.994205212675, -0.0760460534359, 0.0759802135198), (-0.0762988657645, -0.997084901957, 0.000425878376362), (0.0757263373783, -0.00622061461385, -0.997109234628)0.310320748885, 66.7920817497, 63.2079645144
7given(-0.146683070882, -0.436620825604, -0.887607081633), (-0.614798707261, -0.662711843841, 0.427592752023), (-0.774923626087, 0.608420304297, -0.17122531078)49.2319325391, 74.2244416897, 47.0627969416
8given(-0.177616458582, 0.443826130529, 0.878334081942), (-0.517541749185, 0.717004977394, -0.466962953822), (-0.837020269462, -0.537514863284, 0.102346667057)-37.0573531317, 55.4309118513, 78.1555996142
9given(-0.183933869623, 0.464794430586, 0.866103035962), (0.518281751494, -0.702835226842, 0.487243953249), (0.835195999555, 0.538506064224, -0.111619268588)-32.6102557409, 10.8971353701, -14.716331051
10given(-0.168653395128, -0.441295154319, -0.88137087488), (0.629358144664, 0.639964947266, -0.440855069173), (0.758593671247, -0.629049642751, 0.169800438452)53.0036227926, -4.64400305756, 15.1571059484

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要素

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タンパク質 / RNA鎖 , 2種, 12分子 ABEJIFDCGLKH

#1: タンパク質
ATP-dependent RNA helicase DbpA


分子量: 49358.754 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: dbpA, b1343, JW1337 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P21693, RNA helicase
#2: RNA鎖
RNA (5'-D(*(POP))-R(P*GP*GP*AP*CP*AP*UP*AP*UP*GP*GP*CP*UP*GP*UP*UP*CP*GP*CP*CP*AP*UP*U)-3')


分子量: 7476.280 Da / 分子数: 6 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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非ポリマー , 4種, 42分子

#3: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM
#4: 化合物
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


分子量: 66.007 Da / 分子数: 6 / 由来タイプ: 合成 / 式: BeF3
#5: 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: 6 / 由来タイプ: 合成 / 式: Mg
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 24 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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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: 2.46 Å3/Da / 溶媒含有率: 50.07 %
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: 8
詳細: 20 % (v/v) PEG 3350, 400 mM KSCN, 100 mM Tris, pH 8.0

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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: EMBL/DESY, HAMBURG / ビームライン: X13 / 波長: 0.9766 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2021年8月5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: 0.9766 Å / 相対比: 1
反射解像度: 2.5→56.88 Å / Num. obs: 108844 / % possible obs: 96.62 % / 冗長度: 3.6 % / Biso Wilson estimate: 51.89 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.25
反射 シェル解像度: 2.5→2.589 Å / 冗長度: 3.6 % / Mean I/σ(I) obs: 1.75 / Num. unique obs: 10869 / CC1/2: 0.75 / % possible all: 96.52

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874+SVN精密化
PHENIX1.18.2_3874+SVN位相決定
XDSデータ削減
XDSデータスケーリング
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 2db3, 3moj

2db3

3moj


解像度: 2.5→56.88 Å / SU ML: 0.3521 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 28.2317
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2469 5440 5 %
Rwork0.2133 103374 -
obs0.2149 108814 96.62 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 69.07 Å2
精密化ステップサイクル: LAST / 解像度: 2.5→56.88 Å
タンパク質核酸リガンド溶媒全体
原子数20580 2753 192 24 23549
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003524195
X-RAY DIFFRACTIONf_angle_d0.83433470
X-RAY DIFFRACTIONf_chiral_restr0.04834041
X-RAY DIFFRACTIONf_plane_restr0.00453833
X-RAY DIFFRACTIONf_dihedral_angle_d18.889375
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.64269744328
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.77888609011
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.828230347365
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.867433739566
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.802428733745
ens_2d_2JX-RAY DIFFRACTIONTorsion NCS0.767227981401
ens_2d_3JX-RAY DIFFRACTIONTorsion NCS3.05740376433
ens_2d_4JX-RAY DIFFRACTIONTorsion NCS1.63812116603
ens_2d_5JX-RAY DIFFRACTIONTorsion NCS1.05911061611
ens_2d_6JX-RAY DIFFRACTIONTorsion NCS1.55011720814
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.37321810.30753443X-RAY DIFFRACTION96.33
2.53-2.560.34351830.30893462X-RAY DIFFRACTION96.28
2.56-2.590.34251800.30673419X-RAY DIFFRACTION96.96
2.59-2.620.3431800.30893435X-RAY DIFFRACTION96.07
2.62-2.660.32271850.29873497X-RAY DIFFRACTION96.44
2.66-2.690.34851780.29093383X-RAY DIFFRACTION96.01
2.69-2.730.30351780.27553381X-RAY DIFFRACTION95.8
2.73-2.770.31081810.27913449X-RAY DIFFRACTION95.75
2.77-2.820.30351780.27373386X-RAY DIFFRACTION95.32
2.82-2.860.36081720.27743252X-RAY DIFFRACTION92.24
2.86-2.910.28891870.27453556X-RAY DIFFRACTION97.68
2.91-2.960.31461810.27873443X-RAY DIFFRACTION97.29
2.96-3.020.27881810.27623445X-RAY DIFFRACTION97.5
3.02-3.080.31921860.27893522X-RAY DIFFRACTION97.48
3.08-3.150.31991790.28883431X-RAY DIFFRACTION97.65
3.15-3.220.33821850.26963512X-RAY DIFFRACTION97.6
3.22-3.30.26841820.2533459X-RAY DIFFRACTION97.43
3.3-3.390.25921830.23433481X-RAY DIFFRACTION97.21
3.39-3.490.25911840.23283479X-RAY DIFFRACTION97.39
3.49-3.610.29881820.22293461X-RAY DIFFRACTION97.12
3.61-3.730.25071800.22033434X-RAY DIFFRACTION97.05
3.73-3.880.21821810.20093434X-RAY DIFFRACTION95.84
3.88-4.060.20421780.19833378X-RAY DIFFRACTION94.62
4.06-4.270.25381740.18063307X-RAY DIFFRACTION93.58
4.27-4.540.19771870.15613551X-RAY DIFFRACTION98.32
4.54-4.890.18461850.15573522X-RAY DIFFRACTION98.25
4.89-5.380.20051840.17183488X-RAY DIFFRACTION98.26
5.39-6.160.22361820.19183455X-RAY DIFFRACTION97.74
6.16-7.760.21421810.18743449X-RAY DIFFRACTION96.65
7.76-56.880.18111820.15713460X-RAY DIFFRACTION96.78
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)
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472.345673744930.0868388521937-0.8228336939571.945369047640.5126789670462.621272318160.138084375360.0128636891223-0.64836909329-0.238523452109-0.04545180164850.4117578346010.614158213666-0.490389295186-0.06957329267551.00038680854-0.110464978229-0.2226163728010.6764333947830.0778741926810.832396786677-5.647354924642.85162532633-17.7976409277
481.782881101610.659561520092-0.2606907771373.27713241224-1.070245567974.34820763529-0.152966163866-0.03342025559750.138396906415-0.03626125201580.140065004785-0.155888500719-0.459977713751-0.3355456376930.01108408513070.487199505180.153739257820.002723483371680.421737992611-0.0194651505860.41810313922615.1039391079-29.5332607892-2.83741139579
490.8510507598190.435660078283-0.147444946581.82365231478-1.378437933181.448819601880.120397426153-0.04760763703460.2982325815970.4383799934190.4318095586830.474880151621-1.12105197672-1.4986667531-0.3382978845351.053422898070.7957432435490.2139886854191.264075887920.1822557136540.606436530596-2.89672739559-21.048095503112.7035306258
501.4949481915-0.345187093985-0.4511282962051.54444753607-1.291455560742.16560917558-0.0110069591897-0.250652823290.3712623420480.5328174896770.08306629776920.0429157057907-1.24669263987-0.557854030038-0.1187902910961.364750818120.442574159280.01842742612970.870811127978-0.07407338324430.612722611488.7327979037-9.1174162245612.8908812056
517.094082415760.1839373025960.683633067011.492170329762.377073638789.068682315920.109844975932-0.167376542471-1.59444394554-1.757989862140.613757679363-0.8148301953140.8265210863580.934026256493-0.6843256859321.015314601710.225796271004-0.05852350118940.564781449987-0.1460826652160.91207362410131.02352873449.68458030829-18.4486383798
523.549068115590.430373231817-0.2128542306584.430308813312.258691259441.22074993566-0.3183777016190.4519885137130.427211245101-0.4588938088920.34432064112-0.148626988928-0.6009955469210.1679696799220.001352181355870.865246717404-0.0419865117356-0.07259316349220.71901585520.08144777659410.87069650506926.5966490637-9.62269632641-8.999789483
531.74394931197-1.16684381709-3.286858785740.7691763671792.196616253336.35585319144-0.852168983031-1.040241530190.1824190663021.21496037320.71335839538-0.225989838321-0.7296964279021.374540855020.2311169939621.377123114330.146723934201-0.1994894984560.942430144097-0.02862035759280.8196368401827.9388506837-9.0523749474411.0878709359
543.9403610595-1.7714082841-0.9390065440914.67678948045-3.597594753616.50953100431-0.30867165917-0.4288110582380.2868194748950.07593127099360.64647619626-1.22751141565-1.07029696480.363482879903-0.2719505566561.07426021128-0.0305567712372-0.01878013920170.692570099543-0.01177332629561.114219339634.9337521852-7.659774972530.0956982024304
552.167757287431.85712633108-1.096413305482.22248291936-2.909557872986.764149654331.185834811462.14779543553-1.02211322289-1.31348529314-1.0574196313-0.632946587688-0.5005752456830.662286690239-0.04799720678941.33941098795-0.1144060450390.3597545247741.21071964154-0.2506349587791.3539288293432.444145795-16.6436350093-13.4330935098
562.76395770952-0.02475856190381.435943629513.3977924263-0.5244545727982.68162957068-0.1015429088470.889427564531-0.320952299601-0.08896779762760.27004986629-0.492840097361-0.0383209854470.499540197414-0.2100200888640.74321500127-0.249122431510.1891048605040.684052380506-0.1607680953770.64032369638717.979675526104.00727779553.6060349237
572.81437347019-1.72625913762.12682963142.333645736570.4404800056514.042783017010.321323086480.008879269506-1.228129560490.626851238240.197695974076-0.1066715862380.07300964076760.214920645868-0.4857972066180.871710671418-0.2035746564950.04920287325020.446277377262-0.02514595986060.86712712738414.267695028593.254624667164.4513442421
583.244781881760.6882508948831.085907585191.471514615170.1378608277813.270651289580.278398617798-1.06844606596-0.8558900325980.4667674322190.08104293281050.09035662965630.537809961402-0.626701332582-0.3665206717351.08119537678-0.2749223988770.1104169498550.6975722889050.1620322669770.7840097270695.9386488063795.131350598973.6019062318
594.735199013711.772097415822.845429668792.8292136960.9023164801693.54728073254-0.0606150063188-0.03137415653630.06242981698290.2011663611990.08890208562530.371817283595-0.493245782769-0.109349447461-0.01516045760540.784727013533-0.1350982209090.1436078097840.44059115206-0.02208446281390.569306382975-1.20294580803106.53602048356.6106731088
603.42549336381-0.02383157328311.553671335061.96399118751-0.446318645552.460975146570.5102550242660.167610706699-1.26094422583-0.2289765773850.02898490753130.557273544490.657549210252-0.314508663221-0.4693181878420.767715764249-0.233457430952-0.00692080815310.600201917142-0.1638463553181.12659062466-9.391123442689.821131127947.7584395221
612.16184184626-0.6487790996190.7332974389020.742384057288-0.9660738393351.322604962640.6456563637410.188030660786-0.99841613323-0.152079151167-0.130957379081-0.2664151147090.2086956261670.77114542694-0.5626103394171.37172447511-0.175782750596-0.3813985005670.795616524115-0.25756882561.6053117272814.414451519172.905175782652.909453563
621.131548304050.7320866333580.1351578354971.767948468091.244544817521.414174578890.345136972137-0.125557904454-0.3504108341520.88718797343-0.457051599198-0.4381871066581.07535481296-0.02458790844120.006531629463131.24316058617-0.215230450712-0.2493601745610.751352384167-0.2187365616911.57133841439.9982215610966.354373978452.7464056179
634.82708184436-1.51954327534-0.1407747115717.719618916932.846545295556.64773928782-0.516748390806-0.130061200441.25931665261-0.1366593293180.679574143725-1.36702880723-0.5514356003871.01940777123-0.1739324822380.649653919853-0.175345632526-0.07168764178670.5548025534910.01933641339450.76581327389227.14321596758.119984242882.341531669
645.02929724409-3.445411103681.576786351352.40077014222-1.356894880636.034432747270.954753715023-1.26788639076-0.4480039357710.1953708772810.821271095724-0.3105344491060.9332406114480.117875608023-1.639288863361.55146156932-0.308226503771-0.4416405926540.7501451560080.2162021816841.535023045921.123644804478.585778575672.241171679
651.70029052927-0.80716147913-0.555325648652.567478574730.2099571752190.198456961004-0.2110774775530.1728892643720.3596475880470.5469234403210.560411533193-0.843272024517-0.09760279193640.87462274543-0.3503133368441.19792572472-0.052753582098-0.4562456954980.884735063496-0.1924518884332.252930580526.490964514376.266330101357.7261362321
666.610851215763.89657688151-0.8796462867045.797529794752.199744947217.283863374442.169685492080.655845836965-3.912023551420.399277425939-0.710804449295-0.7495914583661.277360293320.218979355977-1.517375237721.710851445170.25869659993-0.873873838161.54036664237-0.4701290474282.0694747935328.646241684884.330018390175.9634104176
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 52 )AA1 - 521 - 52
22chain 'A' and (resid 53 through 80 )AA53 - 8053 - 80
33chain 'A' and (resid 81 through 111 )AA81 - 11181 - 111
44chain 'A' and (resid 112 through 148 )AA112 - 148112 - 148
55chain 'A' and (resid 149 through 198 )AA149 - 198149 - 198
66chain 'A' and (resid 199 through 301 )AA199 - 301199 - 301
77chain 'A' and (resid 302 through 346 )AA302 - 346302 - 346
88chain 'A' and (resid 347 through 381 )AA347 - 381347 - 381
99chain 'A' and (resid 382 through 423 )AA382 - 423382 - 423
1010chain 'A' and (resid 424 through 457 )AA424 - 457424 - 457
1111chain 'D' and (resid 1 through 5 )DE1 - 5
1212chain 'D' and (resid 6 through 10 )DE6 - 10
1313chain 'D' and (resid 11 through 20 )DE11 - 20
1414chain 'D' and (resid 21 through 22 )DE21 - 22
1515chain 'B' and (resid 1 through 27 )BF1 - 271 - 27
1616chain 'B' and (resid 28 through 52 )BF28 - 5228 - 52
1717chain 'B' and (resid 53 through 80 )BF53 - 8053 - 80
1818chain 'B' and (resid 81 through 124 )BF81 - 12481 - 124
1919chain 'B' and (resid 125 through 198 )BF125 - 198125 - 198
2020chain 'B' and (resid 199 through 346 )BF199 - 346199 - 346
2121chain 'B' and (resid 347 through 381 )BF347 - 381347 - 380
2222chain 'B' and (resid 382 through 423 )BF382 - 423381 - 422
2323chain 'B' and (resid 424 through 457 )BF424 - 457423 - 456
2424chain 'C' and (resid 1 through 5 )CJ1 - 5
2525chain 'C' and (resid 6 through 10 )CJ6 - 10
2626chain 'C' and (resid 11 through 20 )CJ11 - 20
2727chain 'C' and (resid 21 through 22 )CJ21 - 22
2828chain 'E' and (resid 1 through 111 )EK1 - 1111 - 111
2929chain 'E' and (resid 112 through 173 )EK112 - 173112 - 173
3030chain 'E' and (resid 174 through 346 )EK174 - 346174 - 346
3131chain 'E' and (resid 347 through 381 )EK347 - 381347 - 381
3232chain 'E' and (resid 382 through 423 )EK382 - 423382 - 423
3333chain 'E' and (resid 424 through 457 )EK424 - 457424 - 457
3434chain 'G' and (resid 1 through 5 )GO1 - 5
3535chain 'G' and (resid 6 through 21 )GO6 - 21
3636chain 'J' and (resid 2 through 80 )JP2 - 801 - 79
3737chain 'J' and (resid 81 through 111 )JP81 - 11180 - 110
3838chain 'J' and (resid 112 through 148 )JP112 - 148111 - 147
3939chain 'J' and (resid 149 through 173 )JP149 - 173148 - 172
4040chain 'J' and (resid 174 through 198 )JP174 - 198173 - 197
4141chain 'J' and (resid 199 through 239 )JP199 - 239198 - 238
4242chain 'J' and (resid 240 through 346 )JP240 - 346239 - 345
4343chain 'J' and (resid 347 through 381 )JP347 - 381346 - 378
4444chain 'J' and (resid 382 through 423 )JP382 - 423379 - 420
4545chain 'J' and (resid 424 through 456 )JP424 - 456421 - 453
4646chain 'L' and (resid 1 through 5 )LT1 - 5
4747chain 'L' and (resid 6 through 22 )LT6 - 22
4848chain 'I' and (resid 3 through 198 )IU3 - 1981 - 196
4949chain 'I' and (resid 199 through 346 )IU199 - 346197 - 344
5050chain 'I' and (resid 347 through 456 )IU347 - 456345 - 451
5151chain 'K' and (resid 1 through 5 )KY1 - 5
5252chain 'K' and (resid 6 through 10 )KY6 - 10
5353chain 'K' and (resid 11 through 15 )KY11 - 15
5454chain 'K' and (resid 16 through 20 )KY16 - 20
5555chain 'K' and (resid 21 through 22 )KY21 - 22
5656chain 'F' and (resid 2 through 52 )FZ2 - 521 - 51
5757chain 'F' and (resid 53 through 111 )FZ53 - 11152 - 110
5858chain 'F' and (resid 112 through 173 )FZ112 - 173111 - 172
5959chain 'F' and (resid 174 through 227 )FZ174 - 227173 - 226
6060chain 'F' and (resid 228 through 381 )FZ228 - 381227 - 376
6161chain 'F' and (resid 382 through 423 )FZ382 - 423377 - 418
6262chain 'F' and (resid 424 through 456 )FZ424 - 456419 - 451
6363chain 'H' and (resid 1 through 5 )HL2 - 6
6464chain 'H' and (resid 6 through 10 )HL7 - 11
6565chain 'H' and (resid 11 through 20 )HL12 - 21
6666chain 'H' and (resid 21 through 22 )HL22 - 23

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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