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- PDB-8afi: GABARAP in complex with LIR motif of HsATG3 -

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基本情報

登録情報
データベース: PDB / ID: 8afi
タイトルGABARAP in complex with LIR motif of HsATG3
要素
  • Gamma-aminobutyric acid receptor-associated protein
  • Ubiquitin-like-conjugating enzyme ATG3
キーワードSIGNALING PROTEIN / Autophagy / LIR / ATG3 / GABARAP
機能・相同性
機能・相同性情報


Atg12 transferase activity / Atg8-family conjugating enzyme activity / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / ubiquitin-like protein transferase activity / positive regulation of protein K48-linked ubiquitination / glycophagy / regulation of cilium assembly / regulation of Rac protein signal transduction / nucleophagy ...Atg12 transferase activity / Atg8-family conjugating enzyme activity / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / ubiquitin-like protein transferase activity / positive regulation of protein K48-linked ubiquitination / glycophagy / regulation of cilium assembly / regulation of Rac protein signal transduction / nucleophagy / mitochondrial fragmentation involved in apoptotic process / GABA receptor binding / autophagy of mitochondrion / phosphatidylethanolamine binding / phagophore assembly site / 転移酵素; アシル基を移すもの; アミノアシル基を移すもの / TBC/RABGAPs / cellular response to nitrogen starvation / protein targeting to membrane / microtubule associated complex / negative regulation of phagocytosis / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / beta-tubulin binding / protein targeting / mitophagy / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / protein ubiquitination / Golgi membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / enzyme binding / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
: / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
ACETATE ION / Ubiquitin-like-conjugating enzyme ATG3 / 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 / シンクロトロン / 分子置換 / 解像度: 2.66 Å
データ登録者Farnung, J. / Benoit, R.M. / Corn, J.E. / Bode, J.W.
資金援助 スイス, European Union, 3件
組織認可番号国
Swiss National Science Foundation188634 スイス
Swiss National Science Foundation310030_201160 スイス
European Research Council (ERC)856581European Union
引用ジャーナル: Acs Cent.Sci. / 年: 2023
タイトル: Semisynthetic LC3 Probes for Autophagy Pathways Reveal a Noncanonical LC3 Interacting Region Motif Crucial for the Enzymatic Activity of Human ATG3.
著者: Farnung, J. / Muhar, M. / Liang, J.R. / Tolmachova, K.A. / Benoit, R.M. / Corn, J.E. / Bode, J.W.
履歴
登録2022年7月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年5月10日Provider: repository / タイプ: Initial release
改定 1.12023年6月7日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Gamma-aminobutyric acid receptor-associated protein
F: Ubiquitin-like-conjugating enzyme ATG3
H: Ubiquitin-like-conjugating enzyme ATG3
B: Ubiquitin-like-conjugating enzyme ATG3
J: Ubiquitin-like-conjugating enzyme ATG3
N: Ubiquitin-like-conjugating enzyme ATG3
P: Ubiquitin-like-conjugating enzyme ATG3
D: Ubiquitin-like-conjugating enzyme ATG3
L: Ubiquitin-like-conjugating enzyme ATG3
E: Gamma-aminobutyric acid receptor-associated protein
G: Gamma-aminobutyric acid receptor-associated protein
I: Gamma-aminobutyric acid receptor-associated protein
K: Gamma-aminobutyric acid receptor-associated protein
M: Gamma-aminobutyric acid receptor-associated protein
O: 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)131,83825
ポリマ－131,07516
非ポリマー7639
水39622
1
A: Gamma-aminobutyric acid receptor-associated protein
B: Ubiquitin-like-conjugating enzyme ATG3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,5364
ポリマ－16,3842
非ポリマー1512
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-2 kcal/mol
Surface area7350 Å2
手法PISA
2
C: Gamma-aminobutyric acid receptor-associated protein
D: Ubiquitin-like-conjugating enzyme ATG3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)16,5364
ポリマ－16,3842
非ポリマー1512
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-2 kcal/mol
Surface area7300 Å2
手法PISA
3
F: Ubiquitin-like-conjugating enzyme ATG3
E: 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)16,4763
ポリマ－16,3842
非ポリマー921
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area7340 Å2
手法PISA
4
H: Ubiquitin-like-conjugating enzyme ATG3
G: 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)16,4763
ポリマ－16,3842
非ポリマー921
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-3 kcal/mol
Surface area7140 Å2
手法PISA
5
J: Ubiquitin-like-conjugating enzyme ATG3
I: 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)16,4763
ポリマ－16,3842
非ポリマー921
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5 kcal/mol
Surface area7390 Å2
手法PISA
6
N: Ubiquitin-like-conjugating enzyme ATG3
M: 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)16,4763
ポリマ－16,3842
非ポリマー921
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-3 kcal/mol
Surface area7040 Å2
手法PISA
7
P: Ubiquitin-like-conjugating enzyme ATG3
O: Gamma-aminobutyric acid receptor-associated protein


分子量 (理論値)分子数
合計 (水以外)16,3842
ポリマ－16,3842
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area7270 Å2
手法PISA
8
L: Ubiquitin-like-conjugating enzyme ATG3
K: 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)16,4763
ポリマ－16,3842
非ポリマー921
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-5 kcal/mol
Surface area7080 Å2
手法PISA
単位格子
Length a, b, c (Å)62.800, 63.800, 73.900
Angle α, β, γ (deg.)64.500, 86.500, 70.300
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
13
23
33

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHETYRTYR(chain 'A' and (resid 3 through 12 or (resid 13...AA3 - 1152 - 114
221PHEPHETYRTYR(chain 'C' and (resid 3 through 12 or (resid 13...CB3 - 1152 - 114
331PHEPHETYRTYR(chain 'E' and (resid 3 through 12 or (resid 13...EK3 - 1152 - 114
441PHEPHETYRTYR(chain 'G' and (resid 3 through 12 or (resid 13...GL3 - 1152 - 114
551PHEPHETYRTYR(chain 'I' and (resid 3 through 12 or (resid 13...IM3 - 1152 - 114
661PHEPHETYRTYR(chain 'K' and (resid 3 through 12 or (resid 13...KN3 - 1152 - 114
771PHEPHETYRTYR(chain 'M' and (resid 3 through 22 or (resid 23...MO3 - 1152 - 114
881PHEPHETYRTYR(chain 'O' and (resid 3 through 12 or (resid 13...OP3 - 1152 - 114
192ALAALATHRTHR(chain 'B' and resid 96 through 110)BE96 - 1107 - 21
2102ALAALATHRTHR(chain 'D' and resid 96 through 110)DI96 - 1107 - 21
3112ALAALATHRTHR(chain 'F' and resid 96 through 110)FC96 - 1107 - 21
4122ALAALATHRTHR(chain 'J' and resid 96 through 110)JF96 - 1107 - 21
5132ALAALATHRTHRchain 'L'LJ96 - 1107 - 21
1143ASPASPTHRTHR(chain 'H' and resid 104 through 110)HD104 - 11015 - 21
2153ASPASPTHRTHR(chain 'N' and resid 104 through 110)NG104 - 11015 - 21
3163ASPASPTHRTHRchain 'P'PH104 - 11015 - 21

NCSアンサンブル:
ID
1
2
3

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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: 13697.693 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: GABARAP, FLC3B, HT004 / プラスミド: pOPINS / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Rosetta-CodonPlus (DE3) RIL / 参照: UniProt: O95166
#2: タンパク質・ペプチド
Ubiquitin-like-conjugating enzyme ATG3


分子量: 2686.685 Da / 分子数: 8 / Mutation: N113G / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: C9JNW8
#3: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H3O2
#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C3H8O3
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 22 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: Sodium acetate, sodium cacodylate, PEG 8,000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2021年11月27日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.66→49.13 Å / Num. obs: 52724 / % possible obs: 98.14 % / 冗長度: 3.5 % / Biso Wilson estimate: 72.38 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.06833 / Rpim(I) all: 0.04274 / Rrim(I) all: 0.0809 / Net I/σ(I): 14.19
反射 シェル解像度: 2.66→2.75 Å / Rmerge(I) obs: 1.126 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2663 / CC1/2: 0.481 / CC star: 0.806 / Rpim(I) all: 0.7205

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
XDS1.16_3549データ削減
XSCALEデータスケーリング
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 6HB9

6hb9


解像度: 2.66→49.1 Å / SU ML: 0.4485 / 交差検証法: FREE R-VALUE / σ(F): 1.31 / 位相誤差: 30.8705
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2618 2637 5 %
Rwork0.2146 50087 -
obs0.217 52724 94.57 %
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: 90.52 Å2
精密化ステップサイクル: LAST / 解像度: 2.66→49.1 Å
タンパク質核酸リガンド溶媒全体
原子数8485 0 50 22 8557
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01158751
X-RAY DIFFRACTIONf_angle_d1.216511787
X-RAY DIFFRACTIONf_chiral_restr0.0681204
X-RAY DIFFRACTIONf_plane_restr0.00891527
X-RAY DIFFRACTIONf_dihedral_angle_d11.38985204
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.710.38461320.38462434X-RAY DIFFRACTION88.48
2.71-2.760.39591400.36712687X-RAY DIFFRACTION95.57
2.76-2.820.40441350.3622628X-RAY DIFFRACTION95.67
2.82-2.880.35241400.33542673X-RAY DIFFRACTION95.75
2.88-2.940.33391460.31672718X-RAY DIFFRACTION95.59
2.94-3.020.3191390.30812608X-RAY DIFFRACTION95.38
3.02-3.10.31911390.2832654X-RAY DIFFRACTION95.98
3.1-3.190.34191430.25932736X-RAY DIFFRACTION95.78
3.19-3.290.2891360.25882609X-RAY DIFFRACTION95.18
3.29-3.410.2891410.24132682X-RAY DIFFRACTION95.44
3.41-3.550.27481420.23962682X-RAY DIFFRACTION95.15
3.55-3.710.2471390.22832685X-RAY DIFFRACTION95.66
3.71-3.90.25781400.21112594X-RAY DIFFRACTION93.82
3.9-4.150.24711400.19592613X-RAY DIFFRACTION94.22
4.15-4.470.22231360.17112602X-RAY DIFFRACTION93.96
4.47-4.920.18961350.15312638X-RAY DIFFRACTION92.62
4.92-5.630.28471380.19512548X-RAY DIFFRACTION93.07
5.63-7.090.24331400.19932692X-RAY DIFFRACTION95.61
7.09-49.10.23291360.17622604X-RAY DIFFRACTION93.84
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)
19.085887801061.20029248541-3.143693489227.28417443575-1.614611162874.85038312819-0.1000851420680.1187576066690.445677730893-1.56554684062-0.124211257254-0.4315391850430.2896113468130.1879206970610.01895234495551.040815438220.02100741055640.06084230941730.995312016834-0.1133091568360.56435595958928.41912389410.0163963286348-46.5281315087
25.646487377440.7248626261280.9392634393887.769709706690.7154181800919.284065164480.171237432998-0.251860300195-0.3943990427770.0340366884708-0.0492153067417-0.2254975717771.10443447838-0.207234124073-0.1645207444030.328783954611-0.005213965728850.033861763120.5429601311330.03195559469480.41098884637526.31823643331.34894016452-30.5008743772
35.86955293446.356348335515.650177813137.635467758596.26216419315.48365777042-1.58989691519-1.046189576831.33874135858-2.25601949241.39255628512.55734653353-1.97215633747-1.594803523690.6279743960921.08526107372-0.0669479012364-0.2563312689091.641416925150.157276656110.78772342485824.352574691121.9304961619-48.5403616006
47.93008090541-0.857066966730.1408695240456.789493617732.899420375075.27827501811-0.313830131861.94673054251.0820995704-1.849871158070.455222638842-0.3128890412720.7354545289820.2293637930260.03475011302751.12823881801-0.07611821293360.2112785387891.340970374590.02740400640170.60391652051434.115808423815.3198476861-55.0246477461
52.977310844272.084686342943.378708153669.276126618121.810515894796.49234343765-0.3521401421311.5401484152-1.48418731728-0.5199425488330.0751131923846-0.454692754892-0.08766849531131.14300836995-0.2400345064430.676077977585-0.1007002539660.03183628762851.067077814270.1343796750460.53967791461938.979963847123.1227336119-47.8481703732
63.223722043932.82797637568-3.715049505859.26853880743-6.048708264546.695430170321.117560159861.074342354432.06269488227-0.4100098734131.269153929390.5241285038111.3889614019-0.161009799687-1.662297798521.158920421550.101424934507-0.06593647882261.50939214158-0.001651845469381.1969358535728.260427787233.141801898-40.6754141104
77.884292116141.748289338094.383322162229.192096184373.629123027664.956847082970.2633029264750.2383839445450.227223535593-0.486706900071-0.033911451801-1.63726655584-0.8076001022891.102386183150.07832944059210.757718827196-0.269481677960.1159461404671.263488366720.1875043420010.82913898711742.219895394229.683121139-41.5878733002
85.520833314880.1190156236682.583036264866.915949673822.917839771447.572036682770.02507636097010.2287300328880.1783989337570.734946664801-0.277236645706-0.4877584535180.2348468007110.3141068575020.1944360095320.678843856506-0.02297343123180.06493323968110.6574601171670.1603152044280.52053499618935.668044923223.6405765295-36.8237849353
91.76096933763-0.0738685835653-0.1379647969441.743611844841.28321386158.401119843663.33597391221.01611508781-0.811893439904-1.93513294198-0.8918152509550.0147058797329-1.68529620567-0.589227766482-1.91696157831.748673468120.067771050157-0.1911293283561.48525347070.1479151011831.43790316771-1.1228719964523.2392549309-40.6944727936
107.35317959685-0.815235336956-2.183431539444.886347582894.886022339135.157144021091.08530387571-0.440705991334-0.2506920440171.611559971840.669498202604-0.559086758173-1.32529300341.68994943144-1.566503785981.45244535961-0.09241773343140.07418693405640.8375643934850.1057436120361.1333947342.771942404719.9392386267-32.0762961293
117.78670145166-3.99713523239-2.598003865525.958094044720.865157434336.86605717005-0.6428695970840.194745007464-0.561662898250.4249938385430.9649299314490.634474903749-0.479568517748-0.386049726278-0.0267358858020.9933881621350.1087813238460.2975552193981.225732891950.1126329931631.1451838991423.97460728117.05266664846.23632988199
124.414372560791.697396925062.191073354313.81819334857-0.4335770160821.56794037811-0.1894150717470.89174720725-1.41999815248-1.16292788316-1.73135877336-0.8253712230980.782395846841-0.7300918042521.439345541611.935556681020.1854417124870.1213055875910.963189739891-0.1413959083881.3984505400926.0069518921-13.3847368079-41.7072260402
139.49543133284-1.82099957838-9.10121594124.492835618482.692881914628.96602822593-3.348177695731.083435180990.00738250850672-0.5301032390890.0751558549338-0.3700836042570.377285073559-1.814975609891.216596409891.17150538152-0.220417825435-0.3198127027190.956208235470.1830510914110.95454734106923.3538444805-9.49077921707-37.5357681597
148.074898117470.1991438009980.9050839186125.41657000374-4.349973183634.495514596290.604659511326-0.331691621264-1.282523541542.23307462684-0.728624154053-1.745811107242.62033618376-0.542168948184-1.097788806192.11170805523-0.3604487302740.03638003146231.75447514688-0.4679888983791.10897362709-6.164665425316.1159538555715.6423045914
155.538405218691.48120218837-2.627191832262.251173026970.5727225502932.10840494226-0.0904737271769-1.47671553092-0.5897406507882.39478905056-0.423878619168-0.3237907161740.107265638737-2.06312789028-0.006310416938491.00236139674-0.282690873351-0.5899958063322.17428154464-0.405004094458-0.0498182003642-6.688829106475.199804653710.0268713245
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175.147425131423.02254268064-4.162116136383.31686903349-1.584830340044.31712080733-0.776220943783-0.223202675119-0.912239727985-0.0609561070364-0.891658721989-0.2882316913591.14175933717-0.5625805284422.01725185041.54553646069-0.2334263454560.2009215488551.52211575067-0.1464819569721.2687295740142.269078072742.88080638-7.11701400113
186.515211710942.66780013832-5.296659146654.30436639437-0.195852796326.61740038099-0.2118434902230.6702627457461.00346941906-1.598465676520.9567051377642.04395351014-0.443280385796-0.1607198487490.3088355099141.69717601174-0.3140309540050.1812686211041.754704835310.3728636348750.99133890008337.091233803629.8448181189-56.4837201308
197.027688187591.307857977994.664023527927.260203629051.641006358633.17450556062-0.7315378131111.07710601265-0.739539057372-1.455953645591.04799450779-1.459685921540.3933152838241.823020028522.005243552551.05763835369-0.2521499676280.07532285178651.433691287450.1326076583410.96552978835942.955794803929.5515351381-50.6513496771
202.569873768580.741654466280.4071303018881.87298127318-1.24688126541.226719172190.426234356719-0.7293661224451.646379534481.335338879550.4132617336121.098022685160.7381635031490.0801089166141-1.539044252961.32858400874-0.1570731639170.1550890633961.497034725260.1779814711531.576475255-2.3914675872128.3566746435-2.49613118347
214.552098976891.90040927898-0.5347309499787.79666069375-0.7960260747926.1628288386-0.3778407029571.195188547030.212919510857-1.564549577350.3680291860460.2253550177590.0369109979152-0.3562524029060.1080108308490.879058312780.0316252531705-0.1105557065050.9367308458130.151844176690.615939705696-0.46343805252810.8752576616-40.8478058866
225.46237905401-0.0827091572035-4.603953912817.64346782022-1.073899559414.74896904079-0.08288369955810.9783776232891.09371799503-0.4373431257110.3022465922110.749670934246-0.709272147192-0.628305742906-0.09214415361620.635069465633-0.0182599253264-0.07277347190640.737378486012-0.04567865188120.676161385714-3.778522721713.7863755352-25.8420026451
238.107334048221.00766556193-1.582308706837.11145971095-1.204139207856.6611011034-0.2860817373650.387759405236-0.04754050729-0.083747073291-0.03549847656640.390768936203-0.196114187751-0.4257143290920.2510276952060.318197541276-0.04259394191-0.07775376560320.551307807483-0.05366021683610.440486849523-2.771480509155.79793584784-26.7674892696
243.970003227910.585054996174-2.145337959558.843535694751.534689645656.67891336389-0.161861058607-0.9378706910530.1120083954791.697071544090.1959578717840.584184664771-1.69721057269-0.6611555126060.05765516460321.092376093780.1605508237340.1687900327651.39879970473-0.03067921638170.51025371617326.763894634317.03563136894.95300464631
253.789603549652.072060848192.021221284215.458982113661.728382097481.1666366486-0.309216249414-1.47378494107-1.334021428840.999491765276-0.3688296017281.85600915349-0.141284775281-2.148332390730.3651545852520.7298187826260.146200768830.01075271582492.22886032761-0.09810166288031.0413448144215.274567346310.1680534818-7.20225448413
267.38661135435-0.2813602385990.01055489546177.48409794240.7258939028035.75445581363-0.06603638101060.0301677179766-0.5141055872530.348503968517-0.08522347474350.0892720971231-0.217377958-0.177842952360.2758929302110.5199558880410.01987193462250.05537788108840.9963404456290.008628372213450.34399171343827.69105552348.9290789451-7.50753490677
271.884115603882.784126398822.187840720745.77557004260.7209126328286.79013120540.604697719384-1.54436121356-0.5440959059440.804931442033-0.939638958236-0.2711371740951.576337742820.7135608664720.3931835826361.134959522060.174682184164-0.0624411378141.645983116940.2357236458550.570585550474-7.94235876983-7.115874348569.33912015771
281.27005460581.248094690461.615118887865.89912405347-2.569754257386.262008834920.0551291310242-1.492009172470.6043506281010.56687565673-0.200188885311-0.767876401462-0.66639041961.7314440281-0.1361318812110.776531108018-0.0429742805131-0.1860950638791.24908408165-0.07857253581020.513394609922-3.020960507072.319648714511.0845407423
297.03923139865-0.819106832614-1.553620272076.636492126870.07141050183483.219078722960.721607782769-1.092539585691.097871834061.00704423161-0.3070326441960.093403579815-0.9313868470070.355337729782-0.2325317540910.6656540638-0.08718985674890.050879101370.969138122483-0.1879559766290.552517092699-8.679200033699.21252109858-1.4247728136
306.31681353932-1.64410671882-0.2147195251196.83589710745-0.7682188788558.907439196310.137807096345-0.3608876724030.2293626051390.395909787859-0.106546858071-0.1212994525590.04198920321080.227001219188-0.1424803620930.477194217811-0.0271787101207-0.09947788032050.865826525203-0.06659613183340.335557597944-7.041926588430.617036155055-6.18806279422
314.865752185322.817161748042.525685925769.82284599154-3.50094791554.55749716482-1.31753896703-1.006934897491.114638417290.6452485958671.344190440591.301789108260.162920427708-2.260041899970.6514639617710.9406408233820.06127521053510.3776278476481.480730497290.003021289178631.15580802943-1.1544411212244.5986910662-0.664568911159
325.133916102680.1010192114832.534073784335.18886681254-1.757842790458.372545869850.211077948975-1.28250118263-1.272928798211.048269521250.3830338820790.6526924937240.539175930833-0.685682751255-0.1675376488560.806776344998-0.01602925962490.2065847977010.9901179687760.221763207170.9218974829134.05735794834.8616637579-4.3349513557
331.059066891970.08743202567961.275615809588.03953775843-1.432244197051.870046540850.7176067428040.851194294902-1.87588945788-0.957781837571-0.626620716287-0.7491675629181.52897750542-1.35821032265-0.2326238989431.19863317732-0.172750254950.3072918549411.00781208921-0.2351503597481.173293965754.3903934369632.7892725285-18.8356636734
348.84510002791-0.717338658969-1.935449832317.29612396934-2.618449849366.47072012304-0.4439524150810.119607904552-0.5997163610910.376133071720.189734560136-0.1028940499410.4713552915060.3267067564750.06645282251310.6624642814570.08059642681780.161346626510.764285149338-0.04948357559980.6992631502498.3390311689441.0375993641-13.1668266697
351.531411744451.29960418107-3.505005690124.00814376623-3.960375706678.52232880984-0.411275690866-1.14173783272-0.308474236403-1.43758065127-0.084040041346-2.088936661261.555982760771.066605709330.6051966589410.889755994396-0.2561157238390.1277426479831.49340920931-0.04903639428831.0064956258324.99152473148.4158034747-43.9270879537
361.56733091322-1.520330364151.819118252025.01440016096-0.4729872311073.602239734130.7436350732871.64991412666-0.505290028286-1.55583451881-0.3297880238640.00980425618092-2.14532834235-0.3204820453120.2634564835771.2572019645-0.25190582354-0.07137260639171.72074138968-0.1821151910340.67380666180215.852240855354.2820426606-52.3499265722
373.872153091083.56404588038-1.578639029686.456536841091.306556804013.05871465538-0.9101436222422.179718013321.16994709392-0.580701203899-0.1209215951020.9076748171990.0356003752659-0.7420031909220.08955632390660.736941411075-0.280490229130.08136749411161.62351657244-0.336831340140.59328775067510.579717644746.4021389765-45.7664233076
387.22430508462-1.837263731452.622676911177.01066054816-1.213623030817.90759987507-0.3411198169120.617206773323-1.05255681386-0.6940614320930.2657473163290.06768944210840.3894164494820.9783187212380.2507919357930.717736867745-0.154743008246-0.002917925115651.21959393913-0.2630692098190.82727829674413.704128233440.5634869817-39.6464915669
399.00223132407-3.587479456281.895023258726.13873997789-1.605897627184.90585302453-0.175319217775-1.18175178239-1.509435094230.0981058631020.2313121397471.561735441941.35123158719-1.07074531872-0.1079954322430.884408032414-0.468880054020.2210698749871.14038401083-0.4163776328541.064119943726.0325220540437.798831967-36.5340476883
409.23275088720.871873704272-2.176552317335.7576458606-1.909522645727.42397740688-0.6292668060040.176189835243-1.18281417310.19952895230.2551135489040.3896469652080.594302485650.09345865300690.3117536832780.528192728605-0.111868582070.1808543453290.66153125407-0.2101915167760.6747262657839.9375781616941.5128749729-30.6580013325
416.381072391612.4538735361-1.913438057327.05130250382-4.552074461925.33082591778-0.123651120630.902246684485-0.1213546185370.04937474490560.0280066057450.283221302586-0.435337249424-0.4729074873610.004579100603680.802876169806-0.1697038721650.06846376189731.07054571253-0.3397662584050.5922077367613.002466322650.5707425506-37.4668548153
422.133669105651.24897045903-1.592721471511.26262691529-1.071055187627.84343303341-0.0350784298964-0.255478497388-0.04175555775872.313640106980.0206666665508-0.4796733316420.139234880869-0.372081398602-0.01510096167881.74859773076-0.049064642068-0.3542572944381.29513541281-0.1384968053720.91035648928136.829749470435.8530987602-1.98127451162
438.85145909486-0.458286024723-0.8840265296219.003548418592.533581851059.93334555130.263087737079-0.483367850470.6206794035610.3734635344440.172803380974-0.391100614306-0.93660581280.404012317016-0.3592204844911.340591439070.0123523534414-0.1100498595240.8045025603120.001559242777340.55698418239937.841315918532.7627194581-16.3894167969
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 116 )
3X-RAY DIFFRACTION3chain 'C' and (resid 3 through 10 )
4X-RAY DIFFRACTION4chain 'C' and (resid 11 through 24 )
5X-RAY DIFFRACTION5chain 'C' and (resid 25 through 35 )
6X-RAY DIFFRACTION6chain 'C' and (resid 36 through 47 )
7X-RAY DIFFRACTION7chain 'C' and (resid 48 through 68 )
8X-RAY DIFFRACTION8chain 'C' and (resid 69 through 116 )
9X-RAY DIFFRACTION9chain 'F' and (resid 96 through 105 )
10X-RAY DIFFRACTION10chain 'F' and (resid 106 through 111 )
11X-RAY DIFFRACTION11chain 'H' and (resid 104 through 111 )
12X-RAY DIFFRACTION12chain 'B' and (resid 95 through 104 )
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 110 )
14X-RAY DIFFRACTION14chain 'J' and (resid 95 through 102 )
15X-RAY DIFFRACTION15chain 'J' and (resid 103 through 111 )
16X-RAY DIFFRACTION16chain 'N' and (resid 103 through 111 )
17X-RAY DIFFRACTION17chain 'P' and (resid 104 through 110 )
18X-RAY DIFFRACTION18chain 'D' and (resid 93 through 107 )
19X-RAY DIFFRACTION19chain 'D' and (resid 108 through 110 )
20X-RAY DIFFRACTION20chain 'L' and (resid 96 through 110 )
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 35 )
22X-RAY DIFFRACTION22chain 'E' and (resid 36 through 67 )
23X-RAY DIFFRACTION23chain 'E' and (resid 68 through 116 )
24X-RAY DIFFRACTION24chain 'G' and (resid 3 through 35 )
25X-RAY DIFFRACTION25chain 'G' and (resid 36 through 47 )
26X-RAY DIFFRACTION26chain 'G' and (resid 48 through 116 )
27X-RAY DIFFRACTION27chain 'I' and (resid 2 through 24 )
28X-RAY DIFFRACTION28chain 'I' and (resid 25 through 47 )
29X-RAY DIFFRACTION29chain 'I' and (resid 48 through 67 )
30X-RAY DIFFRACTION30chain 'I' and (resid 68 through 116 )
31X-RAY DIFFRACTION31chain 'K' and (resid 2 through 10 )
32X-RAY DIFFRACTION32chain 'K' and (resid 11 through 56 )
33X-RAY DIFFRACTION33chain 'K' and (resid 57 through 67 )
34X-RAY DIFFRACTION34chain 'K' and (resid 68 through 116 )
35X-RAY DIFFRACTION35chain 'M' and (resid 3 through 10 )
36X-RAY DIFFRACTION36chain 'M' and (resid 11 through 24 )
37X-RAY DIFFRACTION37chain 'M' and (resid 25 through 35 )
38X-RAY DIFFRACTION38chain 'M' and (resid 36 through 56 )
39X-RAY DIFFRACTION39chain 'M' and (resid 57 through 67 )
40X-RAY DIFFRACTION40chain 'M' and (resid 68 through 90 )
41X-RAY DIFFRACTION41chain 'M' and (resid 91 through 115 )
42X-RAY DIFFRACTION42chain 'O' and (resid 2 through 35 )
43X-RAY DIFFRACTION43chain 'O' and (resid 36 through 116 )

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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