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- PDB-6wxm: X-ray crystallographic structure of a beta-hairpin peptide derive... -

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基本情報

登録情報
データベース: PDB / ID: 6wxm
タイトルX-ray crystallographic structure of a beta-hairpin peptide derived from amyloid beta 16-36
要素Amyloid-beta protein
キーワードDE NOVO PROTEIN / oligomer / alzheimer's
機能・相同性
機能・相同性情報


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / main axon / transition metal ion binding / intracellular copper ion homeostasis / regulation of multicellular organism growth / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / axonogenesis / protein serine/threonine kinase binding / response to interleukin-1 / platelet alpha granule lumen / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / endosome lumen / positive regulation of interleukin-1 beta production / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / adult locomotory behavior / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / recycling endosome / synapse organization / visual learning / response to lead ion / positive regulation of interleukin-6 production / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to amyloid-beta / neuron projection development / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of translation / regulation of gene expression / early endosome membrane / G alpha (i) signalling events / perikaryon / G alpha (q) signalling events / dendritic spine
類似検索 - 分子機能
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
類似検索 - ドメイン・相同性
HEXANE-1,6-DIOL / Amyloid-beta precursor protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 単波長異常分散 / 解像度: 2.3 Å
データ登録者Kreutzer, A.G. / Nowick, J.S.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 米国
引用ジャーナル: Acs Chem Neurosci / 年: 2020
タイトル: X-ray Crystallography Reveals Parallel and Antiparallel beta-Sheet Dimers of a beta-Hairpin Derived from A beta16-36that Assemble to Form Different Tetramers.
著者: Kreutzer, A.G. / Samdin, T.D. / Guaglianone, G. / Spencer, R.K. / Nowick, J.S.
履歴
登録2020年5月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月8日Provider: repository / タイプ: Initial release
改定 1.12020年7月15日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
改定 1.22020年8月26日Group: Database references / Derived calculations / カテゴリ: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
改定 1.32025年4月2日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
F: Amyloid-beta protein
H: Amyloid-beta protein
B: Amyloid-beta protein
I: Amyloid-beta protein
E: Amyloid-beta protein
A: Amyloid-beta protein
C: Amyloid-beta protein
D: Amyloid-beta protein
J: Amyloid-beta protein
G: Amyloid-beta protein
K: Amyloid-beta protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)28,53621
ポリマ－27,35411
非ポリマー1,18210
水1,36976
1
F: Amyloid-beta protein
H: Amyloid-beta protein
B: Amyloid-beta protein
E: Amyloid-beta protein
A: Amyloid-beta protein
C: Amyloid-beta protein
D: Amyloid-beta protein
G: Amyloid-beta protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,72115
ポリマ－19,8948
非ポリマー8277
水1448
タイプ名称対称操作数
identity operation1_555x,y,z1
2
J: Amyloid-beta protein
ヘテロ分子

J: Amyloid-beta protein
ヘテロ分子

I: Amyloid-beta protein
ヘテロ分子

I: Amyloid-beta protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,65610
ポリマ－9,9474
非ポリマー7096
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
3
I: Amyloid-beta protein
ヘテロ分子

I: Amyloid-beta protein
ヘテロ分子

J: Amyloid-beta protein
ヘテロ分子

J: Amyloid-beta protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)10,65610
ポリマ－9,9474
非ポリマー7096
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
4
K: Amyloid-beta protein

K: Amyloid-beta protein


分子量 (理論値)分子数
合計 (水以外)4,9742
ポリマ－4,9742
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
単位格子
Length a, b, c (Å)90.194, 122.127, 58.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDモデル要素
11I-202-

HOH

21E-204-

HOH

31E-205-

HOH

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要素

#1: タンパク質・ペプチド
Amyloid-beta protein / Abeta / Beta-APP


分子量: 2486.754 Da / 分子数: 11 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P05067
#2: 化合物
ChemComp-HEZ / HEXANE-1,6-DIOL


分子量: 118.174 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C6H14O2
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 76 / 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
Has protein modificationY

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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: 2.92 Å3/Da / 溶媒含有率: 57.89 %
結晶化温度: 296.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5
詳細: 0.1 M sodium acetate (pH 5.0), 0.1 M CoCl2, 1.1 M 1,6-hexanediol
PH範囲: 4.5-6.0

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データ収集

回折平均測定温度: 113.15 K / Serial crystal experiment: N
放射光源由来: 回転陽極 / タイプ: RIGAKU MICROMAX-007 HF / 波長: 1.54 Å
検出器タイプ: RIGAKU SATURN 92 / 検出器: CCD / 日付: 2015年6月2日
放射モノクロメーター: Cu anode / 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: 1.54 Å / 相対比: 1
反射解像度: 2.3→36.28 Å / Num. obs: 27084 / % possible obs: 98.46 % / 冗長度: 16.1 % / Biso Wilson estimate: 32.34 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.07937 / Rpim(I) all: 0.07937 / Rrim(I) all: 0.1122 / Net I/σ(I): 15.9
反射 シェル解像度: 2.3→2.382 Å / 冗長度: 4.1 % / Rmerge(I) obs: 0.4408 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 2540 / CC1/2: 0.357 / CC star: 0.726 / Rpim(I) all: 0.4408 / Rrim(I) all: 0.6233 / % possible all: 87.34

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
MOSFLMデータ削減
Aimlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.3→36.28 Å / SU ML: 0.2832 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 20.6638
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2185 2715 10.02 %
Rwork0.1713 24369 -
obs0.176 27084 97.88 %
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: 66.35 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→36.28 Å
タンパク質核酸リガンド溶媒全体
原子数1793 0 80 76 1949
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01071874
X-RAY DIFFRACTIONf_angle_d1.52242458
X-RAY DIFFRACTIONf_chiral_restr0.0686275
X-RAY DIFFRACTIONf_plane_restr0.0078308
X-RAY DIFFRACTIONf_dihedral_angle_d16.70671172
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.38571170.32541034X-RAY DIFFRACTION77.98
2.34-2.390.33711300.30141158X-RAY DIFFRACTION88.22
2.39-2.440.34451330.27561234X-RAY DIFFRACTION95.26
2.44-2.490.30111450.26361283X-RAY DIFFRACTION98.76
2.49-2.550.27761490.24981320X-RAY DIFFRACTION100
2.55-2.610.29761430.22641314X-RAY DIFFRACTION100
2.61-2.680.2891420.22291293X-RAY DIFFRACTION100
2.68-2.760.23451450.19091319X-RAY DIFFRACTION100
2.76-2.850.20911460.18041308X-RAY DIFFRACTION100
2.85-2.950.17411440.16791318X-RAY DIFFRACTION100
2.95-3.070.19141470.1541322X-RAY DIFFRACTION100
3.07-3.210.23021440.14081293X-RAY DIFFRACTION100
3.21-3.380.1791440.14261306X-RAY DIFFRACTION100
3.38-3.590.18351460.13621329X-RAY DIFFRACTION100
3.59-3.870.19371500.14521296X-RAY DIFFRACTION100
3.87-4.250.18811460.13431305X-RAY DIFFRACTION100
4.25-4.870.16631470.12321306X-RAY DIFFRACTION100
4.87-6.130.1981480.14811313X-RAY DIFFRACTION100
6.13-36.280.24831490.19751318X-RAY DIFFRACTION99.93
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)
13.603981408122.329133768841.431091073893.460321542530.7593520592820.6709605403870.178229149592-1.34892343844-0.430492497310.413521083795-0.508319191094-0.522609355615-1.454107988890.940129487132-0.1158484547230.33648230971-0.237091795128-0.03477716693690.496827645050.08279653394550.34272089765318.308546316133.79091910844.613135302
24.61174522069-0.3674992803580.5496075480050.709024241193-0.4168160031130.271336403079-0.2445728918980.888024656502-0.985859104574-2.120098226241.50316923782-1.85975784084-0.3632913384140.56830010118-1.040249891530.826473675416-0.3033707395820.1279143121130.5002934042090.01153432827710.7083211643814.10929355628.574504253630.4480181014
39.89024189959-1.756308902884.776963634865.07228794634-2.714671445523.480263217620.1260569039190.908731239024-1.14022109716-0.5970508572630.1988264899860.1668323894980.02530865561961.55934777495-0.01615772796910.475675832545-0.03006791589040.0339376566510.498309530290.1017760402240.48564446061114.327374361427.376057180237.9770039221
42.00533089213-6.94706830141.022765642455.19196564864-2.453791248155.467293737960.0553300960414-0.9365012037260.9583096581411.646439594460.02542938398470.234607705398-0.390003708657-0.0998155355176-0.1964372911680.423354935074-0.1664420392670.131537589440.3489085365090.02694216148990.53436903616917.172853491639.62350144339.0396855958
59.395892320033.07024961807-6.625000218471.17968027776-1.638021064576.57383506359-1.469331626641.38664085005-2.9755549079-0.411221654007-0.3460759463150.1937351825952.30625745412-1.077714464560.4734637183620.701316462494-0.1414839826020.09831330267710.441737939719-0.1226222239350.60844723086420.189618867528.731552308329.9457348707
64.081261255892.825850559221.356677803026.54668544312-3.205357850814.33267176262-0.3843628633340.69601874917-0.751707368187-0.1933235060260.461090695708-0.7106544555861.30705036910.443892888325-0.097959620510.5568748082770.01558377312730.04635207767270.365468011389-0.01933414891990.34355894878422.601508933730.568806805532.9681547111
75.65031487759-0.408055942807-1.630415556295.161129518272.107964980266.084660287510.304242321262-0.7933981018070.206902999419-0.1202167813050.172549583476-0.2440832501920.2639308622510.742174424588-0.1369569281210.2084269577880.01305172042420.01896649399210.365969141749-0.03186892525340.22298604121530.751362792636.929067814332.2368138288
88.15248365471.37058214461-3.859319608522.44409387756-4.439245408198.16275149141-0.556673218758-0.541812000045-0.543307996502-0.4234381951080.572720404272-0.04365585854090.5197637764890.2730294613270.007887633039230.273876189372-0.01312168973840.01285789046840.265037732746-0.045955503510.30149596120527.316591392733.845554886835.0541216198
91.94555379664-1.51971612607-1.558535358727.661207677054.250261880172.737372428130.98404729390.5508942097120.26898151097-0.761730123916-0.8490183247980.490280814216-1.04405787403-1.2185829104-0.1474541559570.3118566773080.0922151680793-0.01622139993360.533934032879-0.04142006767870.27961024386828.146574836636.385395205122.5278265432
101.394017975093.39882264906-1.081863575999.22617749699-1.263860398542.949561799570.279350846436-1.16775977172-2.232802351971.70390387484-1.73247357256-3.248387323841.857682823342.419921215820.492007842460.7882573478840.172862013427-0.1989692260770.8627015174150.174099660520.99057684239836.459185528828.555158987633.7089785901
112.44715865045-0.26255671818-2.648267067454.867856197580.7618993542594.116427259380.470937215012-0.605821209092-0.311791139586-0.0283024297771-0.599081527903-0.07565117300740.807048764246-0.1479163008680.4888585794350.394377134599-0.0179830466052-0.02275842154880.4577561893170.01168096597460.30205999879334.915895709429.673010681428.3852021519
123.775551586782.03883868528-1.297988665549.71337099316-0.9548686003379.310609764760.195738551338-0.3588486027140.4127984931960.245402955815-0.2695909403150.1951222101120.5291452206040.2441289855020.2777483502240.429975052577-0.02938904246980.05606506368410.3446939440010.06742279400660.45101323168522.273054067153.913882355735.3676314319
138.224159414392.17675104331-0.7406106875856.497167973981.76789825833.29592311201-0.738260688339-1.371354841890.3580419043230.8708381371820.490629721258-0.9897158890820.2920898397250.2677882290620.3566820734780.448220388310.06569558631030.09113410178970.39459519510.1736993286010.59847412064720.992347204356.747252448835.2254650254
146.43942173340.8131146767840.9377057421035.391458201912.451101823718.925668941450.0285858382381-0.4015628078240.5382957882640.5957677924890.191881921142-0.0277490312786-0.4665622233020.257416295221-0.0584261897420.3995087268090.0134582448830.06307566350310.2276918825820.02764521913250.39103822680124.894256924850.012509467537.7390130409
152.689163690321.84440169281.260502030433.310953565091.622281669331.0135174914-0.173642046764-0.69151721923-0.281313928421-0.1723841036650.3498204491610.0323947313856-1.03389042896-0.241481526031-0.4655269860970.423639976898-0.07030279190540.03242692233360.3764648477750.0251931675520.3185920384126.362038186447.846370100937.6890436021
162.457142352440.6159374841191.570417440354.421329545812.246325800419.355526977250.347994559004-0.458830392979-0.201517852119-0.174272825671-0.2145947988860.0893096997310.0692154116031-0.656580932514-0.1259752148770.4471009316080.00312840044848-0.1605949137870.4099646136410.08254485401740.40503901594538.621830634947.937287696644.8350785378
173.36575910209-2.349628102361.341808571318.570695584493.439820977754.68599821994-0.0813341160694-0.1621218793410.9734384350830.0647570306065-0.0103948781857-0.653798186567-1.965619116490.0380338653751-0.07402099630510.792756138725-0.112884809759-0.2313503311330.376501779230.0936021884230.58143413731241.015771467356.687125819740.8627286795
189.48380399529-1.22809878733-1.349702626420.4434947358631.475258431927.74883879150.165092521571-0.140529618212-0.02921376648710.197643786968-0.0221528314005-0.1763682441-0.00215746615483-0.352218555452-0.2632014763630.330309981904-0.0268226512254-0.09770119466230.2455716743560.04505504231520.34520941615135.246127010551.996102329638.3493244673
195.022851204340.9478175087271.522284658422.931027565043.217803338393.54232838335-0.316154290501-0.151719676710.1670127121790.4190546412720.426562650318-0.520288819719-0.3333925122230.0868899757627-0.2176171648760.400212469841-0.0296026881876-0.07492088480290.2821327144220.03986462587220.23699463759533.318867314450.848401949437.4397886128
207.31278199019-3.18885662389-0.0810067955082.01806599310.6127927359363.519210140420.03947355480040.5241791276960.5546130823-0.1510878672040.0333571823841-0.217662148165-0.629692597979-0.214897225289-0.2272191288110.278373339954-0.0097092871546-0.007099588484510.3767114035350.1377558480.4181560143345.5013600595136.836293751542.2053631128
212.00353752676-4.09780657524-2.455446075763.599872088254.959143560118.167812903071.6793217583-0.0317587953081-2.194170827890.119206897778-1.961109558190.1714844587372.57725918268-1.4884218604-1.113118285890.8188039302710.0322021006158-0.3346031310590.825229163920.1462852708380.573492218666.9487243738720.86538687643.9018619953
223.15088539974-2.977631905181.277904192014.0600866434-2.901724573938.66138194710.3139011838730.276784542079-0.497085903849-1.02746828170.215967911228-0.2530070600761.10417416878-0.331371645502-0.4611637563960.473039854699-0.119437895721-0.1103467932860.3940757971020.04927027156540.4850499511958.4065958745825.7974803740.8248180587
239.24202428419-2.208918844492.466170789142.494259380042.796247385786.75509989647-0.0830915436575-0.1025921669740.0317214104974-0.005915921933510.09816907574360.720364746667-0.2647712781710.5437511853910.07859030684310.30808293896-0.1084419903650.0648566803160.445042714279-0.008549384985770.23014721729239.927088042331.189100834321.5215572121
245.354805337772.21749365486-0.3936745906552.034520337722.081211957458.00900997297-0.818890133667-1.42143379951-0.9042496787910.6859322451880.46234284054-0.3040417332330.2728654631921.85102055814-0.6058851463150.3621679323340.159615587381-0.003825463682720.546960382247-0.01046302046170.43531163265838.43119594928.478228359123.6402108159
252.5827624254-0.815526847588-3.733031591790.2660419857241.174630531525.39126211350.09313692316261.37563605341-0.021872849452-2.047819110640.5472790829132.890919801431.47297097301-1.31255832035-0.6134709251110.668932856421-0.171746627616-0.3789690824350.7027449971880.2955672076081.1949956583611.306341318852.0814921527.726614396
262.508236375384.40003675522-4.755321336397.71483643091-8.274599285618.96770416738-0.0572387702583-1.921562699830.008450063776492.66971979315-0.8042028906641.43805056365-2.2856495751-0.3299399601310.322800300970.7760729645280.2609203086970.20208338881.02634304090.3125060236211.181698576814.544291628666.459764109136.8294163454
277.50419743751-2.93475357945-4.90649770885.35912767524-1.822106097846.561476096670.485493091907-0.195200539568-0.217187375042.190429014071.202281116840.887196898429-0.157117019291-1.29418015218-0.6572692112130.7108778577560.08246651752310.07642176740950.6300286752760.1478281690420.80218003168414.756219531958.841014780236.1433776388
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 12 )
3X-RAY DIFFRACTION3chain 'A' and (resid 13 through 22 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 6 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 22 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 12 )
8X-RAY DIFFRACTION8chain 'C' and (resid 13 through 22 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 7 )
10X-RAY DIFFRACTION10chain 'D' and (resid 8 through 12 )
11X-RAY DIFFRACTION11chain 'D' and (resid 13 through 22 )
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 14 )
13X-RAY DIFFRACTION13chain 'E' and (resid 15 through 22 )
14X-RAY DIFFRACTION14chain 'F' and (resid 1 through 14 )
15X-RAY DIFFRACTION15chain 'F' and (resid 15 through 22 )
16X-RAY DIFFRACTION16chain 'H' and (resid 1 through 9 )
17X-RAY DIFFRACTION17chain 'H' and (resid 10 through 22 )
18X-RAY DIFFRACTION18chain 'G' and (resid 1 through 14 )
19X-RAY DIFFRACTION19chain 'G' and (resid 15 through 22 )
20X-RAY DIFFRACTION20chain 'I' and (resid 1 through 7 )
21X-RAY DIFFRACTION21chain 'I' and (resid 8 through 12 )
22X-RAY DIFFRACTION22chain 'I' and (resid 13 through 22 )
23X-RAY DIFFRACTION23chain 'J' and (resid 1 through 13 )
24X-RAY DIFFRACTION24chain 'J' and (resid 14 through 22 )
25X-RAY DIFFRACTION25chain 'K' and (resid 1 through 6 )
26X-RAY DIFFRACTION26chain 'K' and (resid 7 through 13 )
27X-RAY DIFFRACTION27chain 'K' and (resid 14 through 22 )

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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