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- PDB-5npw: Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) -

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基本情報

登録情報
データベース: PDB / ID: 5npw
タイトルStructure of human ATG5-ATG16L1(ATG5BD) complex (C2)
要素
  • Autophagy protein 5
  • Autophagy-related protein 16-1
キーワードCELL CYCLE / autophagy / ATG16L1 / ATG5
機能・相同性
機能・相同性情報


otolith development / regulation of autophagosome maturation / positive regulation of viral translation / C-terminal protein lipidation / regulation of cytokine production involved in immune response / Atg8-family ligase activity / response to fluoride / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / antigen processing and presentation of endogenous antigen ...otolith development / regulation of autophagosome maturation / positive regulation of viral translation / C-terminal protein lipidation / regulation of cytokine production involved in immune response / Atg8-family ligase activity / response to fluoride / Atg12-Atg5-Atg16 complex / negative regulation of dendrite extension / antigen processing and presentation of endogenous antigen / positive regulation of mucus secretion / vacuole-isolation membrane contact site / phagophore / negative regulation of autophagic cell death / negative regulation of defense response to virus / positive regulation of stress granule assembly / ubiquitin-like protein transferase activity / cellular response to nitrosative stress / microautophagy / ventricular cardiac muscle cell development / transferase complex / regulation of cilium assembly / aggrephagy / dendrite arborization / mucus secretion / mitochondria-associated endoplasmic reticulum membrane contact site / response to fungus / xenophagy / corpus callosum development / protein localization to phagophore assembly site / negative thymic T cell selection / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / negative stranded viral RNA replication / regulation of release of sequestered calcium ion into cytosol / endolysosome membrane / cellular response to nitrogen starvation / negative regulation of cardiac muscle cell apoptotic process / regulation of reactive oxygen species metabolic process / negative regulation of phagocytosis / negative regulation of type I interferon production / axonal transport / response to iron(II) ion / Receptor Mediated Mitophagy / Macroautophagy / chaperone-mediated autophagy / heart contraction / autophagosome membrane / axoneme / autophagosome assembly / blood vessel remodeling / regulation of postsynaptic membrane neurotransmitter receptor levels / postsynaptic modulation of chemical synaptic transmission / mitophagy / protein-membrane adaptor activity / sperm midpiece / cardiac muscle cell apoptotic process / negative regulation of protein ubiquitination / positive regulation of autophagy / PINK1-PRKN Mediated Mitophagy / post-translational protein modification / autophagosome / Negative regulators of DDX58/IFIH1 signaling / negative regulation of innate immune response / hippocampus development / macroautophagy / autophagy / Schaffer collateral - CA1 synapse / vasodilation / phagocytic vesicle membrane / protein transport / chromatin organization / GTPase binding / defense response to virus / protein ubiquitination / postsynapse / response to xenobiotic stimulus / axon / innate immune response / glutamatergic synapse / protein-containing complex / identical protein binding / membrane / cytosol / cytoplasm
類似検索 - 分子機能
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 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 / 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) / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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
Autophagy-related protein 16-1 / Autophagy protein 5
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: 3.1 Å
データ登録者Archna, A. / Scrima, A.
引用ジャーナル: Acta Crystallogr F Struct Biol Commun / 年: 2017
タイトル: Identification, biochemical characterization and crystallization of the central region of human ATG16L1.
著者: Archna, A. / Scrima, A.
履歴
登録2017年4月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年10月11日Provider: repository / タイプ: Initial release
改定 1.12017年11月1日Group: Database references / カテゴリ: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年1月17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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Autophagy protein 5
B: Autophagy-related protein 16-1
C: Autophagy protein 5
D: Autophagy-related protein 16-1
E: Autophagy protein 5
F: Autophagy-related protein 16-1
G: Autophagy protein 5
H: Autophagy-related protein 16-1


分子量 (理論値)分子数
合計 (水以外)271,9118
ポリマ－271,9118
非ポリマー00
水1267
1
A: Autophagy protein 5
B: Autophagy-related protein 16-1


分子量 (理論値)分子数
合計 (水以外)67,9782
ポリマ－67,9782
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-18 kcal/mol
Surface area14910 Å2
手法PISA
2
C: Autophagy protein 5
D: Autophagy-related protein 16-1


分子量 (理論値)分子数
合計 (水以外)67,9782
ポリマ－67,9782
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-13 kcal/mol
Surface area14770 Å2
手法PISA
3
E: Autophagy protein 5
F: Autophagy-related protein 16-1


分子量 (理論値)分子数
合計 (水以外)67,9782
ポリマ－67,9782
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-18 kcal/mol
Surface area14640 Å2
手法PISA
4
G: Autophagy protein 5
H: Autophagy-related protein 16-1


分子量 (理論値)分子数
合計 (水以外)67,9782
ポリマ－67,9782
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-14 kcal/mol
Surface area14850 Å2
手法PISA
単位格子
Length a, b, c (Å)200.860, 75.990, 142.440
Angle α, β, γ (deg.)90.000, 131.410, 90.000
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 4 or (resid 5 and (name...
21(chain C and ((resid 4 and (name N or name...
31(chain E and ((resid 4 and (name N or name...
41(chain G and ((resid 4 and (name N or name...
12(chain D and ((resid 10 and (name N or name...
22(chain B and ((resid 10 and (name N or name...
32(chain F and (resseq 10:14 or (resid 15 and (name...
42(chain H and ((resid 10 and (name N or name...

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
111ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA411
121LYSLYSLYSLYS(chain A and (resseq 4 or (resid 5 and (name...AA512
131ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
141ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
151ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
161ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
171ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
181ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
211ASPASPASPASP(chain C and ((resid 4 and (name N or name...CC411
221METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
231METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
241METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
251METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
261METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
271METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
281METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
291METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
2101METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
2111METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
311ASPASPASPASP(chain E and ((resid 4 and (name N or name...EE411
321ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
331ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
341ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
351ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
361ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
371ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
381ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
391ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
3101ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
3111ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
411ASPASPASPASP(chain G and ((resid 4 and (name N or name...GG411
421METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
431METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
441METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
451METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
461METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
471METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
481METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
491METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
4101METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
4111METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
112ARGARGARGARG(chain D and ((resid 10 and (name N or name...DD104
122GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
132GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
142GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
152GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
162GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
212ARGARGARGARG(chain B and ((resid 10 and (name N or name...BB104
222GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
232GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
242GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
252GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
262GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
312ARGARGLYSLYS(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 144 - 8
322ARGARGARGARG(chain F and (resseq 10:14 or (resid 15 and (name...FF159
332ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
342ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
352ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
362ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
372ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
382ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
412ARGARGARGARG(chain H and ((resid 10 and (name N or name...HH104
422GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42
432GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42
442GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42
452GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42
462GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Autophagy protein 5 / APG5-like / Apoptosis-specific protein


分子量: 33187.992 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: ATG5, APG5L, ASP / プラスミド: pET15b-derived / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9H1Y0
#2: タンパク質
Autophagy-related protein 16-1 / APG16-like 1


分子量: 34789.879 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: ATG16L1, APG16L, UNQ9393/PRO34307 / プラスミド: pCOLA-derived / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q676U5
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 7 / 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: 0.4 M KCl and 18 % PEG 3350

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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: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2015年9月8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: 3.1→48.316 Å / Num. obs: 29428 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / 冗長度: 3.698 % / Biso Wilson estimate: 62.2 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.147 / Χ2: 0.962 / Net I/σ(I): 9.48
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.23.8410.7452.0826430.6870.86599.3
3.2-3.33.7980.5043.0423660.8260.58699.3
3.3-43.5760.2285.9106140.9560.26899.2
4-63.8260.09412.9896460.990.10999.1
6-103.5050.0616.3232300.9960.0798.9
10-48.3163.7710.03727.669290.9970.04396.7

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHASER位相決定
PHENIX1.10.1_2155精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4GDK

4gdk


解像度: 3.1→48.316 Å / SU ML: 0.5 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 28.52
Rfactor反射数%反射
Rfree0.2639 1472 5 %
Rwork0.2175 --
obs0.2198 29416 99.6 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 206.4 Å2 / Biso mean: 68.1332 Å2 / Biso min: 4.46 Å2
精密化ステップサイクル: final / 解像度: 3.1→48.316 Å
タンパク質核酸リガンド溶媒全体
原子数9945 0 0 7 9952
Biso mean---18.24 -
残基数----1221
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00310225
X-RAY DIFFRACTIONf_angle_d0.50413895
X-RAY DIFFRACTIONf_chiral_restr0.0391499
X-RAY DIFFRACTIONf_plane_restr0.0031783
X-RAY DIFFRACTIONf_dihedral_angle_d8.9636104
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5734X-RAY DIFFRACTION5.965TORSIONAL
12C5734X-RAY DIFFRACTION5.965TORSIONAL
13E5734X-RAY DIFFRACTION5.965TORSIONAL
14G5734X-RAY DIFFRACTION5.965TORSIONAL
21D812X-RAY DIFFRACTION5.965TORSIONAL
22B812X-RAY DIFFRACTION5.965TORSIONAL
23F812X-RAY DIFFRACTION5.965TORSIONAL
24H812X-RAY DIFFRACTION5.965TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1001-3.20020.37091330.357525132646
3.2002-3.31450.34311330.294425352668
3.3145-3.44720.33451330.286925332666
3.4472-3.6040.29821320.254825022634
3.604-3.7940.28491340.223725372671
3.794-4.03160.26251320.207525162648
4.0316-4.34270.24171340.190125392673
4.3427-4.77940.20441330.165125302663
4.7794-5.47010.23621340.182925552689
5.4701-6.88860.26771350.229225522687
6.8886-48.32190.24261390.197426322771
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)
11.92740.12670.86731.72770.72664.7994-0.0657-0.01270.1704-0.11820.1835-0.1911-0.4669-0.021-0.12130.37770.0630.03950.4420.03410.4205-61.8908-5.8694118.2184
23.9635-1.48271.17952.8216-0.96814.8322-0.07870.108-0.2933-0.18860.15350.05240.28290.025-0.05840.48640.0060.10110.4712-0.02030.3993-61.8931-26.26110.7073
32.6275-0.09190.00097.52763.60325.2194-0.5016-0.2914-0.08770.46830.12170.79830.3745-0.460.4280.3982-0.06690.0060.57020.03010.5086-71.6716-16.9182129.4802
41.57490.0753-0.3912.1651.93016.88650.1085-0.09640.14340.0384-0.1834-0.0685-0.05230.14680.03160.3669-0.02830.0210.43080.02570.4242-48.9649-16.161588.1377
52.6259-0.80030.25383.7756-0.19652.04830.0188-0.15080.0443-0.07610.0011-0.14770.02620.1701-0.0070.3768-0.0057-0.04110.3707-0.03560.3651-41.9863-31.616872.5577
61.5104-2.2164-2.74325.5825.08175.3982-0.14410.05290.0074-0.15410.06160.4332-0.1439-0.12580.06190.5358-0.0086-0.14710.55110.09120.4721-59.4183-17.010173.2412
73.5685-1.302-0.48210.6140.762.61530.0827-0.2048-0.58220.0111-0.1297-0.230.61750.57570.37220.5987-0.0843-0.10760.3720.15680.3394-80.7059-17.522385.4974
84.42021.95211.13965.8574-1.2023.2531-0.00970.43310.63570.11730.1380.4541-0.3254-0.0546-0.10630.4331-0.04570.06430.47840.09060.4616-80.019-2.228574.339
93.69950.14860.22823.79362.29294.84360.0285-0.2036-0.23870.1066-0.30730.27860.0848-0.29030.27280.4387-0.00690.04640.48770.01480.5099-94.9717-23.132578.8527
106.06624.9134-0.30054.0993-0.30923.43330.40570.2546-2.01051.28250.0302-1.12010.42680.2841-0.40360.72960.1277-0.0460.5362-0.01330.8826-77.8185-30.397183.3097
113.8412-2.2462-0.43632.43671.20016.7899-0.5345-0.6060.16471.01091.1215-0.5248-0.1279-0.1391-0.53660.41930.08190.06940.5938-0.00570.4705-67.6853-5.47888.561
128.4896-2.11582.36013.1897-0.40472.84730.1138-0.49890.45060.2014-0.20.1486-0.1433-0.55820.11220.5104-0.0375-0.00830.5188-0.00110.4143-75.447-12.4204152.5049
1330.4228-0.51013.1809-0.34423.34230.15-0.1357-0.1490.2109-0.2443-0.32770.12160.11940.07570.3701-0.0551-0.03290.37140.10110.4743-60.1964-25.8383162.2421
143.4961-1.50732.91984.8782-1.23366.04810.41970.4979-0.6977-0.61890.1835-0.92060.11330.1629-0.47980.50960.02380.09870.34520.08610.8098-52.2309-23.571145.4839
156.1462-0.46882.18172.4466-2.77966.26870.2325-0.88110.21890.3324-0.23210.176-0.68651.14190.07140.46990.00980.00570.5815-0.02570.5161-68.9196-0.5406140.8652
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 136 )A4 - 136
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 275 )A137 - 275
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 48 )B9 - 48
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 117 )C1 - 117
5X-RAY DIFFRACTION5chain 'C' and (resid 118 through 274 )C118 - 274
6X-RAY DIFFRACTION6chain 'D' and (resid 8 through 47 )D8 - 47
7X-RAY DIFFRACTION7chain 'E' and (resid 3 through 22 )E3 - 22
8X-RAY DIFFRACTION8chain 'E' and (resid 23 through 117 )E23 - 117
9X-RAY DIFFRACTION9chain 'E' and (resid 118 through 274 )E118 - 274
10X-RAY DIFFRACTION10chain 'F' and (resid 10 through 28 )F10 - 28
11X-RAY DIFFRACTION11chain 'F' and (resid 29 through 48 )F29 - 48
12X-RAY DIFFRACTION12chain 'G' and (resid 1 through 117 )G1 - 117
13X-RAY DIFFRACTION13chain 'G' and (resid 118 through 275 )G118 - 275
14X-RAY DIFFRACTION14chain 'H' and (resid 8 through 28 )H8 - 28
15X-RAY DIFFRACTION15chain 'H' and (resid 29 through 48 )H29 - 48

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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