8opl

Virus-like Particle based on PVY coat protein with T43C and D136C mutation with helical architecture encapsidating ssRNA

Method: ELECTRON MICROSCOPY D_max: 186.4 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8opl
沉积日期 deposition_date	2023-04-07
结构标题 title	Virus-like Particle based on PVY coat protein with T43C and D136C mutation with helical architecture encapsidating ssRNA
关键词 keywords	helical, VLP, ssRNA, Potyvirus, PVY, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	57.56 Å
回转半径 Rg (电子) rg_electron	57.59 Å
零角强度 I(0) i0	8285750000.00
分子量 molecular_weight	726920.0 kDa
排除体积 excluded_volume	892000 Å³
包络体积 envelope_volume	1271200 Å³
水化壳体积 shell_volume	170310 Å³
包络直径 envelope_diameter	220.9 Å
壳层 Rg shell_rg	69.55 Å
包络 Rg envelope_rg	57.19 Å
形状 Rg shape_rg	57.57 Å
总 Rg total_rg	57.85 Å
总原子数 total_atoms	50679
残基数 n_residues	6183
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	186.4 Å
Rg (实空间) rg_real	57.26 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	8.2850e+09
I(0) 误差 (实空间) i0_real_error	1.6430e+08
Rg (倒空间) rg_reciprocal	57.81 Å
I(0) (倒空间) i0_reciprocal	8293000000.0000
解质量估计 total_estimate	0.8547
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	75.9 Å
偏度 Skewness skewness	0.203
峰度 Kurtosis kurtosis	-0.147
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	4757000000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.821

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	Genome polyprotein (Fragment)
分子量 formula_weight	29925.9 kDa
来源方法 src_method	man
拷贝数 entity_count	27

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	Aa,Ab,Ac,Ad,Ae,Af,Ag,Ah,Ai,As,At,Au,Av,Aw,Ax,Ay,Az,Ba,Bk,Bl,Bm,Bn,Bo,Bp,Bq,Br,Bs
原子数 atom_count	50679

GNDTIDAGGSTKKDAKQEQGSIQPNLNKEKEKDVNVGTSGTHCVPRIKAITSKMRMPKSKGATVLNLEHLLEYAPQQIDISNTRATQSQFDTWYEAVQLAYDIGETEMPTVMNGLMVWCIENGTSPNINGVWVMMCGDEQVEYPLKPIVENAKPTLRQIMAHFSDVAEAYIEMRNKKEPYMPRYGLVRNLRDGSLARYAFDFYEVTSRTPVRAREAHIQMKAAALKSAQSRLFGLDGGISTQEENTERHTTEDVSPSMHTLLGVKNM

来源 Source

来源生物 organism	Potato virus Y strain NTN
NCBI 分类编号 ncbi_taxonomy_id	122280
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	;RNA (5'-R(PUPUPUPUP*U)-3') ;
分子量 formula_weight	1485.9 kDa
来源方法 src_method	man
拷贝数 entity_count	27

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	Aj,Ak,Al,Am,An,Ao,Ap,Aq,Ar,Bb,Bc,Bd,Be,Bf,Bg,Bh,Bi,Bj,Bt,Bu,Bv,Bw,Bx,By,Bz,Ca,Cb

UUUUU

来源 Source

来源生物 organism	Potato virus Y strain NTN
NCBI 分类编号 ncbi_taxonomy_id	122280
宿主生物 host_organism	Escherichia coli BL21(DE3)

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7. 引用文献 (1)

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分辨率 resolution	2.41 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	141112

fit	/app/data/saxs_computation/op/8opl/8opl.fit
pddf	/app/data/pr_computation/op/8opl/8opl.pr.out
profile	/app/data/saxs_computation/op/8opl/8opl.dat

Virus-like Particle based on PVY coat protein with T43C and D136C mutation with helical architecture encapsidating ssRNA

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)