[日本語] English
万見
- PDB-7r86: Structure of mouse BAI1 (ADGRB1) in complex with mouse Nogo recep... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7r86
タイトルStructure of mouse BAI1 (ADGRB1) in complex with mouse Nogo receptor (RTN4R)
要素
  • Reticulon-4 receptor
  • Vasculostatin-120
キーワードCELL ADHESION / adhesion GPCR / O-linked glycosylation / RTN4R / Nogo receptor
機能・相同性
機能・相同性情報


Roundabout binding / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / regulation of postsynapse assembly / ganglioside GT1b binding / negative regulation of axon regeneration / postsynaptic actin cytoskeleton organization / engulfment of apoptotic cell ...Roundabout binding / neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / regulation of postsynapse assembly / ganglioside GT1b binding / negative regulation of axon regeneration / postsynaptic actin cytoskeleton organization / engulfment of apoptotic cell / negative regulation of axon extension / phagocytosis, recognition / corpus callosum development / positive regulation of synapse assembly / negative regulation of endothelial cell migration / muscle organ development / negative chemotaxis / regulation of synapse assembly / positive regulation of myoblast fusion / positive regulation of Rho protein signal transduction / positive regulation of reactive oxygen species biosynthetic process / phagocytosis, engulfment / phosphatidylserine binding / phagocytic cup / axonal growth cone / negative regulation of protein ubiquitination / axonogenesis / negative regulation of angiogenesis / positive regulation of GTPase activity / dendritic shaft / axon guidance / G protein-coupled receptor activity / PDZ domain binding / lipopolysaccharide binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / transmembrane signaling receptor activity / negative regulation of neuron projection development / heparin binding / presynapse / signaling receptor activity / nervous system development / growth cone / perikaryon / postsynaptic membrane / defense response to Gram-negative bacterium / dendritic spine / postsynaptic density / cell surface receptor signaling pathway / neuron projection / membrane raft / external side of plasma membrane / innate immune response / focal adhesion / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / extracellular space / plasma membrane
類似検索 - 分子機能
GPCR, family 2, brain-specific angiogenesis inhibitor / Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / : / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. ...GPCR, family 2, brain-specific angiogenesis inhibitor / Adhesion G protein-coupled receptor B, N-terminal domain / Adhesion GPCR B N-terminal region / : / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
類似検索 - ドメイン・相同性
ACETATE ION / alpha-D-mannopyranose / 4-AMINOBENZOIC ACID / Adhesion G protein-coupled receptor B1 / Reticulon-4 receptor
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.65 Å
データ登録者Miao, Y. / Jude, K.M. / Garcia, K.C.
資金援助 米国, 1件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
引用ジャーナル: Cell / 年: 2021
タイトル: RTN4/NoGo-receptor binding to BAI adhesion-GPCRs regulates neuronal development.
著者: Wang, J. / Miao, Y. / Wicklein, R. / Sun, Z. / Wang, J. / Jude, K.M. / Fernandes, R.A. / Merrill, S.A. / Wernig, M. / Garcia, K.C. / Sudhof, T.C.
履歴
登録2021年6月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年11月10日Provider: repository / タイプ: Initial release
改定 1.12022年5月25日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.32024年10月30日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
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

-
集合体

登録構造単位
A: Reticulon-4 receptor
B: Reticulon-4 receptor
C: Vasculostatin-120
D: Vasculostatin-120
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)79,11727
ポリマ－75,9014
非ポリマー3,21623
水11,367631
1
A: Reticulon-4 receptor
C: Vasculostatin-120
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,81916
ポリマ－37,9502
非ポリマー1,86814
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Reticulon-4 receptor
D: Vasculostatin-120
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,29811
ポリマ－37,9502
非ポリマー1,3489
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)63.468, 95.315, 69.682
Angle α, β, γ (deg.)90.000, 105.390, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 26 through 84 or resid 86...
21(chain B and (resid 26 through 84 or resid 86...
12(chain C and (resid 4 through 28 or (resid 29...
22chain D

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 26 through 84 or resid 86...A26 - 84
121(chain A and (resid 26 through 84 or resid 86...A86 - 89
131(chain A and (resid 26 through 84 or resid 86...A91 - 108
141(chain A and (resid 26 through 84 or resid 86...A210 - 215
151(chain A and (resid 26 through 84 or resid 86...A217 - 246
161(chain A and (resid 26 through 84 or resid 86...A248 - 291
171(chain A and (resid 26 through 84 or resid 86...A297 - 309
181(chain A and (resid 26 through 84 or resid 86...A310 - 311
211(chain B and (resid 26 through 84 or resid 86...B26 - 84
221(chain B and (resid 26 through 84 or resid 86...B86 - 89
231(chain B and (resid 26 through 84 or resid 86...B91 - 108
241(chain B and (resid 26 through 84 or resid 86...B210 - 215
251(chain B and (resid 26 through 84 or resid 86...B217 - 246
261(chain B and (resid 26 through 84 or resid 86...B248 - 291
271(chain B and (resid 26 through 84 or resid 86...B297 - 309
281(chain B and (resid 26 through 84 or resid 86...B310 - 311
112(chain C and (resid 4 through 28 or (resid 29...C4 - 28
122(chain C and (resid 4 through 28 or (resid 29...C29
132(chain C and (resid 4 through 28 or (resid 29...C3 - 501
142(chain C and (resid 4 through 28 or (resid 29...C3 - 501
152(chain C and (resid 4 through 28 or (resid 29...C3 - 501
212chain DD4 - 301

NCSアンサンブル:
ID
1
2

-
要素

-
タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 Reticulon-4 receptor / Nogo receptor / NgR / Nogo-66 receptor / Nogo66 receptor-1 / NgR1


分子量: 31869.578 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Rtn4r, Ngr1, Nogor / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q99PI8
#2: タンパク質 Vasculostatin-120 / Vstat120


分子量: 6080.832 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Adgrb1, Bai1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q3UHD1

-
糖 , 3種, 10分子

#3: 多糖 beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


タイプ: oligosaccharide / 分子量: 326.297 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpb1-3LFucpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Fucp]{[(3+1)][b-D-Glcp]{}}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: 4 / 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
#10: 糖
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / α-D-マンノピラノ-ス


タイプ: D-saccharide, alpha linking / 分子量: 180.156 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C6H12O6
識別子タイププログラム
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
非ポリマー , 6種, 644分子

#5: 化合物 ChemComp-PAB / 4-AMINOBENZOIC ACID / 4-アミノ安息香酸


分子量: 137.136 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C7H7NO2
#6: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
#7: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C2H6O2
#8: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#9: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H3O2
#11: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 631 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.68 Å3/Da / 溶媒含有率: 54.06 %
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 1 M succinic acid, pH 7.0, 0.02% w/v 4-Aminobenzioc acid, 0.02% w/v Azelaic acid, 0.02% w/v o-Sulfobenzoic acid monoammonium salt, 0.02% w/v Sodium 4-aminosalicylate dehydrate, 0.002 M HEPES sodium pH 6.8

-
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: SSRL / ビームライン: BL12-2 / 波長: 0.97946 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2019年4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: 0.97946 Å / 相対比: 1
反射解像度: 1.65→40.24 Å / Num. obs: 94133 / % possible obs: 98.2 % / 冗長度: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.042 / Rrim(I) all: 0.092 / Net I/σ(I): 10.7 / Num. measured all: 435598 / Scaling rejects: 2
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.684.61.5442139046490.4110.7951.744198.5
9.04-40.244.70.02528766060.9990.0130.02842.298.4

-
解析

ソフトウェア
名称バージョン分類
Aimless0.7.4データスケーリング
PHENIX1.14_3260精密化
PDB_EXTRACT3.25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: 1OZN

1ozn


解像度: 1.65→38.871 Å / SU ML: 0.22 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 21.06 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1945 1998 2.12 %
Rwork0.165 92069 -
obs0.1656 94067 98.11 %
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: 107.31 Å2 / Biso mean: 30.2624 Å2 / Biso min: 13.3 Å2
精密化ステップサイクル: final / 解像度: 1.65→38.871 Å
タンパク質核酸リガンド溶媒全体
原子数5151 0 213 631 5995
Biso mean--43.76 39.3 -
残基数----653
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2608X-RAY DIFFRACTION5.535TORSIONAL
12B2608X-RAY DIFFRACTION5.535TORSIONAL
21C469X-RAY DIFFRACTION5.535TORSIONAL
22D469X-RAY DIFFRACTION5.535TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6505-1.69170.31981410.2984657398
1.6917-1.73750.26461420.2691657698
1.7375-1.78860.30851430.2514654498
1.7886-1.84630.26371400.2302643497
1.8463-1.91230.27261420.201658999
1.9123-1.98890.21211440.1857662299
1.9889-2.07940.23541430.1772655798
2.0794-2.1890.22131400.1633649197
2.189-2.32620.18971430.1581657398
2.3262-2.50570.20551440.1641661999
2.5057-2.75780.20861430.1564657298
2.7578-3.15670.18161440.1639660398
3.1567-3.97650.17791440.1404666899
3.9765-38.8710.1421450.1406664897
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)
17.7445-2.27523.91283.0218-1.56162.5162-0.85291.71610.90280.18750.1358-0.5082-0.56460.88060.39930.3895-0.1567-0.07130.54860.17380.379913.379-3.5073.939
27.68360.31623.66171.5366-0.52762.7931-0.34840.66740.3295-0.19080.0784-0.1317-0.16170.24490.19840.2117-0.03630.0130.24360.01640.15067.553-8.8144.848
39.33044.43091.05564.15394.34897.6608-0.10990.2958-0.1343-0.24270.0634-0.118-0.1654-0.2338-0.00620.19130.005-0.01410.2411-0.01340.1429-2.078-12.215.8
44.09571.85581.29943.3851.0673.4681-0.01930.1324-0.0858-0.1692-0.0461-0.33410.04260.20770.0650.19710.02190.01040.18170.01970.165810.173-15.47210.562
56.29794.82422.08669.18161.94698.9414-0.11690.0159-0.3149-0.10280.166-0.10940.0134-0.0267-0.13280.15750.0079-0.00430.21430.00830.1666-3.974-14.98510.21
62.7095-0.63090.28032.2586-0.12821.36620.0166-0.0237-0.1093-0.0687-0.0211-0.07470.0449-0.0470.0140.1833-0.00010.00750.1554-0.00660.1433.921-19.14916.604
72.20130.76351.76132.5382-0.79264.0124-0.19550.1008-0.1276-0.14380.19720.0446-0.0395-0.26570.07350.1934-0.00970.01670.1835-0.00710.1536-1.644-15.52521.462
84.1869-0.83530.87182.1119-0.4512.4513-0.0579-0.03930.02490.00170.0181-0.1537-0.02740.04230.0310.1474-0.00340.01570.14490.00290.1272.791-18.43926.635
95.76742.5474-2.1843.09111.02782.9688-0.21130.3703-0.2056-0.47830.19430.54560.3715-0.6568-0.01360.2099-0.0195-0.01140.2481-0.02580.2009-11.205-19.44826.396
104.70534.04290.2475.173-2.24383.5824-0.1425-0.177-1.0034-0.17780.0865-0.28350.6820.10740.04440.28690.00420.00710.21130.05090.25850.095-25.45133.436
114.6540.3039-0.942.8933-0.83782.01570.0101-0.0648-0.11430.0569-0.0067-0.00060.1279-0.0089-0.00690.164-0.0097-0.00550.1371-0.02180.094-3.817-17.73333.278
125.7297-0.09190.10211.7262-0.12112.82710.0415-0.123-0.04860.0754-0.0561-0.00070.04750.02890.01850.1672-0.0015-0.00550.1185-0.01070.0973-5.44-16.67338.472
132.1447-1.90290.06742.0190.71287.9201-0.0237-0.10740.02580.3903-0.1236-0.56030.14790.61130.14920.2158-0.0124-0.01960.28770.02250.20983.06-14.19743.038
147.22562.819-1.14942.75830.65451.01660.0208-0.345-0.11090.0721-0.16430.04490.0598-0.03120.12010.1707-0.0129-0.00290.16650.01870.1524-13.478-12.10340.42
153.96064.0649-2.89944.673-4.44257.42740.2619-0.3893-0.20160.7514-0.1145-0.2772-0.1350.1824-0.03960.2771-0.0111-0.0220.29680.01260.2319-3.486-13.43249.261
162.10790.5317-0.74781.25-0.10091.53090.02510.0192-0.01850.09480.0106-0.0662-0.0624-0.003-0.03150.1937-0.01840.00430.1631-0.00910.1569-15.344-10.11948.918
174.63844.3246-5.09184.0683-4.73575.60860.5417-0.9280.09060.7545-0.5898-0.2793-0.95880.42070.14880.3447-0.08430.03290.2972-0.03610.268-5.839-3.66353.715
185.33376.568-2.03928.3826-1.5692.9543-0.23160.45270.3839-0.32130.25160.3111-0.1524-0.3476-0.05630.2231-0.00230.00670.2450.01710.1503-20.956-6.21446.697
198.9672-2.69095.58684.13292.08468.5454-0.07050.09720.4312-0.0922-0.14560.1328-0.6974-0.48450.21080.31320.04550.01540.21610.00850.1782-23.968-3.91751.688
206.0464.63350.01173.630.67016.4917-0.07710.3784-0.3861-0.37890.0731-0.5250.3223-0.5977-0.03960.3315-0.01120.01330.3045-0.01780.1833-20.88-11.02960.602
218.5599-0.404-0.48915.0759-1.49196.2901-0.06752.5435-0.6778-0.4594-0.57010.77330.12460.00510.2450.4825-0.0281-0.02630.955-0.3580.41652.0675.816-0.235
227.7275-1.60532.05094.6182-0.09213.4246-0.96280.3271-1.6130.4323-0.37511.30821.6328-1.4631.04990.4042-0.1080.18620.4194-0.22440.6194-5.0832.6629.777
232.2824-0.0058-2.4152.61880.28682.6271-0.22890.8064-0.6176-0.377-0.05170.08180.1214-0.26680.21270.2501-0.0034-0.0130.3063-0.03670.24517.049.2394.916
242.6328-2.40190.22555.404-2.31242.92360.10960.60280.2383-0.3509-0.01740.0256-0.1176-0.154-0.03570.23220.0056-0.03470.2143-0.00180.15459.25419.3565.955
258.22660.4223-1.57482.05290.32952.4855-0.00810.31360.1636-0.14010.00480.2674-0.0838-0.15180.0170.20930.0191-0.01330.15460.02410.19216.26413.85811.397
262.4648-0.5057-0.01072.6047-0.01151.30820.01190.05930.0165-0.0462-0.01040.1202-0.03520.0333-0.00030.17530.00230.00650.16440.00880.18789.32218.24117.666
274.0268-3.3453-2.43353.11753.40217.1907-0.1432-0.34350.4412-0.9010.4992-0.2172-0.60750.6069-0.37430.2465-0.075-0.00360.27940.00160.241322.28519.50219.924
284.26950.2293-0.91943.3877-0.65982.9276-0.01330.12350.2113-0.01960.10780.2177-0.0717-0.0786-0.10260.15790.0074-0.00190.1564-0.00120.18368.58622.27826.707
294.39020.58650.20586.22922.48625.2449-0.14270.06490.10190.11030.0228-0.0792-0.07540.15020.09960.1597-0.0029-0.02360.150.06350.133317.45519.38928.641
303.7946-1.4599-0.07093.2734-0.31412.2471-0.0979-0.195-0.18920.07120.11660.32870.0482-0.13060.00350.1554-0.01510.00590.16160.01640.175311.35314.3331.182
317.26431.82570.85155.33920.20131.56910.077-0.0840.60110.2469-0.10860.179-0.2268-0.1220.0050.18120.0098-0.0050.160.00190.131717.15621.96637.063
328.79811.7354-0.39553.30660.0953.2597-0.10610.21870.134-0.03790.1476-0.00020.04530.0698-0.01850.17720.00990.0040.12480.02960.162422.91214.52935.97
334.40955.85-0.73678.45361.43379.5288-0.1794-0.68140.63920.32410.00270.3793-0.2554-0.02520.17330.19260.0157-0.020.1807-0.04250.212317.94321.99945.037
343.4716-0.5149-0.40411.80320.54642.59710.0341-0.1322-0.11630.1501-0.0285-0.01980.0542-0.114-0.01180.2032-0.0187-0.00710.17050.0230.176921.18312.53740.985
353.57983.35434.35943.48154.37585.55970.2932-1.07380.26580.4556-0.44250.37970.2459-0.30020.1170.2553-0.03170.04030.3006-0.01170.227517.20815.5549.598
362.11330.9370.9681.50710.61432.07070.1292-0.0119-0.12520.1616-0.04210.07180.1645-0.0084-0.09910.1975-0.02-0.01360.15650.01630.195628.2879.79645.827
373.79113.26075.03292.90444.24457.02190.5441-0.568-0.31750.5305-0.28020.09630.5912-0.4512-0.21030.2853-0.04370.01260.26810.04370.210823.0028.06554.42
384.84726.64710.3519.11050.08523.2943-0.1131-0.0012-0.3613-0.30160.0407-0.4320.1540.3284-0.03380.22210.0145-0.01230.20570.01150.219334.1666.64746.741
397.6809-2.4115-3.78123.3904-0.71718.6642-0.0975-0.2172-0.3601-0.129-0.1115-0.07740.67450.63450.22220.27180.0382-0.03880.18640.03780.198436.7944.55552.414
403.53142.4705-3.73793.2297-3.72844.78050.2407-0.28070.65911.73540.0891-0.3893-0.73390.43530.08860.6644-0.0587-0.2270.37640.01730.348534.99112.37960.81
414.20942.76093.54157.84971.99612.99510.1969-0.95140.42722.03750.2896-0.7493-0.39021.0965-0.48760.6979-0.0636-0.09640.7232-0.19230.40151.59712.28853.623
422.6871.61660.37575.20622.54933.5820.14170.02370.00810.01480.00670.07150.1010.1236-0.14160.2461-0.00720.02610.20190.00440.2059-6.1682.30838.186
435.3395-0.85592.60438.20932.52372.3452-0.31730.47960.1699-0.97310.35150.2156-0.4936-0.08030.01250.3728-0.05370.02280.23720.02530.2029-5.045.70432.609
444.4897-1.10311.75628.47685.38475.85260.0278-0.93590.72950.7990.0770.1485-0.86630.3921-0.07950.4272-0.09350.09920.4613-0.13430.2732-3.02711.76948.666
451.35940.70420.70221.67181.59065.4822-0.3107-0.69370.613-0.160.3675-0.5475-0.46830.3209-0.06731.4342-0.38230.29180.7396-0.40340.6302-0.46919.84254.233
463.66020.84540.85625.99476.01156.04870.09080.25880.4233-0.13930.19460.1039-0.72090.1397-0.20290.403-0.0810.03740.26170.00580.2765-1.3599.85838.791
478.4069-0.5962.57398.40140.47841.7842-0.01541.05160.0399-1.77990.620.118-0.74010.3361-0.40930.608-0.07920.08670.39920.03090.2638-5.167-1.35726.357
485.9535-0.68472.04696.45733.20726.4819-0.1225-0.9707-0.67231.31060.2320.56450.8177-1.2933-0.30970.8329-0.2290.06170.96740.27250.517611.849-11.15753.529
492.37791.54610.72545.391-2.29252.73660.0706-0.1545-0.35120.1987-0.1156-0.33530.228-0.05020.07040.2492-0.0219-0.04180.19220.00640.253619.449-1.93338.227
505.0851-0.6189-3.37456.2181-2.22823.3774-0.27790.6274-0.3884-0.76540.0576-0.19570.3481-0.4120.14920.3521-0.0597-0.01520.2367-0.02140.281318.328-5.43832.703
512.8727-1.51690.9163.9652-2.84212.04910.2777-1.0097-0.67391.3109-0.1956-0.30351.0158-0.27610.20480.8296-0.2161-0.21460.6250.31110.377416.616-12.48451.147
526.459-0.7918-1.65329.7296-5.53433.86910.2127-0.4019-1.03030.7524-0.1373-0.42380.7686-0.0874-0.0460.5346-0.1415-0.12350.26390.05180.378114.936-11.39941.321
533.36992.8169-3.90132.5904-3.31734.5445-0.63341.2507-0.115-2.10710.80570.09320.4677-0.6178-0.11780.6487-0.1472-0.07060.4251-0.00150.338218.3831.60926.366
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 26:38 )A26 - 38
2X-RAY DIFFRACTION2( CHAIN A AND RESID 39:63 )A39 - 63
3X-RAY DIFFRACTION3( CHAIN A AND RESID 64:71 )A64 - 71
4X-RAY DIFFRACTION4( CHAIN A AND RESID 72:88 )A72 - 88
5X-RAY DIFFRACTION5( CHAIN A AND RESID 89:95 )A89 - 95
6X-RAY DIFFRACTION6( CHAIN A AND RESID 96:131 )A96 - 131
7X-RAY DIFFRACTION7( CHAIN A AND RESID 132:144 )A132 - 144
8X-RAY DIFFRACTION8( CHAIN A AND RESID 145:162 )A145 - 162
9X-RAY DIFFRACTION9( CHAIN A AND RESID 163:169 )A163 - 169
10X-RAY DIFFRACTION10( CHAIN A AND RESID 170:175 )A170 - 175
11X-RAY DIFFRACTION11( CHAIN A AND RESID 176:197 )A176 - 197
12X-RAY DIFFRACTION12( CHAIN A AND RESID 198:222 )A198 - 222
13X-RAY DIFFRACTION13( CHAIN A AND RESID 223:229 )A223 - 229
14X-RAY DIFFRACTION14( CHAIN A AND RESID 230:241 )A230 - 241
15X-RAY DIFFRACTION15( CHAIN A AND RESID 242:253 )A242 - 253
16X-RAY DIFFRACTION16( CHAIN A AND RESID 254:275 )A254 - 275
17X-RAY DIFFRACTION17( CHAIN A AND RESID 276:280 )A276 - 280
18X-RAY DIFFRACTION18( CHAIN A AND RESID 281:291 )A281 - 291
19X-RAY DIFFRACTION19( CHAIN A AND RESID 292:301 )A292 - 301
20X-RAY DIFFRACTION20( CHAIN A AND RESID 302:309 )A302 - 309
21X-RAY DIFFRACTION21( CHAIN B AND RESID 25:34 )B25 - 34
22X-RAY DIFFRACTION22( CHAIN B AND RESID 35:39 )B35 - 39
23X-RAY DIFFRACTION23( CHAIN B AND RESID 40:67 )B40 - 67
24X-RAY DIFFRACTION24( CHAIN B AND RESID 68:79 )B68 - 79
25X-RAY DIFFRACTION25( CHAIN B AND RESID 80:95 )B80 - 95
26X-RAY DIFFRACTION26( CHAIN B AND RESID 96:138 )B96 - 138
27X-RAY DIFFRACTION27( CHAIN B AND RESID 139:144 )B139 - 144
28X-RAY DIFFRACTION28( CHAIN B AND RESID 145:157 )B145 - 157
29X-RAY DIFFRACTION29( CHAIN B AND RESID 158:175 )B158 - 175
30X-RAY DIFFRACTION30( CHAIN B AND RESID 176:188 )B176 - 188
31X-RAY DIFFRACTION31( CHAIN B AND RESID 189:203 )B189 - 203
32X-RAY DIFFRACTION32( CHAIN B AND RESID 204:216 )B204 - 216
33X-RAY DIFFRACTION33( CHAIN B AND RESID 217:223 )B217 - 223
34X-RAY DIFFRACTION34( CHAIN B AND RESID 224:241 )B224 - 241
35X-RAY DIFFRACTION35( CHAIN B AND RESID 242:251 )B242 - 251
36X-RAY DIFFRACTION36( CHAIN B AND RESID 252:268 )B252 - 268
37X-RAY DIFFRACTION37( CHAIN B AND RESID 269:280 )B269 - 280
38X-RAY DIFFRACTION38( CHAIN B AND RESID 281:291 )B281 - 291
39X-RAY DIFFRACTION39( CHAIN B AND RESID 292:303 )B292 - 303
40X-RAY DIFFRACTION40( CHAIN B AND RESID 304:309 )B304 - 309
41X-RAY DIFFRACTION41( CHAIN C AND RESID 3:7 )C3 - 7
42X-RAY DIFFRACTION42( CHAIN C AND RESID 8:16 )C8 - 16
43X-RAY DIFFRACTION43( CHAIN C AND RESID 17:22 )C17 - 22
44X-RAY DIFFRACTION44( CHAIN C AND RESID 23:27 )C23 - 27
45X-RAY DIFFRACTION45( CHAIN C AND RESID 28:42 )C28 - 42
46X-RAY DIFFRACTION46( CHAIN C AND RESID 43:48 )C43 - 48
47X-RAY DIFFRACTION47( CHAIN C AND RESID 49:54 )C49 - 54
48X-RAY DIFFRACTION48( CHAIN D AND RESID 4:7 )D4 - 7
49X-RAY DIFFRACTION49( CHAIN D AND RESID 8:16 )D8 - 16
50X-RAY DIFFRACTION50( CHAIN D AND RESID 17:22 )D17 - 22
51X-RAY DIFFRACTION51( CHAIN D AND RESID 23:29 )D23 - 29
52X-RAY DIFFRACTION52( CHAIN D AND RESID 41:48 )D41 - 48
53X-RAY DIFFRACTION53( CHAIN D AND RESID 49:54 )D49 - 54

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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