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- PDB-8smo: Crystal structure of the complex between truncated MLLE domain of... -

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基本情報

登録情報
データベース: PDB / ID: 8smo
タイトルCrystal structure of the complex between truncated MLLE domain of PABPC1 and engineered superPAM2 peptide
要素
  • Polyadenylate-binding protein 1
  • superPAM2
キーワードPEPTIDE BINDING PROTEIN / MLLE domain / poly(A) binding protein / PAM2 motif / complex
機能・相同性
機能・相同性情報


mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding ...mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / cell leading edge / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / lamellipodium / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique domain / RNA recognition motif domain, eukaryote / RNA recognition motif ...: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique domain / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
類似検索 - ドメイン・相同性
Polyadenylate-binding protein 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 3 Å
データ登録者Kozlov, G. / Gehring, K.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR) カナダ
引用ジャーナル: To Be Published
タイトル: Crystal structure of the complex between truncated MLLE domain of PABPC1 and engineered superPAM2 peptide
著者: Behvarmanesh, A. / Kozlov, G. / Chen, Y.S. / Gehring, K.
履歴
登録2023年4月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年5月1日Provider: repository / タイプ: Initial release

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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: Polyadenylate-binding protein 1
B: superPAM2
C: Polyadenylate-binding protein 1
D: superPAM2
E: Polyadenylate-binding protein 1
F: superPAM2
G: Polyadenylate-binding protein 1
H: superPAM2
I: Polyadenylate-binding protein 1
J: superPAM2
K: Polyadenylate-binding protein 1
L: superPAM2
M: Polyadenylate-binding protein 1
N: superPAM2
O: Polyadenylate-binding protein 1
P: superPAM2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)86,30622
ポリマ－85,73016
非ポリマー5766
水32418
1
A: Polyadenylate-binding protein 1
B: superPAM2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,8123
ポリマ－10,7162
非ポリマー961
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Polyadenylate-binding protein 1
D: superPAM2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,8123
ポリマ－10,7162
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Polyadenylate-binding protein 1
F: superPAM2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,8123
ポリマ－10,7162
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Polyadenylate-binding protein 1
H: superPAM2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,8123
ポリマ－10,7162
非ポリマー961
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I: Polyadenylate-binding protein 1
J: superPAM2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,8123
ポリマ－10,7162
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K: Polyadenylate-binding protein 1
L: superPAM2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,8123
ポリマ－10,7162
非ポリマー961
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
M: Polyadenylate-binding protein 1
N: superPAM2


分子量 (理論値)分子数
合計 (水以外)10,7162
ポリマ－10,7162
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
O: Polyadenylate-binding protein 1
P: superPAM2


分子量 (理論値)分子数
合計 (水以外)10,7162
ポリマ－10,7162
非ポリマー00
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)108.275, 108.275, 75.866
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
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 554 or (resid 555 through 559...
d_2ens_1(chain "C" and (resid 554 or (resid 555 through 559...
d_3ens_1(chain "E" and (resid 554 or (resid 555 through 559...
d_4ens_1(chain "G" and (resid 554 or (resid 555 through 559...
d_5ens_1(chain "I" and (resid 554 or (resid 555 through 559...
d_6ens_1(chain "K" and (resid 554 or (resid 555 through 559...
d_7ens_1(chain "M" and ((resid 554 through 559 and (name N...
d_1ens_2(chain "B" and ((resid 1 and (name N or name...
d_2ens_2(chain "D" and ((resid 1 and (name N or name...
d_3ens_2(chain "F" and ((resid 1 and (name N or name...
d_4ens_2(chain "H" and (resid 1 through 5 or (resid 6...
d_5ens_2(chain "J" and ((resid 1 and (name N or name...
d_1ens_3(chain "L" and (resid 3 or (resid 4 and (name...
d_2ens_3chain "N"
d_3ens_3chain "P"

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_1GLYGLYGLUGLUAA554 - 5984 - 48
d_12ens_1LEULEUGLUGLUAA603 - 62153 - 71
d_21ens_1GLYGLYGLUGLUCC554 - 5984 - 48
d_22ens_1LEULEUGLUGLUCC603 - 62153 - 71
d_31ens_1GLYGLYGLUGLUEE554 - 5984 - 48
d_32ens_1LEULEUGLUGLUEE603 - 62153 - 71
d_41ens_1GLYGLYGLUGLUGG554 - 5984 - 48
d_42ens_1LEULEUGLUGLUGG603 - 62153 - 71
d_51ens_1GLYGLYGLUGLUII554 - 5984 - 48
d_52ens_1LEULEUGLUGLUII603 - 62153 - 71
d_61ens_1GLYGLYGLUGLUKK554 - 5984 - 48
d_62ens_1LEULEUGLUGLUKK603 - 62153 - 71
d_71ens_1GLYGLYGLUGLUMM554 - 6214 - 71
d_11ens_2SERSERGLYGLYBB1 - 181 - 18
d_21ens_2SERSERGLYGLYDD1 - 181 - 18
d_31ens_2SERSERGLYGLYFF1 - 181 - 18
d_41ens_2SERSERGLYGLYHH1 - 181 - 18
d_51ens_2SERSERGLYGLYJJ1 - 181 - 18
d_11ens_3LEULEUGLYGLYLL3 - 183 - 18
d_21ens_3LEULEUGLYGLYNN3 - 183 - 18
d_31ens_3LEULEUGLYGLYPP3 - 183 - 18

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.498001172535, 0.867172707992, -0.00251528660994), (0.867172047582, 0.497987460427, -0.00459664546639), (-0.00273350430564, -0.00447032107178, -0.999986271998)53.9514566576, -31.5546438443, -93.9805534725
2given(-0.0909318452883, 0.318396603355, -0.943586245387), (0.522176139561, -0.791565482536, -0.317421117966), (-0.847976107438, -0.52158191095, -0.0942805991959)2.02682203397, -64.8260764839, 1.07611454078
3given(0.496936003001, -0.845350596609, 0.196053507327), (0.184906842864, -0.117586450093, -0.975696103414), (0.847858519084, 0.521110156846, 0.0978781694158)-3.05283268657, -61.9611633054, -94.9350541989
4given(-0.0566368956969, 0.866495272368, 0.495961898748), (0.995407562175, 0.0106081804817, 0.0951380663679), (0.0771754313961, 0.499072549306, -0.863116761115)52.571525047, -70.9251469165, -62.3647751075
5given(0.88902946222, -0.4226133113, -0.176138026607), (0.452587700255, 0.753017726781, 0.477628178326), (-0.0692169696175, -0.504343426908, 0.860724531341)-33.8271165718, -21.4576603641, -32.2509358388
6given(-0.00745615693577, 0.158020542762, 0.987407673552), (-0.153977590855, -0.97584007817, 0.155006591319), (0.988046207036, -0.150882901295, 0.0316076392472)84.458469501, -17.6903178251, -73.1207037523
7given(-0.491109941633, 0.869986182752, 0.0439893970139), (0.871097255342, 0.490438360987, 0.0256862961248), (0.000772634942401, 0.0509338383936, -0.998701730819)55.1188036651, -30.867832025, -92.8250931204
8given(-0.0967353590781, 0.339926434204, -0.935463676277), (0.553804774512, -0.762561251203, -0.334365981959), (-0.827008187403, -0.550409263633, -0.114486245791)3.0620746137, -65.6761379829, -1.79093810943
9given(0.517166363258, -0.834425237104, 0.19045596971), (0.183460232847, -0.109277053898, -0.976934423825), (0.835991205503, 0.540178719661, 0.0965694317407)-3.45564664936, -61.5965571194, -93.5609011936
10given(-0.0567530419343, 0.86611823028, 0.496606789531), (0.997062031447, 0.0235392289967, 0.0728917700766), (0.0514431499607, 0.499284604084, -0.864909525007)52.4616692854, -71.1729847551, -61.0259444224
11given(-0.228438462777, 0.505326596114, 0.8321423556), (0.270684915403, -0.788073889847, 0.552873602838), (0.935171398887, 0.351545979071, 0.0432421010316)113.635413831, -11.2782369501, -32.560184215
12given(0.361411349993, -0.929138785311, 0.0779932928361), (-0.0669556479014, 0.0575695456236, 0.996093714783), (-0.92999934264, -0.365221665633, -0.0414048021585)-11.7194557503, 62.0318219967, -61.9725092792

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要素

#1: タンパク質
Polyadenylate-binding protein 1 / PABP-1 / Poly(A)-binding protein 1


分子量: 8284.560 Da / 分子数: 8 / 断片: MLLE domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PABPC1, PAB1, PABP, PABP1, PABPC2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P11940
#2: タンパク質・ペプチド
superPAM2


分子量: 2431.702 Da / 分子数: 8 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 6 / 由来タイプ: 合成 / 式: SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 18 / 由来タイプ: 天然 / 式: H2O
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: 2.99 Å3/Da / 溶媒含有率: 58.93 %
結晶化温度: 294 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M citric acid pH 4.0, 1.6 M ammonium sulfate

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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: CLSI / ビームライン: 08ID-1 / 波長: 1 Å
検出器タイプ: DECTRIS EIGER2 X 9M / 検出器: PIXEL / 日付: 2019年5月27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→50 Å / Num. obs: 27587 / % possible obs: 99.9 % / 冗長度: 9.7 % / Biso Wilson estimate: 51.07 Å2 / CC1/2: 0.995 / Net I/σ(I): 17.1
反射 シェル解像度: 3→3.11 Å / 冗長度: 6.7 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 535 / CC1/2: 0.385

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3→32.11 Å / SU ML: 0.4259 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 32.2055
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2916 2786 10.1 %
Rwork0.2556 24801 -
obs0.2594 27587 69.33 %
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: 62.52 Å2
精密化ステップサイクル: LAST / 解像度: 3→32.11 Å
タンパク質核酸リガンド溶媒全体
原子数4863 0 30 18 4911
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00164988
X-RAY DIFFRACTIONf_angle_d0.52056823
X-RAY DIFFRACTIONf_chiral_restr0.0338814
X-RAY DIFFRACTIONf_plane_restr0.005892
X-RAY DIFFRACTIONf_dihedral_angle_d2.8665699
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.315882571444
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.74790433198
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.729187862468
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.529140047715
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.468572679653
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.986565604705
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.855249039433
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.986249746496
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.962186155421
ens_2d_5BBX-RAY DIFFRACTIONTorsion NCS1.18582217458
ens_3d_2LLX-RAY DIFFRACTIONTorsion NCS0.703430849723
ens_3d_3LLX-RAY DIFFRACTIONTorsion NCS0.622574590744
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.050.3818210.3654228X-RAY DIFFRACTION12.76
3.05-3.110.3074350.2954293X-RAY DIFFRACTION16.47
3.11-3.170.296460.2815359X-RAY DIFFRACTION21.01
3.17-3.230.2934540.2957452X-RAY DIFFRACTION25.22
3.23-3.30.2824750.2777593X-RAY DIFFRACTION32.97
3.3-3.380.2956940.2771795X-RAY DIFFRACTION45.4
3.38-3.460.35681070.26651069X-RAY DIFFRACTION59.82
3.46-3.560.29791200.27081115X-RAY DIFFRACTION63.59
3.56-3.660.28291390.25681254X-RAY DIFFRACTION68.08
3.66-3.780.30531530.25141347X-RAY DIFFRACTION75.53
3.78-3.910.24671590.25691409X-RAY DIFFRACTION81.5
3.91-4.070.25071850.23241647X-RAY DIFFRACTION89.63
4.07-4.250.2842040.24971749X-RAY DIFFRACTION96.78
4.26-4.480.32841880.24331786X-RAY DIFFRACTION100
4.48-4.760.2962160.24461780X-RAY DIFFRACTION100
4.76-5.120.29591980.26461756X-RAY DIFFRACTION100
5.12-5.640.30931960.26881810X-RAY DIFFRACTION100
5.64-6.440.34221980.2951790X-RAY DIFFRACTION100
6.46-8.10.27072040.26411794X-RAY DIFFRACTION100
8.11-32.110.27241940.22981775X-RAY DIFFRACTION98.94
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)
11.39386439610.20649278136-0.5146982152741.08963246337-0.1422163507722.330675599080.136280283020.00955102006620.07073541633650.2522837318660.07781632651610.191810031397-0.200965051408-0.168413069270.4706295952440.1732472013750.172684290610.1641807490790.3237091603810.0239053259098-0.66190769353151.9480913294-29.6579706065-31.6741248224
21.88925293209-3.75007135655-0.9450724307477.474666117161.705900576481.22740926581-0.0828652930538-0.0966534599674-0.400432715532-0.0418776517136-0.1160070932470.5145353834580.116981225445-0.08956301704710.01427859522860.3219612372990.3696198585570.1164615999560.7504244094670.2228184179690.32883524903445.5074023078-35.7717642792-25.806186982
34.15190499458-2.73343070881.282830954673.97516271154-3.324375769835.695947075520.01099008868440.1870295852050.311919175661-0.374280558247-0.001895724445870.772936577317-0.161342742272-0.403184234688-0.2232742227810.3913557970440.238463601413-0.1455466394460.387955096942-0.05584105668470.56295584537840.3285031981-30.2710896808-41.5932610815
42.14093255621-1.6394438462.263147140127.049694727290.2305398262143.05848068198-0.0658732516796-0.3936538903170.128969816661.165057746620.1472507734691.27757215829-0.0331345484479-0.731558082567-0.07538109503670.7958503728630.4280005533850.02234256847050.889043766919-0.1307971324540.44023954432937.8527197218-25.3598333241-33.9941880839
52.179205936270.434791928373-0.8069635508440.4198280476470.3502519036591.08402962518-0.02795798024770.3026967904890.249279900829-0.216379313578-0.1233934677220.00966861486371-0.345829976406-0.185786242278-0.07413078557990.4536234942620.2640623583550.02784970683080.1890590438370.08881007763640.068007639912353.1385007133-21.8710712578-34.5185534451
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206.61420034626-0.6519277255333.533332876674.90405674808-2.841159599279.128948055380.0192427196127-0.64538394335-0.2669135947460.484942934102-0.02336836854250.206598795762-0.0132635064804-0.127051928289-0.08100589716670.401533971398-0.01515595384730.1392467359950.2885625613480.1204597147610.18577342295734.0570977005-16.6126163654-69.0565504191
211.99997192833-8.38276038766-2.598022781446.536586330562.257190372491.71367774693-0.175336596661-0.0789181324254-0.7996889152520.442465832726-0.2481778651070.9126213235330.438409296255-0.5507952145420.4853008371621.015484294090.1336185072530.679420195711.463596221740.06605138117641.2766617640234.1145673756-21.8933891091-64.6446260385
225.08228124244-0.117286841905-0.9797960086971.552790598310.6542499653281.394054256420.156964858170.203390203457-0.233273942561-0.1124952311630.0531972981552-0.5479752932150.04755062738910.1613240634760.0005067066455680.3867396538550.4701147843770.154124006730.6246651891010.1803570421680.6225038160847.4740720203-20.2229435064-47.8954519483
231.956954646310.3949593291610.2020179447650.3324432073150.4748070706070.7804721079450.576068757397-0.222877486557-1.21690355551-0.181047474737-0.2396262787690.1459339300390.292978009582-0.0835470244586-0.2671710450140.5099138021610.3343174586040.0312055651280.8128391084990.3504083667681.444519791294.94159235052-31.0049865115-42.8987897962
241.174340861060.06617633408760.1659603866050.00422943435630.00767946468930.03396340333790.1126310278690.169430882577-0.1645684254730.2071745152480.21429359165-0.2089207023120.6134312147550.340012473759-0.3026795548141.2080545840.494174175849-0.1067184280151.375441978120.1225123212490.96916416812911.6105281227-36.4133322808-42.3666544121
252.35856144167-0.9293028283080.2302558475490.4230269713390.07146329106980.492912063807-0.0974136418421-0.802452975867-0.8009681522920.3013159705660.3878361915960.573658493420.329930704399-0.243810463924-0.249847237450.5643274342170.330470708536-0.1914429994271.015273989480.4003433567511.3062893584513.1694787521-20.6172437019-39.4820799547
267.200523244840.5893738725942.536363435682.065840733871.997249935615.04109057811-0.102543489096-0.2857158147880.2013674064120.1417550483650.048676514089-0.5892751789030.1225689650210.4833861913480.0413709824570.6173707246020.322814638194-0.32014815550.9135160585860.2182018510570.95678830267317.2236830443-23.3046333012-43.0554809414
272.23028369781-0.202275131040.2381239995641.16030160748-0.7096793406190.9611269922820.115451154719-0.08623239783190.18650439584-0.06069230042810.145504501630.534996867056-0.109641126284-0.46084459028-0.06890366252960.4192297316180.371102191741-0.2818701303010.715883649035-0.1474575501970.91472561380830.7967259066-36.2050561124-48.6349623915
280.463157038994-0.6022001146890.3415463791261.87589688988-0.08892145629970.3558107661840.00811922984025-0.0395652248768-0.494803566871-0.471270501135-0.1009883316911.01823886347-0.0619329900246-0.08287540859960.183836009340.4024177857160.2265377753-0.1516757748561.18849214061-0.2511757374981.5428497618223.3162980955-43.4192921388-50.3062308078
292.069374932821.83244539375-3.551212577392.11587624239-3.559966187526.44415367318-0.1545682069190.248402482508-0.12100339505-0.2049980112930.2047357756220.0975155408170.326943975207-0.452186783991-0.04652828999111.112291905470.0722208281283-0.3193309802591.16997174710.06846733983270.92029227112317.4787932155-38.1852569855-53.2727773929
303.3536787012-1.845647559314.133999354891.03738324083-2.473498546486.898634778870.2171049614720.856630688172-0.33219970062-0.168278767778-0.01596613828790.1868139820940.2550939650990.0674663719175-0.195133680970.790473813650.273767622973-0.6235727037430.8762610922-0.2734647139641.4425453600328.2684404041-32.0314759722-55.2123342104
310.10008183244-0.1061044560030.01370343840310.319240077007-0.1071654776050.04186095187580.02829150979570.04468350023090.0312847151198-0.0365217941007-0.03435916019880.145082031919-0.0588095195506-0.07641300197160.02360295821520.6027737091790.469268873901-0.3815479120930.8831403595040.2859969796980.9759175981531.4646485055-27.3526066822-51.9120109334
329.604956727122.84108639772-0.7761518478575.75262712863-6.075575845527.02007281051-0.699813610483-0.333533690166-0.5360473633110.2605465260960.2645758877270.008914657101610.3169374502720.1512955652580.4083729710160.837472574670.281263094671-0.1854040609920.3633166982510.0810218493381.012634698823.0901366653-26.9591115864-50.8959558705
330.731621139397-0.6828295977360.181433602053.60595621028-0.1037604593381.39674298916-0.3265472668490.0743371861436-0.428393536921-0.0405942018750.133147795431-0.5764465680360.1393010382420.3165713159410.07043288159590.441864309210.0978097653682-0.08059390740381.680093880150.3140410168741.1653086510549.7930213562-0.205187364022-16.0833755375
343.59057666954-3.610050128062.08797667467.304563586523.021574976378.35102255932-0.02551972704230.08155423410810.010586901273-0.05999330715080.0427077641331-0.198972999880.2853671067040.299335120882-0.006926919564640.782224890624-0.1211961155050.248192764741.77629809830.348042106471.1396230986242.4932240016-2.69016316908-21.8448344829
352.081124322381.107568891860.8395434712122.0090973843-1.349730197082.613158306790.0841070037246-0.06659298711930.07307059222170.189672169779-0.269075167513-0.445440283286-0.38732434730.3304377095990.2014781642051.0999272182-0.384220122822-0.03565228509651.082768853670.1892314150271.6237420512553.7216175065.4162128547-23.5736513207
361.30454270745-0.584524575677-0.7269512646521.6082341974-0.694045765031.178318742850.08951290784260.585334946796-0.415415202256-0.168049377656-0.2000305597570.0161235275451-0.0103076107354-0.1057532443260.06447875799281.09542713215-0.0244372977941-0.216303494580.952523868729-0.05027381012531.3654906813637.8446336896-2.29299254275-31.1222145149
376.765790879035.390286970141.900813917565.203473780023.273309214593.94199041253-0.2734746296480.3867889835920.160461452436-0.7878703350150.4099847219370.955859248020.272895049592-0.591838085947-0.1315360446911.04811329729-0.166830247384-0.3573292342311.68105655501-0.006155609580691.7719769956644.6524930199-7.00610165528-30.3007582912
385.642201221212.2257230214-3.585297154582.14878123141-2.296554214372.904585971180.1226682917990.221357259077-0.371043290196-0.136591441701-0.000571812029015-0.1816709274130.3472749305950.214030757019-0.1053615957311.04425717351-0.301094529728-0.5281420866041.494970767850.1627025172721.2387447491445.7160806379-8.54666016399-17.3351373389
393.42578635644-2.03583538177-4.061640664451.523984707782.673663078795.58630464563-0.1963794241430.2948937494570.507723877353-0.176604845648-0.154164478161-0.297790650539-0.5446700935360.7179733574480.3445655278911.055431047320.0997054851604-0.3880458348681.392739406370.6573074106451.2434947496550.7090596345-10.9961046905-17.2269282614
400.565825304870.346056499112-0.07881681997620.9062620000090.379252421261.503577924-0.01890856071310.03765795204740.1891458416190.4415281279340.04495334572730.509644470946-0.1824726859940.006930987716660.008113940321061.345883743850.68590734829-0.1342380270131.044250224750.05118667524931.2511835984428.064318307111.8604392598-77.668786674
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434.288739626995.5547946948-3.437607687819.57019197076-4.480129767942.762105356890.200219783872-0.192934609524-0.3973295163040.665611134746-0.13942673435-0.7995639697280.08483872398710.436942203851-0.07266895464081.268954529910.392224857686-0.06065963800750.9140996636740.352704007111.0459605677825.61012556493.84792484594-63.7674912156
442.008191591960.850590568259-1.011369206965.406429408553.876099858614.181421592790.0765160982484-0.1167386853650.2118992664570.2102605973060.1707525120510.471414530834-0.259264641592-0.477932992508-0.2243615394021.27067376816-0.233007901398-0.3151475841250.938070291860.5531702390981.239186194123.98700292473.98709498878-76.7036633877
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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 552 through 587 )AA552 - 5871 - 36
22chain 'A' and (resid 588 through 599 )AA588 - 59937 - 48
33chain 'A' and (resid 600 through 625 )AA600 - 62549 - 74
44chain 'B' and (resid 1 through 5 )BB1 - 51 - 5
55chain 'B' and (resid 6 through 15 )BB6 - 156 - 15
66chain 'B' and (resid 16 through 20 )BB16 - 2016 - 20
77chain 'C' and (resid 552 through 587 )CC552 - 5871 - 36
88chain 'C' and (resid 588 through 599 )CC588 - 59937 - 48
99chain 'C' and (resid 600 through 625 )CC600 - 62549 - 74
1010chain 'D' and (resid 1 through 5 )DD1 - 51 - 5
1111chain 'D' and (resid 6 through 15 )DD6 - 156 - 15
1212chain 'D' and (resid 16 through 20 )DD16 - 2016 - 20
1313chain 'E' and (resid 552 through 587 )EE552 - 5871 - 36
1414chain 'E' and (resid 588 through 599 )EE588 - 59937 - 48
1515chain 'E' and (resid 600 through 625 )EE600 - 62549 - 74
1616chain 'F' and (resid 1 through 15 )FF1 - 151 - 15
1717chain 'F' and (resid 16 through 20 )FF16 - 2016 - 20
1818chain 'G' and (resid 552 through 587 )GG552 - 5871 - 36
1919chain 'G' and (resid 588 through 625 )GG588 - 62537 - 74
2020chain 'H' and (resid 1 through 15 )HH1 - 151 - 15
2121chain 'H' and (resid 16 through 19 )HH16 - 1916 - 19
2222chain 'I' and (resid 554 through 573 )II554 - 5731 - 20
2323chain 'I' and (resid 574 through 624 )II574 - 62421 - 71
2424chain 'J' and (resid 1 through 5 )JJ1 - 51 - 5
2525chain 'J' and (resid 6 through 15 )JJ6 - 156 - 15
2626chain 'J' and (resid 16 through 18 )JJ16 - 1816 - 18
2727chain 'K' and (resid 554 through 587 )KK554 - 5871 - 34
2828chain 'K' and (resid 588 through 624 )KK588 - 62435 - 71
2929chain 'L' and (resid 2 through 6 )LL2 - 61 - 5
3030chain 'L' and (resid 7 through 11 )LL7 - 116 - 10
3131chain 'L' and (resid 12 through 16 )LL12 - 1611 - 15
3232chain 'L' and (resid 17 through 18 )LL17 - 1816 - 17
3333chain 'M' and (resid 553 through 573 )MM553 - 5731 - 21
3434chain 'M' and (resid 574 through 587 )MM574 - 58722 - 35
3535chain 'M' and (resid 588 through 603 )MM588 - 60336 - 47
3636chain 'M' and (resid 604 through 621 )MM604 - 62148 - 65
3737chain 'N' and (resid 3 through 7 )NN3 - 71 - 5
3838chain 'N' and (resid 8 through 12 )NN8 - 126 - 10
3939chain 'N' and (resid 13 through 18 )NN13 - 1811 - 16
4040chain 'O' and (resid 552 through 573 )OO552 - 5731 - 22
4141chain 'O' and (resid 574 through 587 )OO574 - 58723 - 36
4242chain 'O' and (resid 588 through 614 )OO588 - 61437 - 61
4343chain 'P' and (resid 3 through 7 )PP3 - 71 - 5
4444chain 'P' and (resid 8 through 12 )PP8 - 126 - 10
4545chain 'P' and (resid 13 through 18 )PP13 - 1811 - 16

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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