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- PDB-7ler: Netrin-1 filament assembly -

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基本情報

登録情報
データベース: PDB / ID: 7ler
タイトルNetrin-1 filament assembly
要素Netrin-1
キーワードSIGNALING PROTEIN / heparin binding protein / filament
機能・相同性
機能・相同性情報


regulation of glial cell migration / chemorepulsion of axon / Cdc42 protein signal transduction / anterior/posterior axon guidance / motor neuron migration / negative regulation of axon extension / substrate-dependent cell migration, cell extension / inner ear morphogenesis / nuclear migration / positive regulation of cell motility ...regulation of glial cell migration / chemorepulsion of axon / Cdc42 protein signal transduction / anterior/posterior axon guidance / motor neuron migration / negative regulation of axon extension / substrate-dependent cell migration, cell extension / inner ear morphogenesis / nuclear migration / positive regulation of cell motility / regulation of synapse assembly / basement membrane / positive regulation of axon extension / glial cell proliferation / positive regulation of glial cell proliferation / cell periphery / cell-cell adhesion / actin cytoskeleton / Ras protein signal transduction / glutamatergic synapse / extracellular region / nucleoplasm / cytosol
類似検索 - 分子機能
Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain ...Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-like domain signature 1. / Galactose-binding-like domain superfamily
類似検索 - ドメイン・相同性
生物種Gallus gallus (ニワトリ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 5.99 Å
データ登録者McDougall, M. / Gupta, M. / Stetefeld, J.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR)RPA-109759 カナダ
引用ジャーナル: Nat Commun / 年: 2023
タイトル: The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation.
著者: Meier, M. / Gupta, M. / Akgul, S. / McDougall, M. / Imhof, T. / Nikodemus, D. / Reuten, R. / Moya-Torres, A. / To, V. / Ferens, F. / Heide, F. / Padilla-Meier, G.P. / Kukura, P. / Huang, W. / ...著者: Meier, M. / Gupta, M. / Akgul, S. / McDougall, M. / Imhof, T. / Nikodemus, D. / Reuten, R. / Moya-Torres, A. / To, V. / Ferens, F. / Heide, F. / Padilla-Meier, G.P. / Kukura, P. / Huang, W. / Gerisch, B. / Morgelin, M. / Poole, K. / Antebi, A. / Koch, M. / Stetefeld, J.
履歴
登録2021年1月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年2月23日Provider: repository / タイプ: Initial release
改定 1.12023年3月15日Group: Database references / カテゴリ: 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
改定 1.22023年8月16日Group: Data collection / Other
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.pdb_format_compatible
改定 1.32023年10月25日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model
改定 1.42024年11月20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: Netrin-1
B: Netrin-1
C: Netrin-1
E: Netrin-1
D: Netrin-1
F: Netrin-1
G: Netrin-1
H: Netrin-1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)410,86140
ポリマ－396,6398
非ポリマー14,22132
水00
1
A: Netrin-1
B: Netrin-1
C: Netrin-1
E: Netrin-1
D: Netrin-1
F: Netrin-1
G: Netrin-1
H: Netrin-1
ヘテロ分子
x 6


分子量 (理論値)分子数
合計 (水以外)2,465,163240
ポリマ－2,379,83648
非ポリマー85,327192
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_344-y-2,x-y-1,z-1/31
crystal symmetry operation3_434-x+y-1,-x-2,z-2/31
crystal symmetry operation4_334-x-2,-y-2,z-1/21
crystal symmetry operation5_545y,-x+y-1,z+1/61
crystal symmetry operation6_454x-y-1,x,z-1/61
単位格子
Length a, b, c (Å)196.690, 196.690, 476.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 40 through 255 or resid 272...
21(chain B and (resid 40 through 255 or resid 272...
31(chain C and (resid 40 through 255 or resid 272...
41(chain D and (resid 40 through 334 or (resid 335...
51(chain E and (resid 40 through 255 or resid 272...
61(chain F and (resid 40 through 255 or resid 272...
71(chain G and (resid 40 through 255 or resid 272...
81(chain H and (resid 40 through 255 or resid 272...
12chain I
22chain J
32chain K
42chain L
52chain M
62chain N
72chain O
82chain P

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 40 through 255 or resid 272...A40 - 255
121(chain A and (resid 40 through 255 or resid 272...A272 - 334
131(chain A and (resid 40 through 255 or resid 272...A335
141(chain A and (resid 40 through 255 or resid 272...A40 - 457
151(chain A and (resid 40 through 255 or resid 272...A40 - 457
161(chain A and (resid 40 through 255 or resid 272...A40 - 457
171(chain A and (resid 40 through 255 or resid 272...A40 - 457
211(chain B and (resid 40 through 255 or resid 272...B40 - 255
221(chain B and (resid 40 through 255 or resid 272...B272 - 334
231(chain B and (resid 40 through 255 or resid 272...B335
241(chain B and (resid 40 through 255 or resid 272...B40 - 457
251(chain B and (resid 40 through 255 or resid 272...B40 - 457
261(chain B and (resid 40 through 255 or resid 272...B40 - 457
271(chain B and (resid 40 through 255 or resid 272...B40 - 457
311(chain C and (resid 40 through 255 or resid 272...C40 - 255
321(chain C and (resid 40 through 255 or resid 272...C272 - 389
331(chain C and (resid 40 through 255 or resid 272...C390
341(chain C and (resid 40 through 255 or resid 272...C40 - 457
351(chain C and (resid 40 through 255 or resid 272...C40 - 457
361(chain C and (resid 40 through 255 or resid 272...C40 - 457
371(chain C and (resid 40 through 255 or resid 272...C40 - 457
411(chain D and (resid 40 through 334 or (resid 335...D40 - 334
421(chain D and (resid 40 through 334 or (resid 335...D335
431(chain D and (resid 40 through 334 or (resid 335...D40 - 457
441(chain D and (resid 40 through 334 or (resid 335...D40 - 457
451(chain D and (resid 40 through 334 or (resid 335...D40 - 457
461(chain D and (resid 40 through 334 or (resid 335...D40 - 457
511(chain E and (resid 40 through 255 or resid 272...E40 - 255
521(chain E and (resid 40 through 255 or resid 272...E272 - 334
531(chain E and (resid 40 through 255 or resid 272...E335
541(chain E and (resid 40 through 255 or resid 272...E40 - 457
551(chain E and (resid 40 through 255 or resid 272...E40 - 457
561(chain E and (resid 40 through 255 or resid 272...E40 - 457
571(chain E and (resid 40 through 255 or resid 272...E40 - 457
611(chain F and (resid 40 through 255 or resid 272...F40 - 255
621(chain F and (resid 40 through 255 or resid 272...F272 - 334
631(chain F and (resid 40 through 255 or resid 272...F335
641(chain F and (resid 40 through 255 or resid 272...F40 - 457
651(chain F and (resid 40 through 255 or resid 272...F40 - 457
661(chain F and (resid 40 through 255 or resid 272...F40 - 457
671(chain F and (resid 40 through 255 or resid 272...F40 - 457
711(chain G and (resid 40 through 255 or resid 272...G40 - 255
721(chain G and (resid 40 through 255 or resid 272...G272 - 334
731(chain G and (resid 40 through 255 or resid 272...G335
741(chain G and (resid 40 through 255 or resid 272...G40 - 457
751(chain G and (resid 40 through 255 or resid 272...G40 - 457
761(chain G and (resid 40 through 255 or resid 272...G40 - 457
771(chain G and (resid 40 through 255 or resid 272...G40 - 457
811(chain H and (resid 40 through 255 or resid 272...H40 - 255
821(chain H and (resid 40 through 255 or resid 272...H272 - 334
831(chain H and (resid 40 through 255 or resid 272...H335
841(chain H and (resid 40 through 255 or resid 272...H40 - 457
851(chain H and (resid 40 through 255 or resid 272...H40 - 457
861(chain H and (resid 40 through 255 or resid 272...H40 - 457
871(chain H and (resid 40 through 255 or resid 272...H40 - 457
112chain II501 - 531
212chain JJ501 - 531
312chain KK501 - 531
412chain LL501 - 531
512chain MM501 - 531
612chain NN501 - 531
712chain OO501 - 531
812chain PP501 - 531

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Netrin-1


分子量: 49579.926 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Gallus gallus (ニワトリ) / 遺伝子: NTN1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q90922
#2: 多糖
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 8 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 8 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 16 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 6.71 Å3/Da / 溶媒含有率: 81.66 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 / 詳細: 40% MPD, 100 mM Tris

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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: CLSI / ビームライン: 08B1-1 / 波長: 0.97952 Å
検出器タイプ: RAYONIX MX300HE / 検出器: CCD / 日付: 2017年9月12日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97952 Å / 相対比: 1
Reflection twinOperator: k,h,-l / Fraction: 0.5
反射解像度: 5.99→49.17 Å / Num. obs: 26042 / % possible obs: 99.5 % / 冗長度: 11.1 % / CC1/2: 0.997 / Net I/σ(I): 8
反射 シェル解像度: 5.995→6.208 Å / Num. unique obs: 2565 / CC1/2: 0.777

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2-3874_3874精密化
XSCALEデータスケーリング
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: 4OVE

4ove


解像度: 5.99→49.17 Å / 交差検証法: THROUGHOUT / σ(F): 3.44 / 位相誤差: 38.74 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.3681 1336 5.13 %
Rwork0.3044 24692 -
obs0.3838 26028 99.94 %
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: 1162.7 Å2 / Biso mean: 304.5544 Å2 / Biso min: 102.85 Å2
精密化ステップサイクル: final / 解像度: 5.99→49.17 Å
タンパク質核酸リガンド溶媒全体
原子数25469 0 936 0 26405
Biso mean--290.38 --
残基数----3249
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01427044
X-RAY DIFFRACTIONf_angle_d1.08136602
X-RAY DIFFRACTIONf_dihedral_angle_d31.5374126
X-RAY DIFFRACTIONf_chiral_restr0.074054
X-RAY DIFFRACTIONf_plane_restr0.0084746
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A9824X-RAY DIFFRACTION9.809TORSIONAL
12B9824X-RAY DIFFRACTION9.809TORSIONAL
13C9824X-RAY DIFFRACTION9.809TORSIONAL
14D9824X-RAY DIFFRACTION9.809TORSIONAL
15E9824X-RAY DIFFRACTION9.809TORSIONAL
16F9824X-RAY DIFFRACTION9.809TORSIONAL
17G9824X-RAY DIFFRACTION9.809TORSIONAL
18H9824X-RAY DIFFRACTION9.809TORSIONAL
21I528X-RAY DIFFRACTION9.809TORSIONAL
22J528X-RAY DIFFRACTION9.809TORSIONAL
23K528X-RAY DIFFRACTION9.809TORSIONAL
24L528X-RAY DIFFRACTION9.809TORSIONAL
25M528X-RAY DIFFRACTION9.809TORSIONAL
26N528X-RAY DIFFRACTION9.809TORSIONAL
27O528X-RAY DIFFRACTION9.809TORSIONAL
28P528X-RAY DIFFRACTION9.809TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.99-6.210.5111390.50112426256594
6.21-6.460.44941190.45222475259495
6.46-6.750.55321200.44322500262095
6.75-7.10.48331500.44052433258394
7.1-7.550.65161380.48822481261995
7.55-8.130.50871220.42382482260495
8.13-8.940.47981410.41182472261395
8.94-10.230.44361310.35352464259595
10.23-12.840.32141290.30692467259695
12.85-49.170.39581470.34422492263994
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)
11.15380.54840.92721.73161.86952.18560.58810.2074-0.9518-0.6091.2850.2011-1.12140.63371.43790.3934-0.79571.0250.96640.64954.2936-112.7383-111.043635.3154
20.1023-0.1202-0.15520.45320.13570.2222-0.6450.1741-0.7911-0.0854-0.23110.63910.4002-0.4946-0.37190.6845-1.08531.290.20020.91983.5462-114.2056-92.198333.0021
30.29670.088-0.63040.22730.2184-0.26710.03790.4466-0.01450.18690.50690.28941.2306-0.0869-0.3916-0.2223-1.23560.2993-1.0307-1.16172.8487-92.4277-97.413726.798
40.57910.46840.21460.64250.18490.146-0.1499-0.41730.3399-0.0606-0.33310.24560.2777-0.5702-0.00980.851-0.74860.3951.6553-0.94982.7269-35.0258-87.968518.6216
50.15730.0449-0.4060.38450.02740.76080.732-0.5620.20080.46920.2861-0.1518-0.4403-0.18531.17561.1390.21731.4445-0.5867-1.41493.4702-51.953-116.5526-1.1358
60.54650.4561-0.08340.5894-0.0880.73160.58860.44470.6229-0.5059-0.15850.47-0.6168-0.4025-0.0197-0.59030.47340.01321.01450.14582.4577-36.8958-111.848-10.5691
70.81930.33840.12780.33450.3356-0.16380.2925-0.4433-0.12540.0368-0.1470.7030.6501-0.39322.08580.3614-0.3596-0.39881.6005-1.86212.2814-36.061-129.8621-7.8223
80.85420.9644-0.38980.96530.05710.2287-0.4080.0233-0.7972-0.1540.4878-0.2432-0.9231-1.03792.9062-0.4084-1.8471-1.0552-1.1018-0.61554.6693-4.0044-163.8826-19.8822
90.62740.2062-0.02030.03230.0560.35820.31890.19230.23890.41950.4249-0.12140.40960.17330.54320.38750.4702-0.49780.65170.96554.1288-134.937-207.9218-7.2712
100.4292-0.05690.35340.3143-0.04430.57670.5795-0.3176-0.13590.28740.2634-0.4280.6189-0.17870.76410.65361.302-0.48590.48280.98944.2681-126.3282-222.17744.0213
110.11740.2183-0.08450.487-0.27110.15130.48530.3504-0.5564-0.8229-0.8559-0.42220.77950.7025-0.00030.18160.8667-0.14421.47830.28183.3456-145.6675-220.7004-10.4415
120.18180.24490.04890.1441-0.070.01710.156-0.1165-0.2593-0.033-0.1805-0.1907-0.55790.1247-0.1809-0.5617-0.1018-0.01392.09451.4192.4985-139.2391-213.4799-3.3891
130.06170.0937-0.13990.115-0.14910.10760.2518-0.4279-0.36180.3626-0.05280.12460.36340.0506-0.3701-0.23190.02612.53980.83011.20852.5969-160.9577-189.7889-16.1923
140.2120.0906-0.15321.0722-0.30050.33960.1475-0.15520.78120.01930.627-0.07120.54850.74951.15751.44290.21161.19110.03810.47032.6015-182.9416-159.9164-20.7015
151.26890.28561.03730.7477-0.0040.93631.14210.163-0.5861-0.49310.6933-0.29120.0339-0.28410.96060.89140.57181.64890.11680.18324.3639-140.9201-128.7041-14.0015
160.1923-0.17770.03320.2633-0.20640.2639-0.1829-0.75970.32430.52-0.3805-0.7133-1.1096-0.46460.2301-0.46580.1424-0.76322.0083-0.5673.1022-156.1787-122.2206-7.8108
170.2558-0.19350.04420.38280.11660.39510.5020.4279-0.24430.2996-0.5806-0.20170.66010.2309-0.43030.0995-0.1389-0.5531.52391.03663.7217-167.2303-146.7379-5.0034
180.8861-0.00460.0430.2532-0.1118-0.1121-0.11210.4962-0.28390.0559-0.01060.1455-0.16850.8628-1.02851.28432.1076-0.72670.20930.18152.6438-199.5013-182.56471.8012
190.1898-0.32380.21360.3941-0.32970.38330.2449-0.0096-0.0565-0.0593-0.0994-0.54760.1158-0.64050.34730.25760.9801-0.9840.33861.09164.2854-121.309-236.9208-53.914
200.488-0.2304-0.28120.51380.08310.16560.0469-0.0004-0.06870.18850.4214-0.42040.56870.5050.17320.99770.6755-0.56092.1891-0.18822.857-123.969-245.2022-55.4823
210.46920.15090.33460.29050.51920.12230.1472-1.09450.3677-0.12110.7907-0.3227-1.00920.7862-0.5897-0.80791.3374-0.0096-0.5465-0.95553.3031-104.4389-252.2106-45.6281
220.0002-0.0016-0.01520.26980.17510.113-0.51950.1586-0.11590.276-0.71190.4992-0.1994-0.8982-0.47520.83370.4511-0.1493-0.4309-1.55223.7649-45.2172-256.5863-37.8082
230.6811-0.35740.08170.7729-0.15860.7620.77890.0313-0.2176-0.34910.68010.35540.18990.35951.3883-0.7831-0.95221.7040.8909-0.4134.0848-76.215-119.9722-56.6039
242.7254-0.18960.16810.3649-0.0268-0.00210.17880.33350.05930.0760.11310.3898-0.01830.4362-0.70461.05661.19760.13432.18031.24513.3978-78.6077-111.8135-51.2258
250.42510.39440.17820.44520.14480.2666-0.05270.3121-0.57130.001-0.1148-0.16280.05320.1045-0.34330.02450.1298-0.17490.7359-0.87112.606-79.6172-97.8656-50.2152
260.0908-0.7112-0.44852.8827-0.19631.04330.95250.4586-0.2940.02250.91571.98010.2147-1.66278.86820.10520.7033-0.09030.33151.17393.1465-114.584-106.1345-42.9008
271.05170.34760.11320.2293-0.07590.54330.48170.0373-0.0950.1587-0.11920.7551-0.1666-0.49621.01810.9251-0.4075-1.13320.2979-0.25024.2065-63.7155-225.5239-16.4072
280.47110.02580.08110.0959-0.12340.16140.0555-0.3092-0.36260.1787-0.31110.36220.1806-0.09940.08791.2248-0.4993-0.02331.8693-0.26222.4113-57.5181-231.4469-17.306
290.5335-0.119-0.45760.19440.52940.9828-0.2126-0.0546-0.80990.5602-1.3627-0.16140.48410.4488-1.25860.7947-0.1788-0.70250.52720.08372.6139-46.1264-231.5842-7.5464
300.0908-0.15490.05870.2070.26150.4492-0.00140.7658-0.1660.459-0.90560.445-0.1097-0.4114-0.74011.4551-1.44760.26740.688-2.24694.3789-42.6485-205.372-6.475
310.1368-0.07260.24590.31780.16550.8371-0.41310.1533-0.4012-0.3899-0.1273-0.3247-0.08380.6066-0.11172.2014-0.93651.53032.2789-0.51773.5762-25.2563-176.5809-4.0719
320.7235-0.1995-0.24270.64270.32211.7107-0.40640.3107-0.46090.1345-0.17510.01880.14940.0987-0.79081.04560.01940.72241.45410.39122.1651-6.6728-159.54942.3115
330.35310.02530.07280.25070.29040.3720.5591-0.18440.5034-0.37760.59610.05090.16420.32380.71551.3378-0.4678-0.16290.8883-0.93533.324-36.7046-180.7742-45.1472
340.21340.04160.01040.13650.02380.00820.3751-0.14760.11980.20440.03280.3584-0.33340.11020.08741.44250.0710.27941.0747-2.15082.948-26.5979-167.1884-34.7105
350.0265-0.0099-0.01310.5643-0.14280.0375-0.37870.3046-0.2398-0.2995-0.23220.1855-0.39960.3732-0.1091.46720.8154-0.84970.4744-1.06084.3043-23.8536-183.7498-45.0872
360.3537-0.06140.51730.1620.01270.5777-1.0863-0.15940.7341-0.5098-0.05850.1260.2670.0228-0.55842.3096-0.8150.50211.0306-0.56641.8664-19.1944-181.9343-50.4693
371.5219-0.17450.65580.0422-0.07320.19151.2813-1.09091.72820.33390.5229-0.4353-1.42912.22741.3556-1.96672.3709-2.7611-0.76381.06233.2007-50.4028-225.1654-56.0509
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 153 )A40 - 153
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 199 )A154 - 199
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 386 )A200 - 386
4X-RAY DIFFRACTION4chain 'A' and (resid 387 through 457 )A387 - 457
5X-RAY DIFFRACTION5chain 'B' and (resid 40 through 138 )B40 - 138
6X-RAY DIFFRACTION6chain 'B' and (resid 139 through 251 )B139 - 251
7X-RAY DIFFRACTION7chain 'B' and (resid 252 through 331 )B252 - 331
8X-RAY DIFFRACTION8chain 'B' and (resid 332 through 457 )B332 - 457
9X-RAY DIFFRACTION9chain 'C' and (resid 40 through 85 )C40 - 85
10X-RAY DIFFRACTION10chain 'C' and (resid 86 through 136 )C86 - 136
11X-RAY DIFFRACTION11chain 'C' and (resid 137 through 243 )C137 - 243
12X-RAY DIFFRACTION12chain 'C' and (resid 244 through 303 )C244 - 303
13X-RAY DIFFRACTION13chain 'C' and (resid 304 through 367 )C304 - 367
14X-RAY DIFFRACTION14chain 'C' and (resid 368 through 457 )C368 - 457
15X-RAY DIFFRACTION15chain 'E' and (resid 40 through 136 )E40 - 136
16X-RAY DIFFRACTION16chain 'E' and (resid 137 through 258 )E137 - 258
17X-RAY DIFFRACTION17chain 'E' and (resid 259 through 376 )E259 - 376
18X-RAY DIFFRACTION18chain 'E' and (resid 377 through 457 )E377 - 457
19X-RAY DIFFRACTION19chain 'D' and (resid 40 through 116 )D40 - 116
20X-RAY DIFFRACTION20chain 'D' and (resid 117 through 160 )D117 - 160
21X-RAY DIFFRACTION21chain 'D' and (resid 161 through 376 )D161 - 376
22X-RAY DIFFRACTION22chain 'D' and (resid 377 through 457 )D377 - 457
23X-RAY DIFFRACTION23chain 'F' and (resid 40 through 138 )F40 - 138
24X-RAY DIFFRACTION24chain 'F' and (resid 139 through 163 )F139 - 163
25X-RAY DIFFRACTION25chain 'F' and (resid 164 through 204 )F164 - 204
26X-RAY DIFFRACTION26chain 'F' and (resid 205 through 457 )F205 - 457
27X-RAY DIFFRACTION27chain 'G' and (resid 40 through 116 )G40 - 116
28X-RAY DIFFRACTION28chain 'G' and (resid 117 through 159 )G117 - 159
29X-RAY DIFFRACTION29chain 'G' and (resid 160 through 255 )G160 - 255
30X-RAY DIFFRACTION30chain 'G' and (resid 271 through 367 )G271 - 367
31X-RAY DIFFRACTION31chain 'G' and (resid 368 through 406 )G368 - 406
32X-RAY DIFFRACTION32chain 'G' and (resid 407 through 457 )G407 - 457
33X-RAY DIFFRACTION33chain 'H' and (resid 40 through 85 )H40 - 85
34X-RAY DIFFRACTION34chain 'H' and (resid 86 through 138 )H86 - 138
35X-RAY DIFFRACTION35chain 'H' and (resid 139 through 182 )H139 - 182
36X-RAY DIFFRACTION36chain 'H' and (resid 183 through 279 )H183 - 279
37X-RAY DIFFRACTION37chain 'H' and (resid 280 through 457 )H280 - 457

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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