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- PDB-7vec: Crystal structure of GABARAP complexed with the TEX264 LIR phosph... -

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基本情報

登録情報
データベース: PDB / ID: 7vec
タイトルCrystal structure of GABARAP complexed with the TEX264 LIR phosphorylated at Ser271 and Ser272
要素
  • Gamma-aminobutyric acid receptor-associated protein
  • TEX264 phospho-LIR
キーワードSIGNALING PROTEIN / Autophagy / ER-phagy
機能・相同性
機能・相同性情報


positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / protein targeting / sperm midpiece / autophagosome / microtubule cytoskeleton organization / protein transport / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / synapse / plasma membrane / cytosol
類似検索 - 分子機能
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
類似検索 - ドメイン・相同性
Gamma-aminobutyric acid receptor-associated protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 分子置換 / 解像度: 3 Å
データ登録者Noda, N.N.
資金援助 日本, 2件
組織認可番号国
Japan Science and TechnologyJPMJCR20E3 日本
Japan Society for the Promotion of Science (JSPS)19H05707 日本
引用ジャーナル: Embo Rep. / 年: 2022
タイトル: Phosphorylation by casein kinase 2 enhances the interaction between ER-phagy receptor TEX264 and ATG8 proteins.
著者: Chino, H. / Yamasaki, A. / Ode, K.L. / Ueda, H.R. / Noda, N.N. / Mizushima, N.
履歴
登録2021年9月8日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年3月30日Provider: repository / タイプ: Initial release
改定 1.12023年10月11日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22023年11月29日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model
改定 1.32024年10月9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: Gamma-aminobutyric acid receptor-associated protein
B: Gamma-aminobutyric acid receptor-associated protein
C: Gamma-aminobutyric acid receptor-associated protein
D: Gamma-aminobutyric acid receptor-associated protein
E: Gamma-aminobutyric acid receptor-associated protein
F: Gamma-aminobutyric acid receptor-associated protein
G: Gamma-aminobutyric acid receptor-associated protein
H: Gamma-aminobutyric acid receptor-associated protein
I: Gamma-aminobutyric acid receptor-associated protein
J: Gamma-aminobutyric acid receptor-associated protein
K: Gamma-aminobutyric acid receptor-associated protein
L: Gamma-aminobutyric acid receptor-associated protein
M: TEX264 phospho-LIR
N: TEX264 phospho-LIR
O: TEX264 phospho-LIR
P: TEX264 phospho-LIR
Q: TEX264 phospho-LIR
R: TEX264 phospho-LIR
S: TEX264 phospho-LIR
T: TEX264 phospho-LIR
U: TEX264 phospho-LIR
V: TEX264 phospho-LIR
X: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)181,68023
ポリマ－181,68023
非ポリマー00
水00
1
A: Gamma-aminobutyric acid receptor-associated protein
M: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-11 kcal/mol
Surface area6950 Å2
手法PISA
2
B: Gamma-aminobutyric acid receptor-associated protein
N: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area6910 Å2
手法PISA
3
C: Gamma-aminobutyric acid receptor-associated protein
O: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area6940 Å2
手法PISA
4
D: Gamma-aminobutyric acid receptor-associated protein
P: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-12 kcal/mol
Surface area7020 Å2
手法PISA
5
E: Gamma-aminobutyric acid receptor-associated protein
Q: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-13 kcal/mol
Surface area7300 Å2
手法PISA
6
F: Gamma-aminobutyric acid receptor-associated protein
R: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area7020 Å2
手法PISA
7
G: Gamma-aminobutyric acid receptor-associated protein
S: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-11 kcal/mol
Surface area7130 Å2
手法PISA
8
H: Gamma-aminobutyric acid receptor-associated protein
T: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-13 kcal/mol
Surface area7240 Å2
手法PISA
9
I: Gamma-aminobutyric acid receptor-associated protein
U: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-10 kcal/mol
Surface area7000 Å2
手法PISA
10
J: Gamma-aminobutyric acid receptor-associated protein
V: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area7180 Å2
手法PISA
11
K: Gamma-aminobutyric acid receptor-associated protein


分子量 (理論値)分子数
合計 (水以外)13,9831
ポリマ－13,9831
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6870 Å2
手法PISA
12
L: Gamma-aminobutyric acid receptor-associated protein
X: TEX264 phospho-LIR


分子量 (理論値)分子数
合計 (水以外)15,2452
ポリマ－15,2452
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-6 kcal/mol
Surface area6790 Å2
手法PISA
単位格子
Length a, b, c (Å)200.480, 201.383, 211.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

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要素

#1: タンパク質
Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


分子量: 13983.056 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GABARAP, FLC3B, HT004 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O95166
#2: タンパク質・ペプチド
TEX264 phospho-LIR


分子量: 1262.107 Da / 分子数: 11 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
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: 3 Å3/Da / 溶媒含有率: 59.01 %
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: 30% PEG 4000, 0.2M ammonium acetate, 0.1M bis-Tris pH 5.6

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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: 回転陽極 / タイプ: RIGAKU MICROMAX-007 HF / 波長: 1.54178 Å
検出器タイプ: RIGAKU HyPix-6000HE / 検出器: PIXEL / 日付: 2021年6月4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: 1.54178 Å / 相対比: 1
反射解像度: 3→30.48 Å / Num. obs: 42776 / % possible obs: 99.9 % / 冗長度: 8.7 % / CC1/2: 0.964 / Net I/σ(I): 6.5
反射 シェル解像度: 3→3.11 Å / 冗長度: 8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4477 / CC1/2: 0.608 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.17.1_3660: ???)精密化
CrysalisPro1.171.40.14aデータ削減
Aimlessデータスケーリング
MrBUMP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5YIR

5yir


解像度: 3→28.89 Å / SU ML: 0.43 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 28.35 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3007 2233 5.34 %
Rwork0.257 --
obs0.2594 41787 97.65 %
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: 3→28.89 Å
タンパク質核酸リガンド溶媒全体
原子数12376 0 0 0 12376
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00312703
X-RAY DIFFRACTIONf_angle_d0.67117160
X-RAY DIFFRACTIONf_dihedral_angle_d19.1924791
X-RAY DIFFRACTIONf_chiral_restr0.051764
X-RAY DIFFRACTIONf_plane_restr0.0052204
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.41331550.37362477X-RAY DIFFRACTION99
3.07-3.140.32871000.31742525X-RAY DIFFRACTION100
3.14-3.210.32121750.27612495X-RAY DIFFRACTION100
3.21-3.30.29711550.26882502X-RAY DIFFRACTION100
3.3-3.40.30411520.25932524X-RAY DIFFRACTION100
3.4-3.510.31221340.26732468X-RAY DIFFRACTION100
3.51-3.630.56031180.46151912X-RAY DIFFRACTION76
3.63-3.780.52891280.47022307X-RAY DIFFRACTION92
3.78-3.950.37451420.30412470X-RAY DIFFRACTION98
3.95-4.160.24061860.23652449X-RAY DIFFRACTION100
4.16-4.420.23111640.1932517X-RAY DIFFRACTION100
4.42-4.760.2131930.16692572X-RAY DIFFRACTION100
4.76-5.230.18871600.16122531X-RAY DIFFRACTION100
5.23-5.980.2181310.17832554X-RAY DIFFRACTION100
5.98-7.520.22131160.19042604X-RAY DIFFRACTION100
7.52-28.890.20821240.16682647X-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)
10.0024-0.00170.00290.00120.0024-0.0039-0.04770.029-0.00240.0166-0.01350.01060.04660.017-00.1627-0.00850.0549-0.0115-0.11140.1454-62.057535.5256-17.0322
20.0030.00560.00480.00040.00430.0006-0.01330.0362-0.02990.03490.0325-0.0432-0.0326-0.02470-0.0438-0.1971-0.3231-0.1536-0.31580.0607-68.434324.2741-22.7653
30.0192-0.041-0.02880.02150.0207-0.0137-0.20090.225-0.1224-0.1474-0.0585-0.09690.12290.24020-0.49230.01320.2172-0.7383-0.4358-0.1733-50.286926.4453-20.1825
40.0021-0.0003-0.0010.00010.0006-0.0003-0.0056-0.00320.00630.01330.02060.008-0.00570.0152-00.12140.15880.01730.0624-0.13960.0991-44.619734.9764-9.907
5-0.00020.0011-0.00240.00130.0017-0.00210.0258-0.02220.00970.010.03110.0024-0.0007-0.0031-00.1280.18880.31720.0417-0.37780.1368-36.52910.6498-18.2483
60.00030.0047-0.00540.00420.0005-0.0019-0.05820.01370.0391-0.0389-0.04190.039-0.06410.026700.08470.13850.311-0.092-0.3750.0298-30.935118.1056-29.4378
7-0.00230.00390.00280.00910.00540.00470.04350.01620.01080.0666-0.0624-0.0530.04460.0097-00.1869-0.05310.0966-0.0245-0.1549-0.1159-28.69186.4713-29.6655
80.01010.00930.00770.0017-0.0051-0.0030.02840.07380.02870.0389-0.0803-0.04420.078-0.0583-0-0.0352-0.1418-0.17550.096-0.1479-0.1252-29.22660.6526-23.9337
90-0.00280.00280.0016-0.0006-0.0012-0.0223-0.041-0.0343-0.04-0.03480.02110.04510.03170-0.0654-0.2027-0.08690.1619-0.0798-0.2191-27.0309-6.5541-27.3238
10-0.0074-0.0080.00610.0020.0053-0.00110.11770.00580.10330.019-0.02030.06850.07550.0121-0-0.0846-0.2643-0.2051-0.1117-0.4838-0.4386-35.2523-7.7216-26.4407
110.00070.0002-0.00060.0010.0020.00230.00080.01260.0034-0.01560.01570.0271-0.01380.01060-0.12130.20660.1180.2083-0.245-0.0093-37.164.1099-36.4437
120.00040.00370.0060.00170.00180.00230.1124-0.03930.03960.05190.016-0.01920.0408-0.0687-00.0795-0.01830.05360.0928-0.0160.0329-36.52397.4904-27.3722
130.0009-0.0020.00030.00370.0020.001-0.0043-0.00680.00360.0119-0.0143-0.00280.0054-0.014500.0778-0.03880.19280.0136-0.24130.0777-41.941-6.9942-18.9815
140.00120.00280.0028-0.00150.00040.0030.0130.0140.0027-0.02530.0012-0.01680.0107-0.04070-0.17440.0164-0.15020.1247-0.06580.0714-32.4687-13.0575-43.8317
15-0.0009-0.0007-0.0026-0.0005-0.00140.00140.0057-0.0119-0.08310.0609-0.0480.0077-0.002-0.0365-0-0.1440.36530.2077-0.1644-0.13330.0041-21.7892-19.1909-35.4455
16-0.0002-0.00360.010.00430.00750.01230.0330.0521-0.02220.06750.0607-0.09820.0413-0.067-00.0720.0036-0.05290.1043-0.04280.0718-24.353-20.9366-50.8984
170.0012-0.00630.00070.00220.00450.00030.04950.0207-0.0387-0.03130.1280.0310.05120.0412-0-0.1507-0.0797-0.1727-0.0016-0.1383-0.1322-24.6279-20.8646-62.034
180.0022-0.0022-0.00610.0036-0.00330.0006-0.04520.03020.0315-0.06040.0376-0.0097-0.00130.092300.102-0.04450.10860.1347-0.0025-0.0895-15.7626-11.8634-53.03
190.01110.007-0.0011-0.0043-0.01420.0017-0.0860.07790.03820.121-0.0423-0.0318-0.0153-0.07820-0.28050.2292-0.4562-0.07670.2106-0.2691-23.0137-13.5396-46.1759
200.00020.0005-0.00060.0015-0.0006-0.00070.008-0.00330.0354-0.0057-0.01270.0090.0179-0.016400.0841-0.06020.0990.2104-0.0080.1338-30.0319-7.7215-61.1912
21-0.0003-0.0036-0.00530.0002-0.00250.00310.02580.0398-0.0388-0.020.0582-0.03330.01790.01950-0.05810.06610.18770.09830.0215-0.0756-16.505555.518-32.1112
22-0.00180.00090.0026-0.0075-0.0048-0.0006-0.10040.0512-0.01980.08540.0929-0.072-0.0250.02420-0.3006-0.16450.12360.06090.27770.0196-20.487163.9608-20.7548
230.006-0.00390.00740.0003-0.00140.0012-0.04590.0372-0.06150.03230.0386-0.0534-0.0359-0.031-0-0.00030.0681-0.13110.00730.2316-0.0695-23.247252.8491-19.5988
240.00070.0037-0.00190.0036-0.0032-0.00080.02290.00640.0046-0.01140.0450.0071-0.02030.03200.15350.07990.02020.22910.12480.2098-21.785143.9178-32.9327
250.00420.0008-0.0023-0.0008-0.00280.0005-0.0491-0.0178-0.0614-0.0075-0.0141-0.00180.01760.01240-0.1491-0.03350.1010.2174-0.03050.0204-24.87349.3788-16.0365
26-0.00020.00250.0051-0.0014-0.0034-0.0023-0.01490.0239-0.02470.0261-0.05240.0060.0466-0.0085-0-0.0036-0.04730.0690.07580.05780.0953-25.716239.8803-20.7904
27-0.00010.0044-0.0018-0.0014-0.0009-0.00020.00440.0114-0.0122-0.0373-0.0130.01160.0459-0.07160-0.07150.03090.3115-0.00440.13290.041-21.956434.4435-26.2041
280.0007-0.0058-0.00070.001-0.00380.00080.0135-0.01650.00390.07560.05980.00330.02020.00190-0.13250.24770.0434-0.0280.09070.2749-12.519542.6074-17.49
290.0005-0.00070.00130.0002-0.0021-0.00140.0194-0.0257-0.02070.03410.02660.01820.04310.007100.08160.1999-0.22690.10080.1328-0.2564-14.632750.6988-13.5579
30-0.00260.00240.0007-0-0.00460.0062-0.02530.03420.10750.0123-0.0385-0.01730.07850.0536-00.06340.11780.0424-0.2344-0.01860.0211-15.638853.1496-22.7667
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440.0066-0.01130.00870.0046-0.00080.00280.0096-0.04920.1743-0.01310.0594-0.0508-0.0105-0.0022-00.21590.0498-0.14320.08020.0774-0.2369-64.2477-22.2612-18.9984
450.0027-0.00020.002-0.00060.00180.0031-0.0184-0.01820.0570.04410.01590.1052-0.00770.0189-00.0129-0.057-0.08660.0878-0.0590.194-49.0014-15.692-18.4946
460.00520.0053-0.00280.00170.0030-0.08080.03350.00210.0164-0.08250.05820.01760.0361-0-0.0122-0.0761-0.031-0.0324-0.2013-0.0005-56.1543-25.129-19.6217
470.00450.00180.00390.00230.00250.0062-0.00780.0095-0.0150.01570.00610-0.0026-0.005100.24330.00270.06080.2916-0.07490.2755-66.1014-29.85-13.0237
480.00130.00340.0058-0.00510.01-0.01150.0695-0.05940.02220.00510.0241-0.0603-0.05780.12470-0.24230.12610.2418-0.5604-0.09540.0105-26.974330.2791-8.7783
490.00010.01920.00060.0179-0.01280.01610.1007-0.01760.0302-0.09910.1740.13520.00260.0608-00.08120.01530.0088-0.0410.0130.1917-29.019226.22096.305
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550.00320.0099-0.0005-0.0050.0095-0.00270.00040.0351-0.0836-0.0860.04020.07660.0261-0.09670-0.5107-0.29930.5133-0.41390.2874-0.133-26.2723-62.5644-32.8263
560.00090.0022-0.00210.0010.0023-0.0007-0.1187-0.03150.02910.037-0.0817-0.0153-0.01470.03030-0.1792-0.27070.0216-0.1109-0.00650.0639-18.1951-53.558-22.9025
570.0068-0.00830.01240.0057-0.01230.00260.0381-0.01530.0657-0.0516-0.029-0.03090.0670.110600.0717-0.0379-0.0122-0.0541-0.03620.0139-18.8445-50.0868-31.803
580.00150.001-0.00060.0013-0.0015-0.00110.0157-0.00060.00430.0078-0.00020.01620.0025-0.0116-00.2260.00040.16170.3011-0.02650.2212-8.50214.3465-29.4047
590.0021-0.0054-0.0010.00240.00020.0012-0.0450.0281-0.09060.05290.05910.0316-0.0048-0.0535-00.0710.0450.02870.0859-0.04350.2773-14.255525.9686-23.2413
600.00740.00020.0010.0019-0.00460.0055-0.0752-0.02920.01040.023-0.0215-0.0263-0.0173-0.0337-00.03840.37780.1588-0.06360.02440.072-2.54325.163-22.307
610.0038-0.0053-0.0063-0.00110.0061-0.00510.03-0.0914-0.05120.04120.02520.0099-0.01420.002600.26270.09580.070.26370.04010.20652.793918.4089-23.887
620.0083-0.0055-0.0172-0.0153-0.00990.0025-0.107-0.07790.050.0659-0.0647-0.05040.0183-0.01480-0.74660.31740.7529-0.0788-0.2549-0.497810.272820.9335-27.2483
63-0.0002-0.0008-0.0021-0.00070.00120.0008-0.0273-0.0186-0.0062-0.0031-0.02680.0148-0.00440.0209-00.03150.11020.26140.161-0.07790.1897-0.430231.5872-30.4524
640.00120.0028-0.00870.0024-0.012-0.0033-0.0291-0.0464-0.0133-0.024-0.07-0.0135-0.01690.01730-0.26830.35410.352-0.36340.12870.1506-4.498123.0315-29.9989
65-0.0010.0009-0.00020.0009-0.00120.0011-0.0095-0.0142-0.01870.0143-0.00750.02620.01890.0258-00.15880.1047-0.01370.03290.07590.03678.559813.4773-37.0969
660.00490.00680.01-0.0055-0.00420.00340.10970.0096-0.0103-0.07360.0929-0.1198-0.03440.07790-0.05520.2041-0.2512-0.61820.4728-0.0811.21224.1554-70.3054
670.01350.00450.0308-0.0026-0.00560.01090.1193-0.0276-0.0473-0.08680.09870.0214-0.0675-0.00530-0.42840.3928-0.6137-0.24820.4382-0.2601-1.226726.0906-74.5314
68-0.001-0.00510.0069-0.00510.0036-0.0038-0.06490.04460.00250.04920.00650.00060.0273-0.01230-0.33930.162-0.3179-0.25730.4095-0.1486-9.883729.0207-77.1724
69-0.00170.00480.00560.0037-0.0091-0.0010.0346-0.03810.0512-0.03730.05910.01150.0160.03360-0.01720.0243-0.0823-0.04330.547-0.0105-15.335324.679-72.6293
70-0.00150.0088-0.0003-0.00510.0031-0.0010.0002-0.14380.23430.06640.01150.0334-0.0781-0.1021-0-0.40580.4318-0.2147-0.1760.219-0.01340.289432.2037-66.5395
710.0033-0.00080.00060.0001-0.00070.00170.01580.0029-0.01540.00840.00740.00460.0036-0.0056-00.3477-0.0129-0.05290.45190.22630.2377-11.743321.8925-61.6337
720.0020.00060.0007-0.00120.00040.00140.0263-0.0266-0.02430.01180.0058-0.00580.004-0.0151-00.5209-0.00230.03980.64180.20750.4063-88.272631.27469.2102
73-0.003-0.0092-0.001-0.0039-0.00830.00230.044-0.0259-0.03450.02710.0006-0.04-0.0019-0.0709-00.2271-0.1398-0.00880.49560.1916-0.0477-76.941124.379815.3928
74-0.0027-0.0077-0.0016-0.00180.00770.00890.0283-0.0133-0.06150.0384-0.0757-0.0599-0.002-0.0387-00.32480.23-0.01240.36320.00960.333-77.646722.84243.9067
750.00180.01-0.00080.00560.00210.00870.12390.01980.0268-0.00210.07220.05710.1334-0.114900.46150.0893-0.02680.14160.0296-0.0707-82.878123.7262-4.8254
760.00020.013-0.0016-0.0096-0.01640.0095-0.0861-0.0193-0.00330.0460.03530.00510.1479-0.0638-00.1818-0.21720.13880.12410.0171-0.4923-81.837331.2476-9.442
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780.00110.00010.0005-0.0006-0.00130.0017-0.0075-0.00440.0088-0.0099-0.00870.0097-0.0245-0.005700.3557-0.06090.10730.55570.02360.2644-35.847124.1639-59.7706
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820.001-0.000200.000600.0002-0.00220.00620.00420.01110.0054-0.00470.0008-0.007800.5482-0.0260.01390.5249-0.06460.5132-36.99516.4995-42.7139
830.0007-0.00160.00130.0003-0.00060.0020.02360.0277-0.0025-0.00290.04920.01830.0202-0.004500.13280.08090.0870.2006-0.01760.14-52.666824.354-31.1768
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 116 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 10 )
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 35 )
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 56 )
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 68 )
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 90 )
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 98 )
12X-RAY DIFFRACTION12chain 'B' and (resid 99 through 110 )
13X-RAY DIFFRACTION13chain 'B' and (resid 111 through 116 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 10 )
15X-RAY DIFFRACTION15chain 'C' and (resid 11 through 24 )
16X-RAY DIFFRACTION16chain 'C' and (resid 25 through 56 )
17X-RAY DIFFRACTION17chain 'C' and (resid 57 through 79 )
18X-RAY DIFFRACTION18chain 'C' and (resid 80 through 98 )
19X-RAY DIFFRACTION19chain 'C' and (resid 99 through 110 )
20X-RAY DIFFRACTION20chain 'C' and (resid 111 through 116 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 10 )
22X-RAY DIFFRACTION22chain 'D' and (resid 11 through 24 )
23X-RAY DIFFRACTION23chain 'D' and (resid 25 through 35 )
24X-RAY DIFFRACTION24chain 'D' and (resid 36 through 47 )
25X-RAY DIFFRACTION25chain 'D' and (resid 48 through 56 )
26X-RAY DIFFRACTION26chain 'D' and (resid 57 through 68 )
27X-RAY DIFFRACTION27chain 'D' and (resid 69 through 79 )
28X-RAY DIFFRACTION28chain 'D' and (resid 80 through 90 )
29X-RAY DIFFRACTION29chain 'D' and (resid 91 through 98 )
30X-RAY DIFFRACTION30chain 'D' and (resid 99 through 110 )
31X-RAY DIFFRACTION31chain 'D' and (resid 111 through 116 )
32X-RAY DIFFRACTION32chain 'E' and (resid 1 through 10 )
33X-RAY DIFFRACTION33chain 'E' and (resid 11 through 24 )
34X-RAY DIFFRACTION34chain 'E' and (resid 25 through 35 )
35X-RAY DIFFRACTION35chain 'E' and (resid 36 through 56 )
36X-RAY DIFFRACTION36chain 'E' and (resid 57 through 90 )
37X-RAY DIFFRACTION37chain 'E' and (resid 91 through 110 )
38X-RAY DIFFRACTION38chain 'E' and (resid 111 through 116 )
39X-RAY DIFFRACTION39chain 'F' and (resid 1 through 10 )
40X-RAY DIFFRACTION40chain 'F' and (resid 11 through 24 )
41X-RAY DIFFRACTION41chain 'F' and (resid 25 through 35 )
42X-RAY DIFFRACTION42chain 'F' and (resid 36 through 47 )
43X-RAY DIFFRACTION43chain 'F' and (resid 48 through 68 )
44X-RAY DIFFRACTION44chain 'F' and (resid 69 through 90 )
45X-RAY DIFFRACTION45chain 'F' and (resid 91 through 104 )
46X-RAY DIFFRACTION46chain 'F' and (resid 105 through 110 )
47X-RAY DIFFRACTION47chain 'F' and (resid 111 through 115 )
48X-RAY DIFFRACTION48chain 'G' and (resid 1 through 24 )
49X-RAY DIFFRACTION49chain 'G' and (resid 25 through 67 )
50X-RAY DIFFRACTION50chain 'G' and (resid 68 through 79 )
51X-RAY DIFFRACTION51chain 'G' and (resid 80 through 116 )
52X-RAY DIFFRACTION52chain 'H' and (resid 1 through 10 )
53X-RAY DIFFRACTION53chain 'H' and (resid 11 through 24 )
54X-RAY DIFFRACTION54chain 'H' and (resid 25 through 56 )
55X-RAY DIFFRACTION55chain 'H' and (resid 57 through 79 )
56X-RAY DIFFRACTION56chain 'H' and (resid 80 through 98 )
57X-RAY DIFFRACTION57chain 'H' and (resid 99 through 116 )
58X-RAY DIFFRACTION58chain 'I' and (resid 1 through 10 )
59X-RAY DIFFRACTION59chain 'I' and (resid 11 through 24 )
60X-RAY DIFFRACTION60chain 'I' and (resid 25 through 35 )
61X-RAY DIFFRACTION61chain 'I' and (resid 36 through 56 )
62X-RAY DIFFRACTION62chain 'I' and (resid 57 through 90 )
63X-RAY DIFFRACTION63chain 'I' and (resid 91 through 98 )
64X-RAY DIFFRACTION64chain 'I' and (resid 99 through 110 )
65X-RAY DIFFRACTION65chain 'I' and (resid 111 through 116 )
66X-RAY DIFFRACTION66chain 'J' and (resid 1 through 24 )
67X-RAY DIFFRACTION67chain 'J' and (resid 25 through 56 )
68X-RAY DIFFRACTION68chain 'J' and (resid 57 through 68 )
69X-RAY DIFFRACTION69chain 'J' and (resid 69 through 79 )
70X-RAY DIFFRACTION70chain 'J' and (resid 80 through 110 )
71X-RAY DIFFRACTION71chain 'J' and (resid 111 through 116 )
72X-RAY DIFFRACTION72chain 'K' and (resid 1 through 10 )
73X-RAY DIFFRACTION73chain 'K' and (resid 11 through 24 )
74X-RAY DIFFRACTION74chain 'K' and (resid 25 through 35 )
75X-RAY DIFFRACTION75chain 'K' and (resid 36 through 68 )
76X-RAY DIFFRACTION76chain 'K' and (resid 69 through 90 )
77X-RAY DIFFRACTION77chain 'K' and (resid 91 through 116 )
78X-RAY DIFFRACTION78chain 'L' and (resid 1 through 10 )
79X-RAY DIFFRACTION79chain 'L' and (resid 11 through 47 )
80X-RAY DIFFRACTION80chain 'L' and (resid 48 through 79 )
81X-RAY DIFFRACTION81chain 'L' and (resid 80 through 110 )
82X-RAY DIFFRACTION82chain 'L' and (resid 111 through 116 )
83X-RAY DIFFRACTION83chain 'M' and (resid 273 through 278 )
84X-RAY DIFFRACTION84chain 'N' and (resid 273 through 278 )
85X-RAY DIFFRACTION85chain 'O' and (resid 273 through 279 )
86X-RAY DIFFRACTION86chain 'P' and (resid 273 through 279 )
87X-RAY DIFFRACTION87chain 'Q' and (resid 273 through 279 )
88X-RAY DIFFRACTION88chain 'R' and (resid 273 through 278 )
89X-RAY DIFFRACTION89chain 'S' and (resid 273 through 278 )
90X-RAY DIFFRACTION90chain 'T' and (resid 273 through 279 )
91X-RAY DIFFRACTION91chain 'U' and (resid 273 through 277 )
92X-RAY DIFFRACTION92chain 'V' and (resid 273 through 278 )
93X-RAY DIFFRACTION93chain 'X' and (resid 273 through 276 )

+
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