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- PDB-6hoh: Structure of VPS34 LIR motif (S249E) bound to GABARAP -

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基本情報

登録情報
データベース: PDB / ID: 6hoh
タイトルStructure of VPS34 LIR motif (S249E) bound to GABARAP
要素Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
キーワードSIGNALING PROTEIN / Autophagy / ATG8 / LIR
機能・相同性
機能・相同性情報


Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane ...Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / regulation of Rac protein signal transduction / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / GABA receptor binding / protein targeting to lysosome / early endosome to late endosome transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / TBC/RABGAPs / microtubule associated complex / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / Macroautophagy / 1-phosphatidylinositol-3-kinase activity / beta-tubulin binding / axoneme / phosphatidylinositol-mediated signaling / autophagosome membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / smooth endoplasmic reticulum / RHO GTPases Activate NADPH Oxidases / autophagosome / regulation of macroautophagy / protein targeting / cellular response to glucose starvation / sperm midpiece / regulation of cytokinesis / regulation of autophagy / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / autophagy / microtubule cytoskeleton organization / endocytosis / phagocytic vesicle membrane / peroxisome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / late endosome / kinase activity / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / protein kinase activity / endosome / cell cycle / phosphorylation / cell division / Golgi membrane / ubiquitin protein ligase binding / synapse / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
Phosphatidylinositol 3-kinase, Vps34 type / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) ...Phosphatidylinositol 3-kinase, Vps34 type / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / Ubiquitin-like (UB roll) / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Protein kinase-like domain superfamily / Alpha Beta
類似検索 - ドメイン・相同性
TRIETHYLENE GLYCOL / Gamma-aminobutyric acid receptor-associated protein / Phosphatidylinositol 3-kinase catalytic subunit type 3
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: 2.25 Å
データ登録者Mouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. ...Mouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. / Lamark, T. / Johansen, T.
資金援助 ノルウェー, 2件
組織認可番号国
Research Council of Norway214448 ノルウェー
Research Council of Norway249884 ノルウェー
引用ジャーナル: Autophagy / 年: 2019
タイトル: Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs.
著者: Birgisdottir, A.B. / Mouilleron, S. / Bhujabal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S.A. / Lamark, T. / Johansen, T.
履歴
登録2018年9月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年2月27日Provider: repository / タイプ: Initial release
改定 1.12019年3月13日Group: Data collection / Database references
カテゴリ: citation / citation_author / pdbx_database_proc
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.22019年7月10日Group: Data collection / Database references / カテゴリ: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
B: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
C: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
D: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,0845
ポリマ－60,9344
非ポリマー1501
水2,882160
1
A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
ヘテロ分子

A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
ヘテロ分子

A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,1516
ポリマ－45,7013
非ポリマー4513
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6650 Å2
ΔGint-26 kcal/mol
Surface area19790 Å2
手法PISA
2
B: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
C: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein

D: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein


分子量 (理論値)分子数
合計 (水以外)45,7013
ポリマ－45,7013
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area5870 Å2
ΔGint-43 kcal/mol
Surface area19930 Å2
手法PISA
単位格子
Length a, b, c (Å)119.502, 119.502, 119.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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要素

#1: タンパク質
Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein / PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase ...PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase class 3 / hVps34 / GABA(A) receptor-associated protein / MM46


分子量: 15233.520 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PIK3C3, VPS34, GABARAP, FLC3B, HT004 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q8NEB9, UniProt: O95166, phosphatidylinositol 3-kinase
#2: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O4
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 160 / 由来タイプ: 天然 / 式: H2O

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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: 2.4 Å3/Da / 溶媒含有率: 48.77 %
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 / 詳細: 20% PEG 3350, 200 mM magnesium formate

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I04 / 波長: 0.97 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年3月12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: 0.97 Å / 相対比: 1
反射解像度: 2.25→53.443 Å / Num. obs: 27219 / % possible obs: 99.49 % / 冗長度: 5.8 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 10.4
反射 シェル解像度: 2.25→2.33 Å / 冗長度: 5.9 % / Rmerge(I) obs: 0.98 / Num. unique obs: 2654 / CC1/2: 0.65 / Rpim(I) all: 0.44 / Rrim(I) all: 1.07 / Χ2: 39 / % possible all: 99.21

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.12_2829: ???)精密化
xia2データ削減
DIALSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1GNU

1gnu


解像度: 2.25→53.44 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 30.25
Rfactor反射数%反射
Rfree0.2496 1272 4.7 %
Rwork0.2064 --
obs0.2084 27048 99.31 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.25→53.44 Å
タンパク質核酸リガンド溶媒全体
原子数4153 0 10 160 4323
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0024320
X-RAY DIFFRACTIONf_angle_d0.4225843
X-RAY DIFFRACTIONf_dihedral_angle_d16.4792636
X-RAY DIFFRACTIONf_chiral_restr0.044616
X-RAY DIFFRACTIONf_plane_restr0.003761
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2504-2.34050.37711310.34392813X-RAY DIFFRACTION99
2.3405-2.4470.42951610.32822774X-RAY DIFFRACTION99
2.447-2.5760.35781500.30942812X-RAY DIFFRACTION99
2.576-2.73740.31871340.28712870X-RAY DIFFRACTION100
2.7374-2.94870.29761350.25762843X-RAY DIFFRACTION100
2.9487-3.24540.32021460.21742881X-RAY DIFFRACTION100
3.2454-3.71490.22111580.192855X-RAY DIFFRACTION100
3.7149-4.680.16881070.14372943X-RAY DIFFRACTION100
4.68-53.4580.1941500.17112985X-RAY DIFFRACTION99
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)
10.4050.02170.8679-0.1138-0.02791.2621-1.08780.65570.02670.91210.61710.32540.97680.11590.00430.66480.00130.0380.37850.03730.62597.41422.672333.9808
20.12440.09940.1208-0.00190.12830.1905-0.5152-1.09120.16890.23550.58020.1467-0.11670.160300.41420.0280.00070.59-0.03460.456224.8456-4.694422.5499
30.1355-0.24080.18190.321-0.04970.12310.9355-0.2555-1.3505-0.1866-0.2422-0.05830.21450.03490.00040.4934-0.1048-0.11480.54310.08250.556434.464-8.289118.3085
40.3959-0.3565-0.22210.57180.15390.00610.0952-0.0429-0.0346-0.211-0.06890.0340.19750.5269-00.35570.0325-0.06290.52080.00870.316243.62491.373516.6996
5-0.01050.17090.2632-0.16110.30551.27850.1977-0.11130.19350.07-0.01480.3674-0.04970.0564-0.00010.29270.0052-0.0010.3718-0.02410.359734.48925.17211.2996
60.3748-0.85210.46620.6204-0.81320.2743-0.1502-0.2035-1.02070.30920.0073-0.0550.2758-0.1364-0.00010.4424-0.02420.0180.4574-0.06450.553420.8462-4.906510.3895
70.17160.0927-0.12710.02070.05780.07580.10660.52780.2134-0.08780.01490.4853-0.02970.560400.36250.0433-0.00260.4619-0.04170.441432.71019.30498.6733
80.0972-0.04470.2290.3243-0.05210.1940.04610.53670.42910.0663-0.2245-0.01420.1403-0.1976-00.3777-0.0004-0.03120.403-0.00220.40822.70637.92895.7285
9-0.0489-0.00760.2931-0.02310.133-0.2077-0.1953-0.28570.0175-0.15950.00630.1096-0.11530.0373-00.3496-0.0192-0.01440.4653-0.04180.420515.01962.74938.1452
100.1077-0.3770.19850.74880.43870.6164-0.2713-0.85430.34940.78680.08410.248-0.47780.2028-0.00010.42120.0897-0.02230.5012-0.06020.51623.238211.072618.9441
110.0567-0.174-0.04060.2954-0.04910.10770.2771-0.0220.74780.1722-0.49330.0219-0.1402-0.3791-0.00020.3484-0.08970.02720.4373-0.03710.422732.113412.312519.0682
120.4013-0.1728-0.26910.4358-1.58461.0711-0.05870.12780.14270.0048-0.01420.2137-0.20690.1039-0.00010.3189-0.0022-0.02660.3591-0.05060.340829.0572.269418.2668
130.07920.09150.04270.04380.0468-0.02940.5059-1.11761.43670.25110.3313-2.2177-1.18540.19110.00070.946-0.0828-0.09550.7131-0.01440.706454.572840.184363.0743
141.9121-0.3826-0.80540.1871-0.12990.55450.5076-0.5794-0.3435-0.57250.3168-1.19550.45090.8545-0.02880.53910.00430.1230.28280.02020.560457.520631.901151.003
150.01840.04370.04640.0562-0.07210.05871.20970.9462-0.00050.16480.04580.9348-0.8497-0.34930.00030.6967-0.0641-0.040.52730.0260.670864.73220.890737.2596
160.2455-0.2113-0.8122.5311.70713.7921-0.63512.21480.20070.3833-0.832-0.37851.5171.5196-0.10190.3547-0.1870.06540.95850.27960.633469.960516.42427.837
171.0057-0.6250.44070.41230.62850.595-0.0637-0.06780.0431-0.4405-0.4415-0.5261-0.33110.6252-1.01720.515-0.1308-0.04190.80470.19930.452161.289515.807918.0709
180.1056-0.1012-0.38471.0686-0.70950.576-0.14760.2682-0.03350.1626-0.04070.1865-0.53010.3707-00.2957-0.0276-0.02620.43640.02010.33356.274510.441626.4347
191.32941.6182-1.31890.2155-0.32051.08140.3606-0.0746-0.0741-0.1484-0.11070.038-0.07740.20380.00090.2909-0.0343-0.01870.3713-0.010.273159.2218.284434.9444
200.2592-0.42710.07350.1960.35470.5999-0.11360.09920.1468-0.4901-0.03150.07790.3869-0.03090.00010.2814-0.01750.01310.37990.02290.319852.31124.472838.1457
210.23640.3090.31210.1274-0.28430.27790.1835-0.12460.04810.1414-0.15140.0599-0.25950.2367-00.4172-0.00090.0260.3933-0.02450.35858.2796.885846.5229
22-0.02230.13230.11530.2654-0.5410.25070.3521-0.3650.7204-0.3337-0.1361-0.2496-0.5509-0.91330.00020.43120.13880.02360.50180.04260.520149.786917.966737.6124
230.1367-0.04380.14730.1890.0244-0.0341-0.18070.28670.50250.2137-0.16840.1904-0.226-0.30070.00020.48570.0217-0.09030.46840.05410.429849.472118.40228.4255
240.38780.0119-0.33020.0231-0.12150.0967-0.92031.19190.96140.77410.0758-0.5639-1.25740.5684-0.17650.7452-0.0895-0.07340.59990.29960.567358.738420.450724.0064
250.483-0.26630.50770.57370.34720.28240.19040.01950.21790.36770.1058-0.066-0.7360.8943-0.00020.4126-0.0673-0.08080.38170.03260.445459.300214.669239.8672
262.256-0.68870.63932.7834-1.1981.8508-0.4150.6090.3325-0.47060.5032-0.79210.7287-0.31940.19980.3216-0.03140.02080.5303-0.02930.135454.82592.035725.6825
270.07540.02820.06070.424-0.08260.28970.97911.3824-0.06170.39970.00940.208-0.99260.56620.00550.33160.0783-0.00290.57370.1010.506635.7802-5.863436.6418
280.1777-0.1163-0.08080.28970.21580.07060.29150.1569-0.14220.4352-0.4282-0.14360.5566-0.8321-0.00010.4982-0.0067-0.04760.5735-0.02570.66125.7298-9.003540.1774
290.655-0.0645-0.1818-0.15530.25160.36590.188-0.2281-0.0184-0.03860.12280.09590.2337-0.27380.00010.47790.0148-0.06510.61280.06240.491917.4040.874143.0649
300.7025-0.14540.678-0.13360.39190.568-0.1972-0.0761-0.0024-0.15860.2211-0.1552-0.1949-0.0267-0.00010.35480.0149-0.02310.41020.05250.340326.96423.607848.5095
311.04460.35841.31361.153-0.78673.8381-0.2311-0.10060.04290.35160.07280.41490.4179-0.1477-0.00010.2478-0.01270.01090.3673-0.04810.386634.4239-0.272749.8678
320.97880.27490.50610.6076-0.44750.289-0.1948-0.36590.54580.02350.2181-0.1169-0.0967-0.379100.41650.0013-0.02070.38530.01850.436239.04834.603253.8781
330.1811-0.24420.0261-0.0819-0.00630.5933-0.05230.19650.21960.2242-0.5112-0.16830.00230.466-0.00020.356-0.01330.03260.46910.06670.41746.4116-0.759251.2158
340.0809-0.26650.18250.6136-0.47810.3407-0.3060.26760.3022-0.95840.19740.1199-1.3120.7220.00010.4246-0.0493-0.0210.51880.12560.51538.71719.059740.9939
350.52240.44390.05050.21060.2210.59210.08220.3140.3522-0.4908-0.0774-0.0778-0.107-0.180300.38470.0821-0.040.50830.06930.419627.21887.682940.0303
360.1281-0.2144-0.0287-0.12070.3506-0.25360.0418-0.0494-0.1991-0.0802-0.3170.25690.30630.0246-0.00020.36360.0621-0.00260.41370.0540.338238.3997-0.989843.5645
370.62270.1465-0.3412-0.46-0.75680.1279-0.15760.1008-0.48830.00380.3116-0.066-0.4418-0.0836-0.00030.5227-0.08410.05210.4852-0.02120.707960.9829-30.789750.2174
380.0264-0.33830.17481.2337-0.29221.5697-0.10660.1521-0.4243-0.3395-0.0518-0.2767-0.0081-0.452900.5129-0.04350.08940.4462-0.04770.391259.8011-16.067921.4034
39-0.41631.11850.14213.3257-0.42243.2776-0.0832-0.0143-0.07880.17320.0556-0.0527-0.0768-0.1064-00.30880.0420.02650.454-0.02740.30461.2224-9.19938.5309
401.58980.8988-0.16112.39912.32612.7817-0.4689-0.1083-0.8315-0.19460.0714-0.30580.44950.4324-0.34370.39480.08060.17450.39630.09860.46566.2806-19.387832.9673
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -13 through -2 )
2X-RAY DIFFRACTION2chain 'A' and (resid -1 through 3 )
3X-RAY DIFFRACTION3chain 'A' and (resid 4 through 10 )
4X-RAY DIFFRACTION4chain 'A' and (resid 11 through 24 )
5X-RAY DIFFRACTION5chain 'A' and (resid 25 through 35 )
6X-RAY DIFFRACTION6chain 'A' and (resid 36 through 47 )
7X-RAY DIFFRACTION7chain 'A' and (resid 48 through 56 )
8X-RAY DIFFRACTION8chain 'A' and (resid 57 through 67 )
9X-RAY DIFFRACTION9chain 'A' and (resid 68 through 79 )
10X-RAY DIFFRACTION10chain 'A' and (resid 80 through 90 )
11X-RAY DIFFRACTION11chain 'A' and (resid 91 through 98 )
12X-RAY DIFFRACTION12chain 'A' and (resid 99 through 112 )
13X-RAY DIFFRACTION13chain 'B' and (resid -16 through -11 )
14X-RAY DIFFRACTION14chain 'B' and (resid -10 through -2 )
15X-RAY DIFFRACTION15chain 'B' and (resid -1 through 3 )
16X-RAY DIFFRACTION16chain 'B' and (resid 4 through 10 )
17X-RAY DIFFRACTION17chain 'B' and (resid 11 through 24 )
18X-RAY DIFFRACTION18chain 'B' and (resid 25 through 35 )
19X-RAY DIFFRACTION19chain 'B' and (resid 36 through 56 )
20X-RAY DIFFRACTION20chain 'B' and (resid 57 through 67 )
21X-RAY DIFFRACTION21chain 'B' and (resid 68 through 79 )
22X-RAY DIFFRACTION22chain 'B' and (resid 80 through 90 )
23X-RAY DIFFRACTION23chain 'B' and (resid 91 through 98 )
24X-RAY DIFFRACTION24chain 'B' and (resid 99 through 104 )
25X-RAY DIFFRACTION25chain 'B' and (resid 105 through 112 )
26X-RAY DIFFRACTION26chain 'C' and (resid -14 through -2 )
27X-RAY DIFFRACTION27chain 'C' and (resid -1 through 3 )
28X-RAY DIFFRACTION28chain 'C' and (resid 4 through 10 )
29X-RAY DIFFRACTION29chain 'C' and (resid 11 through 24 )
30X-RAY DIFFRACTION30chain 'C' and (resid 25 through 35 )
31X-RAY DIFFRACTION31chain 'C' and (resid 36 through 56 )
32X-RAY DIFFRACTION32chain 'C' and (resid 57 through 67 )
33X-RAY DIFFRACTION33chain 'C' and (resid 68 through 79 )
34X-RAY DIFFRACTION34chain 'C' and (resid 80 through 90 )
35X-RAY DIFFRACTION35chain 'C' and (resid 91 through 104 )
36X-RAY DIFFRACTION36chain 'C' and (resid 105 through 112 )
37X-RAY DIFFRACTION37chain 'D' and (resid -13 through 3 )
38X-RAY DIFFRACTION38chain 'D' and (resid 4 through 35 )
39X-RAY DIFFRACTION39chain 'D' and (resid 36 through 76 )
40X-RAY DIFFRACTION40chain 'D' and (resid 77 through 112 )

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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://pdbjlvh1.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