SAXSdb — 8i10

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8i10
沉积日期 deposition_date	2023-01-12
结构标题 title	Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human Vasopressin V2 receptor, V2R (Local refine)
关键词 keywords	GPCR, Arrestin, SIGNALING PROTEIN, SIGNALING PROTEIN-IMMUNE SYSTEM complex; SIGNALING PROTEIN/IMMUNE SYSTEM
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	44.79 Å
回转半径 Rg (电子) rg_electron	44.21 Å
零角强度 I(0) i0	515773000.00
分子量 molecular_weight	186960.0 kDa
排除体积 excluded_volume	234150 Å³
包络体积 envelope_volume	344240 Å³
水化壳体积 shell_volume	65263 Å³
包络直径 envelope_diameter	142.1 Å
壳层 Rg shell_rg	49.22 Å
包络 Rg envelope_rg	42.79 Å
形状 Rg shape_rg	44.18 Å
总 Rg total_rg	44.54 Å
总原子数 total_atoms	13196
残基数 n_residues	1714
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	142.4 Å
Rg (实空间) rg_real	44.65 Å
Rg 误差 (实空间) rg_real_error	1.15 Å
I(0) (实空间) i0_real	5.1580e+08
I(0) 误差 (实空间) i0_real_error	9.1970e+06
Rg (倒空间) rg_reciprocal	44.79 Å
I(0) (倒空间) i0_reciprocal	515900000.0000
解质量估计 total_estimate	0.8361
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	52.9 Å
偏度 Skewness skewness	0.138
峰度 Kurtosis kurtosis	-0.700
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	44820000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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 (4)

Entity 1 polymer

描述 description	Beta-arrestin-2
分子量 formula_weight	47217.7 kDa
突变 mutation	C17G,C60V,L69V,C126S,C141L,C151V,C243V,C252V,C270S,L278F,S280A
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	13196

MGEKPGTRVFKKSSPNGKLTVYLGKRDFVDHLDKVDPVDGVVLVDPDYLKDRKVFVTLTVAFRYGREDCDVLGLSFRKDLFIANYQAFPPTPNPPRPPTRLQERLLRKLGQHAHPFFFTIPQNLPSSVTLQPGPEDTGKALGVDFEIRAFVAKSLEEKSHKRNSVRLVIRKVQFAPEKPGPQPSAETTRHFLMSDRSLHLEASLDKELYYHGEPLNVNVHVTNNSTKTVKKIKVSVRQYADIVLFSTAQYKVPVAQVEQDDQVSPSSTFSKVYTITPFLANNREKRGLALDGKLKHEDTNLASSTIVKEGANKEVLGILVSYRVKVKLVVSRGGDVSVELPFVLMHPKPHDHIALPRPQSAATHPPTLLPSAVPETDAPVDTNLIEFETNYATDDDIVFEDFARLRLKGLKDEDYDDQFC

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI 分类编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Fab30 Heavy Chain
分子量 formula_weight	25512.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,H,M

EISEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYYGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSRQFWYSGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHHHH

来源 Source

来源生物 organism	Mus musculus
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Fab30 Light Chain
分子量 formula_weight	23435.1 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,L,N

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYKYVPVTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Mus musculus
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	Vasopressin V2 receptor
分子量 formula_weight	3550.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,U,V

ARGRTPPSLGPQDESCTTASSSLAKDTSS

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6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

结构域编号 domain_id	8i10A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	840 —

结构域编号 domain_id	8i10A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	640 —

结构域编号 domain_id	8i10B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	840 —

结构域编号 domain_id	8i10B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	640 —

结构域编号 domain_id	8i10C01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	840 —

结构域编号 domain_id	8i10C02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	640 —

结构域编号 domain_id	8i10D01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8i10E01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8i10H01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8i10L01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8i10M01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8i10N01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (2)

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分辨率 resolution	3.96 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	92018

fit	/app/data/saxs_computation/i1/8i10/8i10.fit
pddf	/app/data/pr_computation/i1/8i10/8i10.pr.out
profile	/app/data/saxs_computation/i1/8i10/8i10.dat

Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human Vasopressin V2 receptor, V2R (Local refine)

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)