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- PDB-4naw: Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fr... -

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基本情報

登録情報
データベース: PDB / ID: 4naw
タイトルCrystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3
要素
  • Autophagy protein 5
  • Autophagy-related protein 16-1
  • Ubiquitin-like protein ATG12
  • Ubiquitin-like-conjugating enzyme ATG3
キーワードPROTEIN TRANSPORT/LIGASE / protein-protein conjugate / ubiquitin-like protein / autophagy / E3 ligase / PROTEIN TRANSPORT-LIGASE complex
機能・相同性
機能・相同性情報


Atg12 transferase activity / Atg8-family conjugating enzyme activity / otolith development / regulation of autophagosome maturation / positive regulation of viral translation / response to fluoride / C-terminal protein lipidation / regulation of cytokine production involved in immune response / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex ...Atg12 transferase activity / Atg8-family conjugating enzyme activity / otolith development / regulation of autophagosome maturation / positive regulation of viral translation / response to fluoride / C-terminal protein lipidation / regulation of cytokine production involved in immune response / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / negative regulation of dendrite extension / vacuole-isolation membrane contact site / phagophore / negative regulation of autophagic cell death / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / cellular response to nitrosative stress / ventricular cardiac muscle cell development / microautophagy / positive regulation of stress granule assembly / glycophagy / regulation of cilium assembly / transferase complex / aggrephagy / dendrite arborization / mitochondrial fragmentation involved in apoptotic process / mucus secretion / mitochondria-associated endoplasmic reticulum membrane contact site / nucleophagy / response to fungus / xenophagy / corpus callosum development / protein localization to phagophore assembly site / negative thymic T cell selection / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / negative stranded viral RNA replication / regulation of release of sequestered calcium ion into cytosol / endolysosome membrane / 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 / protein targeting to membrane / cellular response to nitrogen starvation / response to iron(II) ion / positive regulation of mucus secretion / regulation of reactive oxygen species metabolic process / negative regulation of cardiac muscle cell apoptotic process / negative regulation of phagocytosis / axonal transport / negative regulation of type I interferon production / Receptor Mediated Mitophagy / Macroautophagy / chaperone-mediated autophagy / heart contraction / autophagosome membrane / axoneme / autophagosome assembly / blood vessel remodeling / autophagosome maturation / regulation of postsynaptic membrane neurotransmitter receptor levels / postsynaptic modulation of chemical synaptic transmission / mitophagy / protein-membrane adaptor activity / positive regulation of autophagy / cardiac muscle cell apoptotic process / sperm midpiece / negative regulation of protein ubiquitination / post-translational protein modification / autophagosome / negative regulation of innate immune response / hippocampus development / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / macroautophagy / Schaffer collateral - CA1 synapse / autophagy / protein tag activity / phagocytic vesicle membrane / vasodilation / protein transport / chromatin organization / GTPase binding / defense response to virus / postsynapse / protein ubiquitination / response to xenobiotic stimulus / axon / innate immune response / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / protein-containing complex / nucleoplasm / identical protein binding / membrane / cytosol / cytoplasm
類似検索 - 分子機能
Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / : / : / : ...Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / : / : / : / Autophagy protein ATG5, UblB domain / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Ubiquitin-like protein ATG12 / Autophagy-related protein 16-1 / Autophagy protein 5 / Ubiquitin-like-conjugating enzyme ATG3
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: 2.195 Å
データ登録者Metlagel, Z. / Otomo, C. / Takaesu, G. / Otomo, T.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2013
タイトル: Structural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12.
著者: Metlagel, Z. / Otomo, C. / Takaesu, G. / Otomo, T.
履歴
登録2013年10月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年11月6日Provider: repository / タイプ: Initial release
改定 1.12013年11月27日Group: Database references
改定 1.22013年12月18日Group: Database references
改定 1.32017年11月15日Group: Refinement description / カテゴリ: software
改定 1.42024年10月30日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: Ubiquitin-like protein ATG12
B: Autophagy protein 5
C: Autophagy-related protein 16-1
D: Ubiquitin-like-conjugating enzyme ATG3
E: Ubiquitin-like protein ATG12
F: Autophagy protein 5
G: Autophagy-related protein 16-1
H: Ubiquitin-like-conjugating enzyme ATG3
I: Ubiquitin-like protein ATG12
J: Autophagy protein 5
K: Autophagy-related protein 16-1
L: Ubiquitin-like-conjugating enzyme ATG3
M: Ubiquitin-like protein ATG12
N: Autophagy protein 5
O: Autophagy-related protein 16-1
P: Ubiquitin-like-conjugating enzyme ATG3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,15531
ポリマ－205,00616
非ポリマー1,14915
水10,755597
1
A: Ubiquitin-like protein ATG12
B: Autophagy protein 5
C: Autophagy-related protein 16-1
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)51,4677
ポリマ－51,2514
非ポリマー2153
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-50 kcal/mol
Surface area28620 Å2
2
E: Ubiquitin-like protein ATG12
F: Autophagy protein 5
G: Autophagy-related protein 16-1
H: Ubiquitin-like-conjugating enzyme ATG3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,4677
ポリマ－51,2514
非ポリマー2153
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
I: Ubiquitin-like protein ATG12
J: Autophagy protein 5
K: Autophagy-related protein 16-1
L: Ubiquitin-like-conjugating enzyme ATG3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,6599
ポリマ－51,2514
非ポリマー4075
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
4
M: Ubiquitin-like protein ATG12
N: Autophagy protein 5
O: Autophagy-related protein 16-1
P: Ubiquitin-like-conjugating enzyme ATG3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,5638
ポリマ－51,2514
非ポリマー3114
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)93.584, 120.097, 189.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 2種, 8分子 AEIMBFJN

#1: タンパク質
Ubiquitin-like protein ATG12 / Autophagy-related protein 12 / APG12-like


分子量: 10282.029 Da / 分子数: 4 / 断片: UNP residues 52-140 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APG12, APG12L, ATG12 / プラスミド: pACYC Duet-1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: O94817
#2: タンパク質
Autophagy protein 5 / APG5-like / Apoptosis-specific protein


分子量: 32489.195 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: APG5L, ASP, ATG5 / プラスミド: pACYC Duet-1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9H1Y0

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タンパク質・ペプチド , 2種, 8分子 CGKODHLP

#3: タンパク質・ペプチド
Autophagy-related protein 16-1 / APG16-like 1


分子量: 4657.435 Da / 分子数: 4 / 断片: UNP residues 11-43 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APG16L, ATG16L1, UNQ9393/PRO34307 / プラスミド: pET / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q676U5
#4: タンパク質・ペプチド
Ubiquitin-like-conjugating enzyme ATG3 / Autophagy-related protein 3 / APG3-like / hApg3 / Protein PC3-96


分子量: 3822.822 Da / 分子数: 4 / 断片: UNP residues 140-170 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APG3, APG3L, ATG3 / プラスミド: pET / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: Q9NT62, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ（ペプチド合成）

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非ポリマー , 3種, 612分子

#5: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 11 / 由来タイプ: 合成 / 式: SO4
#6: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Na
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 597 / 由来タイプ: 天然 / 式: H2O

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詳細

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: 2.6 Å3/Da / 溶媒含有率: 52.63 %
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: 7.5
詳細: PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K

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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: ALS / ビームライン: 8.2.1 / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2010年1月1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: 2.195→50 Å / Num. obs: 109340 / % possible obs: 99.9 % / 冗長度: 7 % / Rmerge(I) obs: 0.091 / Χ2: 0.99 / Net I/σ(I): 11.2
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.195-2.2850.859107480.983199.4
2.28-2.376.70.663107930.9461100
2.37-2.487.20.515108400.9681100
2.48-2.617.30.349108590.9821100
2.61-2.777.40.247108391.0081100
2.77-2.997.40.164108830.9871100
2.99-3.297.40.099109190.9911100
3.29-3.767.30.074109780.9631100
3.76-4.747.20.065110481.0391100
4.74-5070.037114331.031100

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
PHENIX1.8.2_1309精密化
PDB_EXTRACT3.11データ抽出
HKL-2000データ収集
HKL-2000データ削減
HKL-2000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 / 解像度: 2.195→48.832 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8544 / SU ML: 0.23 / σ(F): 1.34 / 位相誤差: 21.59 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2153 2000 1.83 %RANDOM
Rwork0.1715 ---
obs0.1723 109211 99.6 %-
all-109211 --
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 max: 170.46 Å2 / Biso mean: 66.975 Å2 / Biso min: 25.38 Å2
精密化ステップサイクル: LAST / 解像度: 2.195→48.832 Å
タンパク質核酸リガンド溶媒全体
原子数13277 0 59 597 13933
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00613680
X-RAY DIFFRACTIONf_angle_d0.7618485
X-RAY DIFFRACTIONf_chiral_restr0.0461962
X-RAY DIFFRACTIONf_plane_restr0.0042334
X-RAY DIFFRACTIONf_dihedral_angle_d11.8915163
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.195-2.24960.30831340.25777214734895
2.2496-2.31040.25721420.22276017743100
2.3104-2.37840.24751420.204275767718100
2.3784-2.45520.25411420.201976627804100
2.4552-2.54290.26321420.18675767718100
2.5429-2.64470.25271430.181976237766100
2.6447-2.76510.20551420.179676397781100
2.7651-2.91090.24061420.183576497791100
2.9109-3.09320.23461430.189176587801100
3.0932-3.3320.20671440.178377037847100
3.332-3.66720.22441430.169176737816100
3.6672-4.19760.17721440.153777507894100
4.1976-5.28750.18051470.135478197966100
5.2875-48.84380.21371500.17180688218100
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)
14.048-2.73030.45472.13761.02075.399-0.169-0.21911.218-0.3353-0.2897-0.2479-0.86010.33120.09271.0203-0.04620.0110.3916-0.12181.03750.424215.80723.2564
23.70571.3425-1.57044.90961.59143.2041-0.6235-0.3521.13320.15050.18481.1991-1.1616-0.60730.32880.83110.0886-0.03770.3618-0.11970.95-7.505410.905624.446
32.8818-0.0945-1.5082.3342-1.33522.5048-0.09140.18070.2575-0.31940.03860.0629-0.70510.0024-0.02440.7984-0.10470.0120.385-0.04160.7503-1.94756.351317.1724
48.7206-1.0397-0.72855.7427-4.38363.6874-0.17910.03041.1197-0.0377-0.0793-0.677-0.55450.32990.25520.7935-0.07380.03630.3849-0.09060.65793.7146.773924.4482
57.57070.20782.84913.2218-0.75283.28430.14420.0913-0.23040.02590.19220.16430.07720.0031-0.30760.27660.00360.07810.2593-0.02410.2239-8.4101-23.494113.4596
62.77820.64590.5861.4816-0.09251.2787-0.049-0.00780.31890.02320.14980.1265-0.2296-0.0403-0.10110.31270.00430.07630.27450.01550.3393-10.6691-13.296114.2609
74.1580.94111.72223.3211.69518.0021-0.19760.29240.14510.03610.2514-0.3655-0.43140.8544-0.05430.2756-0.05630.04010.4281-0.04960.386914.0313-12.217518.5034
82.4263-0.32041.90242.94790.3123.65950.0507-0.70090.22050.57920.05380.1384-0.1485-0.2554-0.09440.3971-0.02870.04490.4184-0.08020.26511.3449-15.831934.8312
92.83744.91912.93088.98645.04413.01480.8694-0.2415-1.15050.76240.1204-0.56030.60870.1991-1.0850.4442-0.0071-0.02480.46320.05580.4363.6809-32.401830.3322
107.7771.82555.0085.80111.36883.5442-0.2250.46-0.1337-0.36040.2256-0.88890.1220.5381-0.06280.3459-0.03250.03550.360.0070.4097-9.5236-35.59929.7966
119.98342.50475.04435.88372.40339.10.5543-0.01580.05330.809-0.45350.58950.7487-0.3642-0.03770.96420.03960.0670.5761-0.09481.3831-11.416318.604928.8676
127.4731-2.56492.81345.9223-0.82596.7721-0.1417-0.0262-1.21440.2473-0.00980.14771.30060.01540.20890.89530.03010.09190.33430.10630.9062-22.055-87.72531.2801
134.01562.1062-0.80444.3576-1.58090.6281-0.2715-0.0537-0.8804-0.32020.039-0.53461.18740.6070.15040.89150.17960.04260.39580.08940.7138-14.7734-83.264827.5252
146.9823-3.9182-2.75274.26515.3958.27260.51221.1032-0.5218-1.65450.0983-0.1984-0.36560.1247-0.40951.1573-0.0669-0.02190.5664-0.02030.8863-24.0984-83.020919.6762
152.45-0.0153-2.78342.76331.53654.40270.0113-0.53410.58970.41970.16140.27870.2640.0245-0.07610.59680.0293-0.06510.3930.10810.5769-22.3448-73.20730.9133
168.9333-1.05140.41872.2344-3.57538.0488-0.2469-1.257-0.8661.3643-0.0233-0.33881.05420.09710.14350.90080.0705-0.06810.51550.18810.5868-18.262-76.833240.1631
179.77031.90250.34436.04112.55663.3677-0.20820.5702-0.7585-0.07210.24051.24660.4571-0.02150.03140.7961-0.0767-0.03770.47380.10310.873-28.5723-80.196228.2147
183.63070.2749-2.3623.9776-0.19855.9366-0.04920.190.0748-0.28840.2722-0.1017-0.08-0.0662-0.15550.286-0.0119-0.09290.2960.06170.3259-18.7848-49.240917.022
193.89781.47710.12854.1067-0.60094.3826-0.23440.3516-0.2715-0.71010.3017-0.29070.41890.0787-0.0770.3888-0.0101-0.00960.28350.00880.3448-13.8641-57.630913.5275
201.60850.7985-1.86030.7078-0.21399.5278-0.0586-0.1633-0.18750.1111-0.08030.08740.482-0.27350.21110.4666-0.0206-0.09580.38610.11760.4661-28.0795-64.878829.7896
217.9326-0.09353.48452.8776-1.7027.92790.1901-0.2607-0.2095-0.21840.58571.03450.6223-1.2741-0.83010.3669-0.0162-0.11370.39690.10510.6201-36.6599-62.742730.2477
227.3097-0.3790.83187.81170.1815.8671-0.1233-0.13880.13820.07220.67581.1607-0.2692-1.0477-0.60080.24030.0402-0.00670.40550.17620.5531-34.8692-52.868931.4802
232.4254-3.7416-3.51497.25323.68978.2369-0.0331-0.5689-0.41281.224-0.28730.49590.7038-0.80680.16030.6042-0.06320.02820.70130.06260.394-29.3709-60.89947.7613
242.57460.5854-1.27583.1392-1.29538.6752-0.0012-0.2976-0.18050.3701-0.1376-0.4060.26320.64370.09730.45590.0813-0.13080.46220.11310.4315-13.7805-61.137743.272
252.2019-0.4233-1.38634.3594-0.04994.11660.1658-0.7064-0.120.6522-0.1472-1.0271-0.03550.8538-0.00880.523-0.0084-0.19880.6030.05590.5252-9.585-50.807740.732
262.4027-0.8948-1.50343.8097-0.34523.739-0.0281-0.29310.04790.29820.0825-0.0456-0.39510.223-0.01380.42280.014-0.06270.38650.06990.3546-18.4515-53.855637.042
274.91271.4935-2.54738.2175-4.86253.54090.2421-0.60270.28151.1631-0.12060.1458-1.404-0.0133-0.14850.51050.016-0.04420.4095-0.0440.3705-18.1874-39.528338.0695
285.5736-1.7385-0.54344.72191.14412.0662-0.51420.48410.1593-0.03550.21380.62130.3352-0.63650.33090.3971-0.0843-0.00470.45910.06020.4263-20.1975-37.320413.1932
296.807-4.8922-2.23968.71017.02467.9142-0.6315-0.2066-0.06460.08650.2883-0.361-0.24350.3230.43451.31840.11780.04820.57270.09661.166-9.0436-90.682727.402
308.5690.0631-1.38326.27310.81194.4226-0.1817-0.77680.12390.69260.3374-0.1549-1.03060.1102-0.22591.12460.21510.01340.518-0.08960.7788-48.90655.085332.8416
312.4611-0.68021.80227.66980.57593.9593-0.2172-0.15810.80440.45650.1022-0.2229-1.1592-0.08150.08011.00550.160.05010.4377-0.04580.6275-45.64995.700524.6612
325.3553-3.20711.71278.2623-5.49233.68070.09120.63920.2705-0.9360.0328-0.90410.31080.46060.10151.0291-0.0321-0.00650.5605-0.02490.7734-38.47012.911318.5622
338.7122-1.11921.7296.06482.24042.062-0.2275-0.5415-0.32680.82290.469-0.1851-0.28110.293-0.21490.70410.1180.03510.4606-0.05760.4304-42.6519-6.582529.3551
346.1677-1.9251-1.19953.30923.70064.39-0.6893-1.24890.62231.92630.0670.7378-0.7138-0.81830.52411.20440.36180.14890.8371-0.11840.5976-48.8839-2.873637.3455
358.91443.01991.43437.5113-0.89363.0629-0.7558-0.09151.070.41390.6456-1.2661-0.86310.2210.06470.85920.1028-0.10250.529-0.05660.6359-36.05030.324627.9701
362.3553-0.36961.12812.24240.04782.65910.0257-0.0781-0.2479-0.03260.19040.09310.1738-0.1715-0.2510.28330.02320.01040.27270.01840.3297-43.2398-30.939814.7585
379.423-0.213-0.24395.90534.65035.24520.28240.75331.0415-1.07570.1558-0.6108-1.3510.7078-0.46920.5372-0.06590.08590.43220.0140.4527-39.6507-23.52891.2708
383.08420.53451.88673.20181.17463.9899-0.0153-0.21910.08660.06730.05670.2491-0.3-0.3098-0.02340.28670.06910.0540.32650.02530.3009-46.2781-20.060618.9713
392.8729-0.1234-0.04743.9263-0.27623.499-0.0704-0.7728-0.04630.91710.23180.3164-0.3398-0.4799-0.11480.55760.16920.09670.54720.08320.2669-44.8329-22.185937.1264
401.78221.0802-0.46644.1192.02752.1033-0.2385-0.8245-0.52691.11260.23260.94411.7844-0.5581-0.15610.71370.04510.11660.76790.29950.592-49.0212-40.01535.9081
414.2958-1.6498-3.16833.86281.36996.8394-0.0991-0.2854-0.55720.35650.1701-0.34580.22010.7364-0.10540.37340-0.1430.36430.02430.48-41.6034-42.82712.2137
423.54030.0856-0.12435.2951.08922.0346-0.32260.06440.03020.21650.280.95040.8459-0.463-0.00081.27160.18150.16560.55980.05320.9803-54.893910.76622.3289
432.3449-1.65531.77735.43252.36557.5332-0.2903-0.1445-0.12120.9929-0.06530.98730.5206-0.28680.23731.146-0.0260.07570.56020.19331.1599-64.1728-93.008221.9297
442.3843-2.68490.15378.29040.96052.620.2253-0.0138-0.46410.4447-0.2883-0.08090.722-0.4494-0.0891.0269-0.03970.00060.48340.19240.8655-60.6651-94.837116.7787
451.5456-0.9290.31564.8485-0.93825.5121-0.2146-0.3474-0.5545-0.66660.002-0.4210.96510.35060.1650.82320.02560.01440.42030.170.8718-53.9971-91.703314.1725
464.9437-6.7857-4.38549.49335.38986.0115-0.25761.16330.3936-0.757-0.321-0.25120.31110.06650.02761.106-0.0735-0.08330.6710.18631.0658-55.4698-90.71756.53
478.2405-4.7576-0.69323.6327-2.15658.1268-0.41670.3244-0.91080.5430.18210.74110.1241-0.25230.16560.6958-0.0473-0.07930.40750.10340.8713-64.2252-81.716514.6038
486.2373-1.7399-0.20647.54313.53392.0775-0.1753-0.0836-0.76340.2542-0.0811.05430.7374-0.21810.26470.8585-0.0879-0.080.47460.2070.9117-67.0557-87.243215.8514
495.6922-0.5222-0.13543.5673-0.99333.03040.02010.1573-0.0449-0.03780.0268-0.21810.19510.1609-0.04740.35960.0012-0.06190.26820.02090.4105-49.8493-60.32679.0667
503.30580.50350.95684.638-0.33691.36840.0655-0.129-0.46790.20630.05370.03760.2852-0.0982-0.08120.4539-0.006-0.05290.2680.08340.4027-55.4771-69.189311.6579
515.14860.9327-2.30116.8772-0.8485.6928-0.24320.4674-0.1824-0.7670.31091.16730.7844-0.8296-0.10720.5094-0.0883-0.21490.54810.15530.7029-73.2552-67.45853.5617
523.47250.8832-1.55474.15930.23273.7974-0.038-0.6367-0.49791.02330.18310.71750.2562-0.3515-0.11290.67620.05430.15630.54490.29110.7167-70.6288-65.985825.7217
538.63263.6282-5.30596.0176-2.28615.76260.3872-0.39570.86121.51020.44461.2147-0.3342-0.4626-0.81530.66580.12290.19720.5340.12210.6452-69.733-48.443822.5083
548.92190.9742-6.65542.3813-0.74887.2168-0.12720.2694-0.3332-0.17420.07240.33150.0892-0.3166-0.00760.40360.0071-0.07010.31870.00740.4494-51.1251-44.54716.2493
556.86133.6694-1.847.5233-1.04315.67550.56840.0390.79041.58830.55530.0704-0.3383-0.4373-1.18131.24640.0639-0.03980.62860.18021.3115-53.2108-98.752123.9436
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 71 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 91 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 115 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 140 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 49 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 137 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 138 through 186 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 187 through 274 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 10 through 28 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 29 through 43 )C0
11X-RAY DIFFRACTION11chain 'D' and (resid 153 through 165 )D0
12X-RAY DIFFRACTION12chain 'E' and (resid 53 through 71 )E0
13X-RAY DIFFRACTION13chain 'E' and (resid 72 through 91 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 92 through 103 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 104 through 115 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 116 through 128 )E0
17X-RAY DIFFRACTION17chain 'E' and (resid 129 through 140 )E0
18X-RAY DIFFRACTION18chain 'F' and (resid 3 through 49 )F0
19X-RAY DIFFRACTION19chain 'F' and (resid 50 through 117 )F0
20X-RAY DIFFRACTION20chain 'F' and (resid 118 through 137 )F0
21X-RAY DIFFRACTION21chain 'F' and (resid 138 through 158 )F0
22X-RAY DIFFRACTION22chain 'F' and (resid 159 through 173 )F0
23X-RAY DIFFRACTION23chain 'F' and (resid 174 through 186 )F0
24X-RAY DIFFRACTION24chain 'F' and (resid 187 through 222 )F0
25X-RAY DIFFRACTION25chain 'F' and (resid 223 through 250 )F0
26X-RAY DIFFRACTION26chain 'F' and (resid 251 through 273 )F0
27X-RAY DIFFRACTION27chain 'G' and (resid 10 through 28 )G0
28X-RAY DIFFRACTION28chain 'G' and (resid 29 through 43 )G0
29X-RAY DIFFRACTION29chain 'H' and (resid 154 through 165 )H0
30X-RAY DIFFRACTION30chain 'I' and (resid 53 through 61 )I0
31X-RAY DIFFRACTION31chain 'I' and (resid 62 through 91 )I0
32X-RAY DIFFRACTION32chain 'I' and (resid 92 through 103 )I0
33X-RAY DIFFRACTION33chain 'I' and (resid 104 through 115 )I0
34X-RAY DIFFRACTION34chain 'I' and (resid 116 through 128 )I0
35X-RAY DIFFRACTION35chain 'I' and (resid 129 through 140 )I0
36X-RAY DIFFRACTION36chain 'J' and (resid 4 through 49 )J0
37X-RAY DIFFRACTION37chain 'J' and (resid 50 through 68 )J0
38X-RAY DIFFRACTION38chain 'J' and (resid 69 through 137 )J0
39X-RAY DIFFRACTION39chain 'J' and (resid 138 through 272 )J0
40X-RAY DIFFRACTION40chain 'K' and (resid 10 through 28 )K0
41X-RAY DIFFRACTION41chain 'K' and (resid 29 through 43 )K0
42X-RAY DIFFRACTION42chain 'L' and (resid 154 through 165 )L0
43X-RAY DIFFRACTION43chain 'M' and (resid 53 through 61 )M0
44X-RAY DIFFRACTION44chain 'M' and (resid 62 through 80 )M0
45X-RAY DIFFRACTION45chain 'M' and (resid 81 through 91 )M0
46X-RAY DIFFRACTION46chain 'M' and (resid 92 through 103 )M0
47X-RAY DIFFRACTION47chain 'M' and (resid 104 through 115 )M0
48X-RAY DIFFRACTION48chain 'M' and (resid 116 through 140 )M0
49X-RAY DIFFRACTION49chain 'N' and (resid 3 through 90 )N0
50X-RAY DIFFRACTION50chain 'N' and (resid 91 through 137 )N0
51X-RAY DIFFRACTION51chain 'N' and (resid 138 through 172 )N0
52X-RAY DIFFRACTION52chain 'N' and (resid 173 through 273 )N0
53X-RAY DIFFRACTION53chain 'O' and (resid 10 through 28 )O0
54X-RAY DIFFRACTION54chain 'O' and (resid 29 through 43 )O0
55X-RAY DIFFRACTION55chain 'P' and (resid 153 through 165 )P0

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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