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- PDB-7yiw: The Crystal Structure of Human Tissue Nonspecific Alkaline Phosph... -

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基本情報

登録情報
データベース: PDB / ID: 7yiw
タイトルThe Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (ALPL) at Acidic pH
要素Alkaline phosphatase, tissue-nonspecific isozyme
キーワードHYDROLASE / alkaline phosphatase / bone mineralization / catalytic network / hypophosphatasia / structural biology
機能・相同性
機能・相同性情報


phosphoamidase / phosphoamidase activity / phosphoethanolamine phosphatase activity / pyridoxal phosphate metabolic process / response to vitamin B6 / futile creatine cycle / pyridoxal phosphatase activity / developmental process involved in reproduction / ADP phosphatase activity / biomineral tissue development ...phosphoamidase / phosphoamidase activity / phosphoethanolamine phosphatase activity / pyridoxal phosphate metabolic process / response to vitamin B6 / futile creatine cycle / pyridoxal phosphatase activity / developmental process involved in reproduction / ADP phosphatase activity / biomineral tissue development / response to macrophage colony-stimulating factor / inhibition of non-skeletal tissue mineralization / pyrophosphatase activity / cementum mineralization / Post-translational modification: synthesis of GPI-anchored proteins / alkaline phosphatase / alkaline phosphatase activity / response to sodium phosphate / phosphate ion homeostasis / inorganic diphosphate phosphatase activity / endochondral ossification / cellular homeostasis / response to vitamin D / bone mineralization / calcium ion homeostasis / side of membrane / extracellular matrix / response to glucocorticoid / skeletal system development / response to insulin / mitochondrial membrane / mitochondrial intermembrane space / osteoblast differentiation / positive regulation of cold-induced thermogenesis / response to lipopolysaccharide / response to antibiotic / calcium ion binding / ATP hydrolysis activity / extracellular exosome / extracellular region / membrane / plasma membrane
類似検索 - 分子機能
Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline-phosphatase-like, core domain superfamily
類似検索 - ドメイン・相同性
Alkaline phosphatase, tissue-nonspecific isozyme
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.89 Å
データ登録者Yu, Y.T. / Yao, D.Q. / Zhang, Q. / Rao, B. / Xia, Y. / Lu, Y. / Qin, A. / Cao, Y.
資金援助 中国, 1件
組織認可番号
National Natural Science Foundation of China (NSFC) 中国
引用ジャーナル: Nat Commun / : 2023
タイトル: The structural pathology for hypophosphatasia caused by malfunctional tissue non-specific alkaline phosphatase.
著者: Yating Yu / Kewei Rong / Deqiang Yao / Qing Zhang / Xiankun Cao / Bing Rao / Ying Xia / Yi Lu / Yafeng Shen / Ying Yao / Hongtao Xu / Peixiang Ma / Yu Cao / An Qin /
要旨: Hypophosphatasia (HPP) is a metabolic bone disease that manifests as developmental abnormalities in bone and dental tissues. HPP patients exhibit hypo-mineralization and osteopenia due to the ...Hypophosphatasia (HPP) is a metabolic bone disease that manifests as developmental abnormalities in bone and dental tissues. HPP patients exhibit hypo-mineralization and osteopenia due to the deficiency or malfunction of tissue non-specific alkaline phosphatase (TNAP), which catalyzes the hydrolysis of phosphate-containing molecules outside the cells, promoting the deposition of hydroxyapatite in the extracellular matrix. Despite the identification of hundreds of pathogenic TNAP mutations, the detailed molecular pathology of HPP remains unclear. Here, to address this issue, we determine the crystal structures of human TNAP at near-atomic resolution and map the major pathogenic mutations onto the structure. Our study reveals an unexpected octameric architecture for TNAP, which is generated by the tetramerization of dimeric TNAPs, potentially stabilizing the TNAPs in the extracellular environments. Moreover, we use cryo-electron microscopy to demonstrate that the TNAP agonist antibody (JTALP001) forms a stable complex with TNAP by binding to the octameric interface. The administration of JTALP001 enhances osteoblast mineralization and promoted recombinant TNAP-rescued mineralization in TNAP knockout osteoblasts. Our findings elucidate the structural pathology of HPP and highlight the therapeutic potential of the TNAP agonist antibody for osteoblast-associated bone disorders.
履歴
登録2022年7月18日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02023年7月19日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _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
A: Alkaline phosphatase, tissue-nonspecific isozyme
D: Alkaline phosphatase, tissue-nonspecific isozyme
C: Alkaline phosphatase, tissue-nonspecific isozyme
B: Alkaline phosphatase, tissue-nonspecific isozyme
G: Alkaline phosphatase, tissue-nonspecific isozyme
H: Alkaline phosphatase, tissue-nonspecific isozyme
F: Alkaline phosphatase, tissue-nonspecific isozyme
E: Alkaline phosphatase, tissue-nonspecific isozyme
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)455,56772
ポリマ-443,6758
非ポリマー11,89164
18010
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)159.364, 166.525, 181.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 1種, 8分子 ADCBGHFE

#1: タンパク質
Alkaline phosphatase, tissue-nonspecific isozyme / AP-TNAP / TNS-ALP / TNSALP / Alkaline phosphatase liver/bone/kidney isozyme / Phosphoamidase / ...AP-TNAP / TNS-ALP / TNSALP / Alkaline phosphatase liver/bone/kidney isozyme / Phosphoamidase / Phosphocreatine phosphatase


分子量: 55459.398 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ALPL / 発現宿主: Trichoplusia ni (イラクサキンウワバ)
参照: UniProt: P05186, alkaline phosphatase, phosphoamidase

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, 2種, 32分子

#2: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 16 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 16 / 由来タイプ: 組換発現 / : C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 4種, 42分子

#4: 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: 8 / 由来タイプ: 合成 / : Mg
#5: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 16 / 由来タイプ: 合成 / : Zn
#6: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 8 / 由来タイプ: 合成 / : Ca
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 10 / 由来タイプ: 天然 / : H2O

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詳細

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: 2.64 Å3/Da / 溶媒含有率: 53.43 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5 / 詳細: 20% (w/v) PEG3350, 640 mM sodium acetate, pH5.0

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データ収集

回折平均測定温度: 77 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL19U1 / 波長: 0.97853 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年1月22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: 0.97853 Å / 相対比: 1
反射解像度: 2.89→48.96 Å / Num. obs: 108466 / % possible obs: 99.78 % / 冗長度: 13.3 % / Biso Wilson estimate: 47 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.2 / Net I/σ(I): 12.79
反射 シェル解像度: 2.89→2.993 Å / Num. unique obs: 10707 / CC1/2: 0.835

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.19.2_4158: ???)精密化
xia2データスケーリング
PDB_EXTRACT3.27データ抽出
HKL-2000データ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1EW2
解像度: 2.89→48.96 Å / SU ML: 0.37 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 23.31 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2304 2002 1.85 %
Rwork0.201 --
obs0.2015 108318 99.75 %
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
精密化ステップサイクル: LAST / 解像度: 2.89→48.96 Å
タンパク質核酸リガンド溶媒全体
原子数30673 0 0 10 30683
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00231329
X-RAY DIFFRACTIONf_angle_d0.57242499
X-RAY DIFFRACTIONf_dihedral_angle_d17.2811469
X-RAY DIFFRACTIONf_chiral_restr0.0454765
X-RAY DIFFRACTIONf_plane_restr0.0045525
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.35481370.32817449X-RAY DIFFRACTION99
2.96-3.040.30361480.26997498X-RAY DIFFRACTION100
3.04-3.130.28051410.2467553X-RAY DIFFRACTION100
3.13-3.230.26651410.22887523X-RAY DIFFRACTION100
3.23-3.350.24641420.22957561X-RAY DIFFRACTION100
3.35-3.480.34941380.26897520X-RAY DIFFRACTION100
3.48-3.640.28661360.22347568X-RAY DIFFRACTION100
3.64-3.830.2341490.21297526X-RAY DIFFRACTION100
3.83-4.070.24471440.20397548X-RAY DIFFRACTION99
4.07-4.390.17231410.15747615X-RAY DIFFRACTION100
4.39-4.830.17621410.14637635X-RAY DIFFRACTION100
4.83-5.520.18941490.16387648X-RAY DIFFRACTION100
5.52-6.960.22311440.18827740X-RAY DIFFRACTION100
6.96-48.960.17381510.16937932X-RAY DIFFRACTION99
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.927-0.01370.14711.14210.50191.70650.0441-0.18120.1630.08630.01980.2274-0.55170.0072-0.03620.26940.02220.09420.3149-0.04980.304328.2974145.3259138.0445
20.29230.29470.21690.76-0.25250.4590.052-0.05850.1082-0.07840.01130.0615-0.1620.0301-0.02360.2779-0.00180.01370.2528-0.03050.247246.9282144.2378123.1784
30.82390.00310.00760.96410.02940.01330.12820.0835-0.0332-0.3373-0.0919-0.0511-0.13950.16530.00390.3350.010.05790.2873-0.02560.248459.1365141.9569106.031
41.01310.4829-0.18350.71430.19610.5924-0.06980.10930.0367-0.14040.0391-0.1627-0.05160.0866-0.0140.2832-0.03520.05310.16820.01060.269767.5028148.6631104.9616
50.7365-0.0988-0.69691.34560.47711.0993-0.1459-0.00050.1628-0.00830.0783-0.2831-0.48580.511-0.03530.4347-0.05940.10210.3101-0.05170.377573.4583160.8205108.4521
61.00050.56180.01060.87630.38060.7233-0.02180.12180.3852-0.1353-0.07050.0142-0.2769-0.0142-0.00750.4559-0.00010.04580.2536-0.03720.347358.0016165.1209108.8961
70.43060.27060.07290.24730.10790.5888-0.0424-0.07050.0459-0.0477-0.0505-0.0555-0.19250.0020.00760.23980.0010.02560.2132-0.04260.242751.7533152.4185124.3715
80.758-0.0871-0.65220.5771-0.27441.68130.0632-0.3747-0.04760.16210.0119-0.0636-0.08260.49310.04640.2872-0.021-0.02040.3859-0.00650.291765.5868138.6673146.5175
90.3547-0.17590.50690.2746-0.40690.51150.0077-0.0307-0.01380.06230.0148-0.0772-0.08840.1401-0.00210.23740.00070.02240.3408-0.04110.242556.3292142.3902130.3876
100.3527-0.24530.19910.9766-0.58451.2681-0.0943-0.20050.0067-0.2630.1410.0364-0.0113-0.3838-0.01180.30020.00260.04580.2236-0.01660.200340.4989138.7934106.2226
110.9667-0.0098-0.00190.660.35420.27740.03330.02170.3130.05770.0277-0.1835-0.14490.0156-0.06110.21140.01110.00280.1765-0.0060.263351.4661104.7986119.4038
120.3342-0.2444-0.15760.74740.03120.69690.0737-0.07260.0496-0.0789-0.0935-0.0138-0.0692-0.1532-0.00040.16530.0001-0.00170.23660.00320.233431.7129104.0666106.1198
130.40240.21230.67751.36710.07031.20320.11460.10680.0447-0.2054-0.0630.14550.0582-0.334-0.0380.21510.0171-0.01610.28740.00820.237911.8499101.275799.3469
140.75160.47790.24220.8117-0.14970.78940.0477-0.00150.1138-0.187-0.06810.3370.028-0.04990.01880.23580.014-0.03460.24080.00480.29318.4023111.546591.4123
151.46750.33830.04721.12950.0330.69430.1060.00640.1256-0.0492-0.13370.1119-0.3411-0.13230.02230.30460.0104-0.07170.3122-0.00330.39739.0961123.764398.2832
160.52490.02140.14840.5325-0.10160.09940.0897-0.03830.0707-0.1798-0.04430.0015-0.035-0.0358-0.02830.28320.01120.01060.22970.02240.28728.8946113.8471101.7843
171.9905-0.0525-0.20720.27290.16610.24410.06280.1898-0.2505-0.4659-0.1361-0.21920.08150.2290.04260.4440.04110.15620.2344-0.00830.340648.3031103.130380.8563
180.6054-0.22960.00940.8630.58820.7058-0.0810.1242-0.0724-0.25590-0.15480.0026-0.1560.05750.25570.0053-0.00450.22690.02140.252535.782104.116594.7916
192.5324-0.2496-0.26391.4114-0.72050.4718-0.1176-0.2876-0.282-0.002-0.060.3591-0.1996-0.0867-0.0430.2091-0.024-0.03660.282-0.02020.244718.25496.5988115.6465
200.5169-0.09970.5880.57660.08160.81030.1425-0.0546-0.1589-0.0095-0.0331-0.09280.1292-0.0647-0.12490.2572-0.00550.00980.19680.02840.262836.783488.5083108.0194
210.9411-0.1453-0.27860.9521-0.00740.73290.08480.0445-0.0428-0.126-0.0229-0.42520.18330.3247-0.04930.31140.0957-0.00340.30590.00960.46566.83285.494108.3554
221.56820.11220.27431.1043-0.04640.24750.18370.0066-0.1442-0.0339-0.1201-0.49750.37120.179-0.02870.33380.07810.02990.39680.03940.570566.199769.052108.8362
230.6095-0.1840.45450.46-0.08050.21140.10950.0642-0.0376-0.2293-0.0719-0.17060.16910.0852-0.0040.33190.04860.04060.2528-0.00320.353946.809779.1381103.6202
241.57360.19380.59490.2126-0.30370.28790.14730.37060.1555-0.7291-0.1551-0.07750.02930.17540.09690.65750.07530.08940.3068-0.01930.312739.219293.36277.6548
250.4611-0.25610.1670.7505-0.01730.88040.08360.0395-0.0664-0.2540.0188-0.1123-0.03490.1689-0.07480.33980.00620.08250.27880.04150.320843.634690.034995.7357
260.9124-0.63390.97941.3783-0.13430.98140.0141-0.13680.34630.10130.1223-0.09510.1686-0.1332-0.16550.2353-0.014-0.03570.24550.05740.287248.376393.9572124.2642
271.5978-0.3331-0.38431.61080.10530.9126-0.22650.1236-0.4288-0.16110.07570.15680.02920.02840.1160.248-0.00130.03260.1696-0.02350.197546.297128.0807107.3714
280.3067-0.20260.02980.4189-0.30930.1164-0.05720.0114-0.17420.1194-0.02850.12690.0358-0.08320.0570.2024-0.00170.01690.2821-0.02230.259441.3978125.0801125.7965
290.4591-0.01750.35290.74320.04550.1453-0.0658-0.32560.03860.3639-0.05110.10190.0295-0.18930.09090.34640.00390.06630.4477-0.05970.32632.803131.7528147.8862
300.46520.20180.250.6025-0.02731.4050.1088-0.2479-0.09920.3131-0.2140.10950.35610.05720.14390.3768-0.02330.0880.5045-0.00840.363734.6288126.9160.691
310.66540.1575-0.46991.06220.27681.12910.1093-0.3889-0.14830.3702-0.05060.04570.2169-0.09730.04180.4635-0.06390.05830.45050.04260.350833.3458112.709156.2887
320.5285-0.4722-0.22671.29940.1591.3756-0.0194-0.2065-0.23070.0899-0.18720.22630.2685-0.27050.0570.3423-0.04180.06780.3947-0.02810.359329.8257107.0987144.8006
330.5493-0.1722-0.33460.11340.15650.36110.0266-0.01-0.17480.0667-0.06620.09060.0193-0.0540.05170.24640.00090.02930.2840.00290.292540.7411118.8606134.5981
340.59110.121-0.43610.59820.3270.57490.0709-0.23120.08530.0376-0.0177-0.302-0.0350.2167-0.02340.2285-0.0007-0.04530.36210.02910.382768.5812127.6655134.7959
350.6598-0.2714-0.00160.25390.31370.56010.0001-0.32380.00860.15710.0684-0.15490.030.0044-0.01910.28180.0378-0.01940.30060.00490.26756.8544126.3386138.7563
361.96161.2461-0.81051.99840.51831.44-0.0203-0.07610.32930.1216-0.07270.4456-0.0471-0.37170.07130.24850.02110.06220.3091-0.03770.317524.8265135.4698130.6218
370.0552-0.2624-0.21550.76330.11190.61040.05260.1114-0.0047-0.2026-0.06920.072-0.0715-0.03060.02430.2884-0.0185-0.03740.2858-0.03910.2322-31.1387130.2545124.2018
381.3267-0.09250.28521.47720.24511.2117-0.1025-0.11050.16410.13240.17980.3643-0.3101-0.13920.03330.2840.0005-0.00710.2732-0.00870.2465-49.2889136.5825147.8922
390.71120.037-0.28460.799-0.34361.66320.04310.1032-0.08580.1012-0.03280.18530.0452-0.2229-0.04540.33960.0327-0.09730.2755-0.03870.3556-58.9851144.1651134.3756
400.6759-0.5159-0.40710.45360.2321.4571-0.06830.21870.0023-0.380.18260.2911-0.22390.0468-0.06450.3480.0331-0.08590.334-0.02170.3332-52.0234148.2831121.5748
41-0.1341-0.05380.06570.61020.11420.73660.07120.1766-0.0272-0.0732-0.09830.0961-0.12120.12720.01020.36930.0355-0.06880.3287-0.03020.2585-42.7882140.44122.5975
420.4694-0.4019-0.2840.75860.26161.44640.09910.0978-0.2752-0.3549-0.03660.31340.12510.0407-0.11130.39850.0257-0.09920.3629-0.07960.4666-44.7018112.1594114.5311
430.6094-0.165-0.00050.4203-0.03280.57640.11470.0467-0.0084-0.1661-0.16320.180.1041-0.17040.03950.3745-0.0177-0.07460.3183-0.02640.3447-43.1163122.9142122.8704
440.4021-0.6514-0.34682.20330.25911.5999-0.0641-0.1617-0.01040.11380.1065-0.0746-0.24520.3363-0.03640.3188-0.03720.00160.2588-0.05660.2894-30.0143139.8016142.5835
450.9322-0.3952-0.40480.49180.33750.3558-0.1119-0.127-0.0306-0.13480.0221-0.02270.02470.17070.05980.3197-0.0446-0.01670.31830.01090.2564-25.4481125.8192142.5459
460.9030.2005-0.24440.6538-0.26120.2377-0.1272-0.0312-0.0719-0.1632-0.02340.12520.03380.17280.08340.22280.0148-0.01890.25720.00090.2217-26.7586115.3674127.7332
470.7595-0.24290.50410.8086-0.4790.82940.03870.2045-0.1936-0.3607-0.0671-0.02080.20220.28140.04730.3920.07710.03770.4655-0.04280.3706-12.9076105.0458112.2326
480.9245-0.6596-0.53410.8459-0.7011.2267-0.02250.0559-0.2302-0.0465-0.09140.00760.18420.07670.11140.40740.0780.06370.4443-0.03380.4382-7.414393.0378124.6719
490.5783-0.70840.01840.31220.00630.49980.0132-0.0231-0.1917-0.1029-0.04750.13780.06410.13530.01940.290.0289-0.00350.2506-0.010.2816-22.9821106.2682133.3499
501.6211-0.3979-0.69420.46070.00521.10540.03740.1718-0.1526-0.4674-0.0740.27150.0521-0.34320.04460.4156-0.0393-0.09310.3684-0.06790.5674-52.0793104.775126.7356
510.88020.07310.18680.67840.09430.5119-0.00860.1361-0.218-0.05660.04820.11540.0528-0.0475-0.03340.2790.0444-0.00570.3314-0.03480.3591-33.9532110.192127.2548
522.1671-1.0303-0.34261.9409-0.24222.6695-0.0729-0.24120.3339-0.3515-0.1228-0.1647-0.09390.2160.19890.2868-0.05080.03630.3811-0.03130.3005-9.6433125.7103122.9557
532.29170.20680.45681.8325-0.66711.5170.00110.24150.1977-0.27240.21660.1080.02190.1306-0.24110.28430.0174-0.020.3237-0.01470.3167-29.7084103.9699155.2987
540.2567-0.144-0.19420.52910.09090.50250.04860.13550.02050.00250.057-0.0192-0.08510.3511-0.10180.2902-0.01010.00570.44110.00660.2837-12.0948117.4723163.9624
550.25950.1188-0.06810.89130.01161.07850.00070.12810.0530.08580.2039-0.167-0.26650.8512-0.21890.3602-0.1367-0.0240.8507-0.00390.43437.0326125.302168.941
560.24830.45210.2710.80960.22020.9225-0.1190.110.2782-0.02950.1618-0.2697-0.39250.4535-0.02670.5664-0.3122-0.02150.83220.00540.47446.6382140.9669166.7763
570.9322-0.0738-0.12320.05870.03930.09370.11340.01180.2854-0.22510.06350.0795-0.36580.6223-0.09970.5001-0.2822-0.00620.84680.03680.4506-0.3091138.964151.2446
580.29510.0230.08290.5774-0.2130.97810.01270.24650.1065-0.11470.0350.0449-0.3360.4078-0.05850.3086-0.10360.03430.488-0.00860.3267-10.0719127.7228157.4653
591.05530.42190.35441.2218-0.09750.61390.0683-0.24530.14850.1615-0.0180.3717-0.26490.0596-0.03590.3628-0.05060.07750.2825-0.0640.3604-29.1127125.7472179.9027
601.08780.04990.08551.07540.1691.28510.0319-0.08520.02440.1111-0.00080.0922-0.15220.2748-0.05360.2733-0.0490.02150.3412-0.03590.3111-17.2495123.7493172.7978
611.81210.4528-0.93320.3997-0.5791.98120.07280.2978-0.2733-0.08710.055-0.62330.33930.4512-0.11320.34890.0770.03520.7604-0.13190.49994.2583108.9374160.5192
620.49080.68750.0631.03510.19560.79530.1422-0.0516-0.07230.2173-0.04080.0010.23060.1355-0.09030.37360.0481-0.03470.2906-0.01090.3095-25.462699.2649174.3254
631.50530.68370.27981.0450.26230.4010.2278-0.3267-0.20220.6166-0.1864-0.08140.48340.0764-0.02070.6644-0.0565-0.09520.4090.06890.4293-31.572784.8672188.2634
640.42410.42030.49561.03710.29150.35190.2039-0.0174-0.06070.3883-0.1482-0.10020.15190.1679-0.02810.3668-0.0083-0.03270.39270.00770.2919-17.5197103.544182.0157
650.87980.54490.46591.16710.01420.51610.0832-0.10270.0060.36-0.13030.12320.10590.1838-0.00450.3559-0.01140.05950.31080.010.2654-21.3165111.0844179.013
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 177 )
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 226 )
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 258 )
6X-RAY DIFFRACTION6chain 'A' and (resid 259 through 297 )
7X-RAY DIFFRACTION7chain 'A' and (resid 298 through 400 )
8X-RAY DIFFRACTION8chain 'A' and (resid 401 through 430 )
9X-RAY DIFFRACTION9chain 'A' and (resid 431 through 473 )
10X-RAY DIFFRACTION10chain 'A' and (resid 474 through 501 )
11X-RAY DIFFRACTION11chain 'D' and (resid 18 through 44 )
12X-RAY DIFFRACTION12chain 'D' and (resid 45 through 119 )
13X-RAY DIFFRACTION13chain 'D' and (resid 120 through 177 )
14X-RAY DIFFRACTION14chain 'D' and (resid 178 through 236 )
15X-RAY DIFFRACTION15chain 'D' and (resid 237 through 282 )
16X-RAY DIFFRACTION16chain 'D' and (resid 283 through 400 )
17X-RAY DIFFRACTION17chain 'D' and (resid 401 through 430 )
18X-RAY DIFFRACTION18chain 'D' and (resid 431 through 473 )
19X-RAY DIFFRACTION19chain 'D' and (resid 474 through 499 )
20X-RAY DIFFRACTION20chain 'C' and (resid 18 through 129 )
21X-RAY DIFFRACTION21chain 'C' and (resid 130 through 236 )
22X-RAY DIFFRACTION22chain 'C' and (resid 237 through 282 )
23X-RAY DIFFRACTION23chain 'C' and (resid 283 through 400 )
24X-RAY DIFFRACTION24chain 'C' and (resid 401 through 430 )
25X-RAY DIFFRACTION25chain 'C' and (resid 431 through 473 )
26X-RAY DIFFRACTION26chain 'C' and (resid 474 through 501 )
27X-RAY DIFFRACTION27chain 'B' and (resid 18 through 44 )
28X-RAY DIFFRACTION28chain 'B' and (resid 45 through 99 )
29X-RAY DIFFRACTION29chain 'B' and (resid 100 through 177 )
30X-RAY DIFFRACTION30chain 'B' and (resid 178 through 203 )
31X-RAY DIFFRACTION31chain 'B' and (resid 204 through 258 )
32X-RAY DIFFRACTION32chain 'B' and (resid 259 through 297 )
33X-RAY DIFFRACTION33chain 'B' and (resid 298 through 390 )
34X-RAY DIFFRACTION34chain 'B' and (resid 391 through 430 )
35X-RAY DIFFRACTION35chain 'B' and (resid 431 through 464 )
36X-RAY DIFFRACTION36chain 'B' and (resid 465 through 501 )
37X-RAY DIFFRACTION37chain 'G' and (resid 18 through 129 )
38X-RAY DIFFRACTION38chain 'G' and (resid 130 through 156 )
39X-RAY DIFFRACTION39chain 'G' and (resid 157 through 271 )
40X-RAY DIFFRACTION40chain 'G' and (resid 272 through 299 )
41X-RAY DIFFRACTION41chain 'G' and (resid 300 through 376 )
42X-RAY DIFFRACTION42chain 'G' and (resid 377 through 430 )
43X-RAY DIFFRACTION43chain 'G' and (resid 431 through 473 )
44X-RAY DIFFRACTION44chain 'G' and (resid 474 through 501 )
45X-RAY DIFFRACTION45chain 'H' and (resid 18 through 63 )
46X-RAY DIFFRACTION46chain 'H' and (resid 64 through 129 )
47X-RAY DIFFRACTION47chain 'H' and (resid 130 through 203 )
48X-RAY DIFFRACTION48chain 'H' and (resid 204 through 285 )
49X-RAY DIFFRACTION49chain 'H' and (resid 286 through 400 )
50X-RAY DIFFRACTION50chain 'H' and (resid 401 through 430 )
51X-RAY DIFFRACTION51chain 'H' and (resid 431 through 473 )
52X-RAY DIFFRACTION52chain 'H' and (resid 474 through 501 )
53X-RAY DIFFRACTION53chain 'F' and (resid 18 through 44 )
54X-RAY DIFFRACTION54chain 'F' and (resid 45 through 119 )
55X-RAY DIFFRACTION55chain 'F' and (resid 120 through 178 )
56X-RAY DIFFRACTION56chain 'F' and (resid 179 through 259 )
57X-RAY DIFFRACTION57chain 'F' and (resid 260 through 297 )
58X-RAY DIFFRACTION58chain 'F' and (resid 298 through 377 )
59X-RAY DIFFRACTION59chain 'F' and (resid 378 through 430 )
60X-RAY DIFFRACTION60chain 'F' and (resid 431 through 473 )
61X-RAY DIFFRACTION61chain 'F' and (resid 474 through 500 )
62X-RAY DIFFRACTION62chain 'E' and (resid 18 through 225 )
63X-RAY DIFFRACTION63chain 'E' and (resid 226 through 326 )
64X-RAY DIFFRACTION64chain 'E' and (resid 327 through 400 )
65X-RAY DIFFRACTION65chain 'E' and (resid 401 through 501 )

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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