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- PDB-8os6: Structure of a GFRA1/GDNF LICAM complex -

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基本情報

登録情報
データベース: PDB / ID: 8os6
タイトルStructure of a GFRA1/GDNF LICAM complex
要素
  • GDNF family receptor alpha
  • Glial cell line-derived neurotrophic factor
キーワードCELL ADHESION / Adhesion / Synapse / Complex / signalling
機能・相同性
機能・相同性情報


diencephalon development / regulation of morphogenesis of a branching structure / positive regulation of ureteric bud formation / postganglionic parasympathetic fiber development / positive regulation of monooxygenase activity / regulation of dopaminergic neuron differentiation / glial cell-derived neurotrophic factor receptor binding / glial cell-derived neurotrophic factor receptor signaling pathway / regulation of dopamine uptake involved in synaptic transmission / enteric nervous system development ...diencephalon development / regulation of morphogenesis of a branching structure / positive regulation of ureteric bud formation / postganglionic parasympathetic fiber development / positive regulation of monooxygenase activity / regulation of dopaminergic neuron differentiation / glial cell-derived neurotrophic factor receptor binding / glial cell-derived neurotrophic factor receptor signaling pathway / regulation of dopamine uptake involved in synaptic transmission / enteric nervous system development / peristalsis / positive regulation of branching involved in ureteric bud morphogenesis / peripheral nervous system development / sympathetic nervous system development / metanephros development / mRNA stabilization / neural crest cell migration / branching involved in ureteric bud morphogenesis / MAP kinase kinase kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / receptor tyrosine kinase binding / neuron projection development / signaling receptor activity / nervous system development / protein-containing complex assembly / negative regulation of neuron apoptotic process / receptor complex / external side of plasma membrane / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
類似検索 - 分子機能
Glial cell line-derived neurotrophic factor receptor, alpha 1 / Glial cell line-derived neurotrophic factor / : / Glial cell line-derived neurotrophic factor receptor, alpha 1/2 / Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / Glial cell line-derived neurotrophic factor family / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain ...Glial cell line-derived neurotrophic factor receptor, alpha 1 / Glial cell line-derived neurotrophic factor / : / Glial cell line-derived neurotrophic factor receptor, alpha 1/2 / Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / Glial cell line-derived neurotrophic factor family / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine
類似検索 - ドメイン・相同性
GDNF family receptor alpha / Glial cell line-derived neurotrophic factor
類似検索 - 構成要素
生物種Danio rerio (ゼブラフィッシュ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.66 Å
データ登録者Houghton, F.M. / Adams, S.E. / Briggs, D.C. / McDonald, N.Q.
資金援助 英国, 1件
組織認可番号
The Francis Crick InstituteCC2068 英国
引用ジャーナル: Nat Commun / : 2023
タイトル: Architecture and regulation of a GDNF-GFRα1 synaptic adhesion assembly.
著者: F M Houghton / S E Adams / A S Ríos / L Masino / A G Purkiss / D C Briggs / F Ledda / N Q McDonald /
要旨: Glial-cell line derived neurotrophic factor (GDNF) bound to its co-receptor GFRα1 stimulates the RET receptor tyrosine kinase, promoting neuronal survival and neuroprotection. The GDNF-GFRα1 ...Glial-cell line derived neurotrophic factor (GDNF) bound to its co-receptor GFRα1 stimulates the RET receptor tyrosine kinase, promoting neuronal survival and neuroprotection. The GDNF-GFRα1 complex also supports synaptic cell adhesion independently of RET. Here, we describe the structure of a decameric GDNF-GFRα1 assembly determined by crystallography and electron microscopy, revealing two GFRα1 pentamers bridged by five GDNF dimers. We reconsitituted the assembly between adhering liposomes and used cryo-electron tomography to visualize how the complex fulfils its membrane adhesion function. The GFRα1:GFRα1 pentameric interface was further validated both in vitro by native PAGE and in cellulo by cell-clustering and dendritic spine assays. Finally, we provide biochemical and cell-based evidence that RET and heparan sulfate cooperate to prevent assembly of the adhesion complex by competing for the adhesion interface. Our results provide a mechanistic framework to understand GDNF-driven cell adhesion, its relationship to trophic signalling, and the central role played by GFRα1.
履歴
登録2023年4月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年11月29日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Database references / カテゴリ: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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: GDNF family receptor alpha
B: Glial cell line-derived neurotrophic factor
C: GDNF family receptor alpha
D: Glial cell line-derived neurotrophic factor
E: GDNF family receptor alpha
F: Glial cell line-derived neurotrophic factor
G: GDNF family receptor alpha
H: Glial cell line-derived neurotrophic factor
I: GDNF family receptor alpha
J: Glial cell line-derived neurotrophic factor
K: GDNF family receptor alpha
L: Glial cell line-derived neurotrophic factor
M: GDNF family receptor alpha
N: Glial cell line-derived neurotrophic factor
O: GDNF family receptor alpha
P: Glial cell line-derived neurotrophic factor
Q: GDNF family receptor alpha
R: Glial cell line-derived neurotrophic factor
S: GDNF family receptor alpha
T: Glial cell line-derived neurotrophic factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)411,87038
ポリマ-405,88220
非ポリマー5,98918
34219
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, Negative stain electron microscopy reveals a particle with the same dimensions, 5-fold symmetry and architecture. Assembly also validated by Native PAGE and mutation of ...根拠: 電子顕微鏡法, Negative stain electron microscopy reveals a particle with the same dimensions, 5-fold symmetry and architecture. Assembly also validated by Native PAGE and mutation of residues in the interface
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area53420 Å2
ΔGint-123 kcal/mol
Surface area139130 Å2
単位格子
Length a, b, c (Å)114.140, 170.044, 130.791
Angle α, β, γ (deg.)90.000, 96.170, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

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タンパク質 , 2種, 20分子 ACEGIKMOQSBDFHJLNPRT

#1: タンパク質
GDNF family receptor alpha


分子量: 29249.277 Da / 分子数: 10 / 由来タイプ: 組換発現
由来: (組換発現) Danio rerio (ゼブラフィッシュ)
遺伝子: gfralpha1a, zgc:110129, gfra1a
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q98TT9
#2: タンパク質
Glial cell line-derived neurotrophic factor / zGDNF


分子量: 11338.884 Da / 分子数: 10 / 由来タイプ: 組換発現
由来: (組換発現) Danio rerio (ゼブラフィッシュ)
遺伝子: gdnf
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q98TU0

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, 4種, 18分子

#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: 4 / 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: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 570.542 Da / 分子数: 3 / 由来タイプ: 合成
記述子タイププログラム
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 多糖 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 367.349 Da / 分子数: 1 / 由来タイプ: 天然
記述子タイププログラム
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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: 10 / 由来タイプ: 天然 / : 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

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非ポリマー , 1種, 19分子

#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 19 / 由来タイプ: 天然 / : H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.67 Å3/Da / 溶媒含有率: 66.48 %
結晶化温度: 303 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 100mM Tris pH 7.5 100mM NaCl 3% (v/v) Acetonitrile 5% (w/v)PEG 20k
Temp details: Room Temperature

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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: Diamond / ビームライン: I04-1 / 波長: 0.92 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2017年4月30日
放射モノクロメーター: Single Bounce / 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: 0.92 Å / 相対比: 1
反射解像度: 2.65→90.45 Å / Num. obs: 140996 / % possible obs: 99.1 % / 冗長度: 13.5 % / Biso Wilson estimate: 77.01 Å2 / CC1/2: 0.99 / Net I/σ(I): 4.75
反射 シェル解像度: 2.65→2.7 Å / 冗長度: 12 % / Mean I/σ(I) obs: 0.25 / Num. unique obs: 6703 / CC1/2: 0.281 / % possible all: 95.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
DIALS2.2.5データ削減
DIALS2.2.5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
開始モデル: 3FUB
解像度: 2.66→90.45 Å / SU ML: 0.529 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 37.4716
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2828 6139 4.9 %Random
Rwork0.2437 119036 --
obs0.2456 125175 88.12 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 82.95 Å2
精密化ステップサイクル: LAST / 解像度: 2.66→90.45 Å
タンパク質核酸リガンド溶媒全体
原子数23416 0 390 19 23825
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.002424243
X-RAY DIFFRACTIONf_angle_d0.46932720
X-RAY DIFFRACTIONf_chiral_restr0.04013694
X-RAY DIFFRACTIONf_plane_restr0.00364245
X-RAY DIFFRACTIONf_dihedral_angle_d12.78199185
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.690.6975410.6183805X-RAY DIFFRACTION18.09
2.69-2.720.5193620.52171280X-RAY DIFFRACTION28.35
2.72-2.760.4248920.46541841X-RAY DIFFRACTION41.16
2.76-2.790.51141040.47591907X-RAY DIFFRACTION42.53
2.79-2.830.42111350.42922901X-RAY DIFFRACTION64.49
2.83-2.870.46171910.43343488X-RAY DIFFRACTION77.58
2.87-2.910.43742320.4224192X-RAY DIFFRACTION94.25
2.91-2.950.39251940.40964310X-RAY DIFFRACTION95.38
2.95-30.41672340.41324429X-RAY DIFFRACTION98.33
3-3.040.46082140.41724457X-RAY DIFFRACTION98.67
3.04-3.10.40012350.38924429X-RAY DIFFRACTION98.75
3.1-3.150.37892320.35724446X-RAY DIFFRACTION98.55
3.15-3.210.36632440.34624377X-RAY DIFFRACTION98.74
3.21-3.280.33921990.33164457X-RAY DIFFRACTION98.62
3.28-3.350.34592260.32034502X-RAY DIFFRACTION99.02
3.35-3.430.32712430.30364408X-RAY DIFFRACTION99.04
3.43-3.520.35232270.29364449X-RAY DIFFRACTION99
3.52-3.610.29682320.28964439X-RAY DIFFRACTION99.24
3.61-3.720.32862290.28354496X-RAY DIFFRACTION99.16
3.72-3.840.29632260.26634463X-RAY DIFFRACTION99.28
3.84-3.970.27392360.23174461X-RAY DIFFRACTION99.24
3.97-4.130.24992210.21614463X-RAY DIFFRACTION99.3
4.13-4.320.26532300.20074481X-RAY DIFFRACTION99.37
4.32-4.550.23812300.19364532X-RAY DIFFRACTION99.56
4.55-4.830.20472380.18554450X-RAY DIFFRACTION99.51
4.83-5.210.21232190.17744532X-RAY DIFFRACTION99.56
5.21-5.730.23532510.18714466X-RAY DIFFRACTION99.6
5.73-6.560.28052510.21714501X-RAY DIFFRACTION99.58
6.56-8.260.24522300.19844528X-RAY DIFFRACTION99.62
8.26-90.450.23492410.17514546X-RAY DIFFRACTION98.68
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.17087445516-3.13016690916-0.9091995396620.9063764268071.820034794865.11186721689-0.3426360511-0.2217809486150.181839428552-0.07627378313830.269334551713-0.5463420628170.230910339351-0.1712700827170.07745012862630.724218808473-0.0211881273035-0.03503372848330.242433378373-0.001044051259310.641617680057-5.7131.81281.67
25.786045883180.3804176367623.145409666171.464029732710.2307237983491.40478816005-0.1095110016020.0227319441755-0.799965566669-0.5028997675830.2872700193660.07425959294170.2745412906230.126109765464-0.1458711499210.713263109481-0.02692439867320.03200516014540.3824927092740.02182630930580.7623891341695.462-3.72989.979
33.45314770727-0.265681996817-2.385386403011.500409161740.6038709672724.70786374565-0.0932465826632-0.220906108625-0.0292886832920.1300557625730.234188916982-0.1953483891680.287610793350.196903151135-0.1550901076770.7996877776410.0377026172885-0.06793665349490.274723465821-0.002022196411730.6742365662692.1284.67299.712
43.083777215122.1196390539-2.665741427713.15840684156-1.97253777519.227853940280.1592687659640.3580508215320.0909077848008-0.01791415109970.3227661315480.408635297991-0.150985850593-1.22963983188-0.4540363969250.6656135381080.00309618060145-0.02873102024720.665967983551-0.0718611837570.657598264487-21.3542.49263.034
57.95712386656-2.258766721383.445591788195.0961128034-0.961260435532.77711497119-1.27780127741-0.124331524991-0.9554007284480.217527861161.469818922631.004406424571.10532679482-1.98748836053-0.07029758874151.08328731667-0.279989669610.2047299158951.19273024970.2090697673770.776407960026-23.6981.03133.893
64.20688185917-1.62537138601-0.3539968707768.09988707562-4.842587996382.69979586620.19370216319-0.006992289757960.30577245735-0.839633115072-0.09317526815-0.6177532607060.0769704900944-0.494228016299-0.1766309467220.661450627542-0.07198911136070.03953646409110.471963411712-0.02918640832140.631579403794-12.2270.57665.244
73.585516113170.505694644416-0.5059716930271.414179923340.3273538390282.808664113290.2006317279820.189875025157-0.229120943993-0.1379269059730.25617152525-0.7323137563770.30240361007-0.225324406226-0.4264649879180.9144235083880.127210075764-0.07678221658690.4118310212290.07170165586720.77393448607-12.6238.98176.927
83.18541202851-1.05957263584-2.573839056264.81302642776-2.883449566479.677123294080.806107433168-0.328844137395-0.5129115442470.759375168158-0.239200805462-0.00719376954913-2.00477571457-0.371579156637-0.5410270218460.9398044189180.033946357591-0.1400253512840.368386858992-0.0782792093640.781071003376-14.5645.88390.124
95.394841417651.732648112410.6891890510542.60069230851-2.876975739034.91686996978-0.7069735504440.3521547392570.3694608663490.2729482211890.3306586441920.977912748636-0.30550093061-0.886802499420.2782010771410.5651782399730.0321515891745-0.1354479054750.448499312055-0.01428700405510.730756970296-20.35238.69185.283
106.51976703731-2.698347188811.80945004251.50114460232-1.625796651511.79896001305-0.334479577590.412474490181-0.3737247445910.4561104342890.09970348501750.410463435346-0.09490602148270.006886250201880.2255711414040.734664266880.1472170695570.00845156294770.3778345653570.02798225038790.803049800441-12.99120.53489.223
112.334361984970.5313228395551.959467509093.085921333380.6395880857644.25606091465-0.6760335392560.574025645830.429132959594-1.191127605860.277113912888-0.1995276076520.4485673969481.493336718690.4189457250781.08183339132-0.03822808026940.1812429089110.5241695308170.1428998343560.733372842998-0.93528.28193.339
121.953436216531.63537747593-0.6156141135931.237236182-0.01748308735717.008004631190.510888464648-0.09365433902930.1690157152080.328717529880.007311280483240.1820705827770.7132784358481.00477939028-0.5755510034630.6259294471830.1144577296930.02544788851340.35453634238-0.02574646275650.639795568053-4.22638.016102.382
133.80606858724-2.48065094347-0.4664486667765.859062449352.367823746285.69147075739-0.016828266483-0.110554923353-0.2772924430020.777116897386-0.9396541396130.3734825391971.52707201059-1.791242106620.487350468130.9002991162140.3042485498970.009682915632830.1717832297510.1935824249780.617300038556-16.63933.16192.764
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 149:222 )A149 - 222
2X-RAY DIFFRACTION2( CHAIN A AND RESID 223:256 )A223 - 256
3X-RAY DIFFRACTION3( CHAIN A AND RESID 257:355 )A257 - 355
4X-RAY DIFFRACTION4( CHAIN B AND RESID 139:178 )B139 - 178
5X-RAY DIFFRACTION5( CHAIN B AND RESID 179:201 )B179 - 201
6X-RAY DIFFRACTION6( CHAIN B AND RESID 202:235 )B202 - 235
7X-RAY DIFFRACTION7( CHAIN C AND RESID 151:202 )C151 - 202
8X-RAY DIFFRACTION8( CHAIN C AND RESID 203:222 )C203 - 222
9X-RAY DIFFRACTION9( CHAIN C AND RESID 223:237 )C223 - 237
10X-RAY DIFFRACTION10( CHAIN C AND RESID 238:256 )C238 - 256
11X-RAY DIFFRACTION11( CHAIN C AND RESID 257:269 )C257 - 269
12X-RAY DIFFRACTION12( CHAIN C AND RESID 270:295 )C270 - 295
13X-RAY DIFFRACTION13( CHAIN C AND RESID 296:314 )C296 - 314
14X-RAY DIFFRACTION14( CHAIN C AND RESID 315:325 )C315 - 325
15X-RAY DIFFRACTION15( CHAIN C AND RESID 326:354 )C326 - 354
16X-RAY DIFFRACTION16( CHAIN D AND RESID 138:150 )D138 - 150
17X-RAY DIFFRACTION17( CHAIN D AND RESID 151:162 )D151 - 162
18X-RAY DIFFRACTION18( CHAIN D AND RESID 163:178 )D163 - 178
19X-RAY DIFFRACTION19( CHAIN D AND RESID 179:190 )D179 - 190
20X-RAY DIFFRACTION20( CHAIN D AND RESID 191:207 )D191 - 207
21X-RAY DIFFRACTION21( CHAIN D AND RESID 208:224 )D208 - 224
22X-RAY DIFFRACTION22( CHAIN D AND RESID 225:235 )D225 - 235
23X-RAY DIFFRACTION23( CHAIN E AND RESID 150:212 )E150 - 212
24X-RAY DIFFRACTION24( CHAIN E AND RESID 213:222 )E213 - 222
25X-RAY DIFFRACTION25( CHAIN E AND RESID 223:237 )E223 - 237
26X-RAY DIFFRACTION26( CHAIN E AND RESID 238:256 )E238 - 256
27X-RAY DIFFRACTION27( CHAIN E AND RESID 257:269 )E257 - 269
28X-RAY DIFFRACTION28( CHAIN E AND RESID 270:284 )E270 - 284
29X-RAY DIFFRACTION29( CHAIN E AND RESID 285:322 )E285 - 322
30X-RAY DIFFRACTION30( CHAIN E AND RESID 323:336 )E323 - 336
31X-RAY DIFFRACTION31( CHAIN E AND RESID 337:354 )E337 - 354
32X-RAY DIFFRACTION32( CHAIN F AND RESID 138:142 )F138 - 142
33X-RAY DIFFRACTION33( CHAIN F AND RESID 143:190 )F143 - 190
34X-RAY DIFFRACTION34( CHAIN F AND RESID 191:235 )F191 - 235
35X-RAY DIFFRACTION35( CHAIN G AND RESID 150:178 )G150 - 178
36X-RAY DIFFRACTION36( CHAIN G AND RESID 179:212 )G179 - 212
37X-RAY DIFFRACTION37( CHAIN G AND RESID 213:222 )G213 - 222
38X-RAY DIFFRACTION38( CHAIN G AND RESID 223:269 )G223 - 269
39X-RAY DIFFRACTION39( CHAIN G AND RESID 270:304 )G270 - 304
40X-RAY DIFFRACTION40( CHAIN G AND RESID 305:322 )G305 - 322
41X-RAY DIFFRACTION41( CHAIN G AND RESID 323:353 )G323 - 353
42X-RAY DIFFRACTION42( CHAIN H AND RESID 140:178 )H140 - 178
43X-RAY DIFFRACTION43( CHAIN H AND RESID 179:202 )H179 - 202
44X-RAY DIFFRACTION44( CHAIN H AND RESID 203:235 )H203 - 235
45X-RAY DIFFRACTION45( CHAIN I AND RESID 151:163 )I151 - 163
46X-RAY DIFFRACTION46( CHAIN I AND RESID 164:188 )I164 - 188
47X-RAY DIFFRACTION47( CHAIN I AND RESID 189:202 )I189 - 202
48X-RAY DIFFRACTION48( CHAIN I AND RESID 203:237 )I203 - 237
49X-RAY DIFFRACTION49( CHAIN I AND RESID 238:269 )I238 - 269
50X-RAY DIFFRACTION50( CHAIN I AND RESID 270:295 )I270 - 295
51X-RAY DIFFRACTION51( CHAIN I AND RESID 296:314 )I296 - 314
52X-RAY DIFFRACTION52( CHAIN I AND RESID 315:353 )I315 - 353
53X-RAY DIFFRACTION53( CHAIN J AND RESID 138:142 )J138 - 142
54X-RAY DIFFRACTION54( CHAIN J AND RESID 143:178 )J143 - 178
55X-RAY DIFFRACTION55( CHAIN J AND RESID 179:235 )J179 - 235
56X-RAY DIFFRACTION56( CHAIN K AND RESID 150:202 )K150 - 202
57X-RAY DIFFRACTION57( CHAIN K AND RESID 203:245 )K203 - 245
58X-RAY DIFFRACTION58( CHAIN K AND RESID 246:304 )K246 - 304
59X-RAY DIFFRACTION59( CHAIN K AND RESID 305:325 )K305 - 325
60X-RAY DIFFRACTION60( CHAIN K AND RESID 326:354 )K326 - 354
61X-RAY DIFFRACTION61( CHAIN L AND RESID 140:170 )L140 - 170
62X-RAY DIFFRACTION62( CHAIN L AND RESID 171:178 )L171 - 178
63X-RAY DIFFRACTION63( CHAIN L AND RESID 179:189 )L179 - 189
64X-RAY DIFFRACTION64( CHAIN L AND RESID 190:207 )L190 - 207
65X-RAY DIFFRACTION65( CHAIN L AND RESID 208:224 )L208 - 224
66X-RAY DIFFRACTION66( CHAIN L AND RESID 225:235 )L225 - 235
67X-RAY DIFFRACTION67( CHAIN M AND RESID 151:269 )M151 - 269
68X-RAY DIFFRACTION68( CHAIN M AND RESID 270:354 )M270 - 354
69X-RAY DIFFRACTION69( CHAIN N AND RESID 141:178 )N141 - 178
70X-RAY DIFFRACTION70( CHAIN N AND RESID 179:202 )N179 - 202
71X-RAY DIFFRACTION71( CHAIN N AND RESID 203:235 )N203 - 235
72X-RAY DIFFRACTION72( CHAIN O AND RESID 150:176 )O150 - 176
73X-RAY DIFFRACTION73( CHAIN O AND RESID 177:188 )O177 - 188
74X-RAY DIFFRACTION74( CHAIN O AND RESID 189:202 )O189 - 202
75X-RAY DIFFRACTION75( CHAIN O AND RESID 203:222 )O203 - 222
76X-RAY DIFFRACTION76( CHAIN O AND RESID 223:256 )O223 - 256
77X-RAY DIFFRACTION77( CHAIN O AND RESID 257:269 )O257 - 269
78X-RAY DIFFRACTION78( CHAIN O AND RESID 270:295 )O270 - 295
79X-RAY DIFFRACTION79( CHAIN O AND RESID 296:314 )O296 - 314
80X-RAY DIFFRACTION80( CHAIN O AND RESID 315:338 )O315 - 338
81X-RAY DIFFRACTION81( CHAIN O AND RESID 339:354 )O339 - 354
82X-RAY DIFFRACTION82( CHAIN P AND RESID 141:162 )P141 - 162
83X-RAY DIFFRACTION83( CHAIN P AND RESID 163:178 )P163 - 178
84X-RAY DIFFRACTION84( CHAIN P AND RESID 179:190 )P179 - 190
85X-RAY DIFFRACTION85( CHAIN P AND RESID 191:202 )P191 - 202
86X-RAY DIFFRACTION86( CHAIN P AND RESID 203:235 )P203 - 235
87X-RAY DIFFRACTION87( CHAIN Q AND RESID 151:230 )Q151 - 230
88X-RAY DIFFRACTION88( CHAIN Q AND RESID 231:295 )Q231 - 295
89X-RAY DIFFRACTION89( CHAIN Q AND RESID 296:314 )Q296 - 314
90X-RAY DIFFRACTION90( CHAIN Q AND RESID 315:354 )Q315 - 354
91X-RAY DIFFRACTION91( CHAIN R AND RESID 141:170 )R141 - 170
92X-RAY DIFFRACTION92( CHAIN R AND RESID 171:190 )R171 - 190
93X-RAY DIFFRACTION93( CHAIN R AND RESID 191:202 )R191 - 202
94X-RAY DIFFRACTION94( CHAIN R AND RESID 203:235 )R203 - 235
95X-RAY DIFFRACTION95( CHAIN S AND RESID 151:178 )S151 - 178
96X-RAY DIFFRACTION96( CHAIN S AND RESID 179:202 )S179 - 202
97X-RAY DIFFRACTION97( CHAIN S AND RESID 203:237 )S203 - 237
98X-RAY DIFFRACTION98( CHAIN S AND RESID 238:256 )S238 - 256
99X-RAY DIFFRACTION99( CHAIN S AND RESID 257:269 )S257 - 269
100X-RAY DIFFRACTION100( CHAIN S AND RESID 270:295 )S270 - 295
101X-RAY DIFFRACTION101( CHAIN S AND RESID 296:311 )S296 - 311
102X-RAY DIFFRACTION102( CHAIN S AND RESID 312:321 )S312 - 321
103X-RAY DIFFRACTION103( CHAIN S AND RESID 322:336 )S322 - 336
104X-RAY DIFFRACTION104( CHAIN S AND RESID 337:353 )S337 - 353
105X-RAY DIFFRACTION105( CHAIN T AND RESID 141:178 )T141 - 178
106X-RAY DIFFRACTION106( CHAIN T AND RESID 179:190 )T179 - 190
107X-RAY DIFFRACTION107( CHAIN T AND RESID 191:202 )T191 - 202
108X-RAY DIFFRACTION108( CHAIN T AND RESID 203:235 )T203 - 235

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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