9kqm

Cryo-EM structure of human VAChT in complex with VSM

Method: ELECTRON MICROSCOPY D_max: 67.0 Å Quality: EXCELLENT

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	9kqm
沉积日期 deposition_date	2024-11-26
结构标题 title	Cryo-EM structure of human VAChT in complex with VSM
关键词 keywords	transporter, VAChT, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	21.43 Å
回转半径 Rg (电子) rg_electron	20.54 Å
零角强度 I(0) i0	52907700.00
分子量 molecular_weight	39842.0 kDa
排除体积 excluded_volume	39601 Å³
包络体积 envelope_volume	62940 Å³
水化壳体积 shell_volume	24768 Å³
包络直径 envelope_diameter	68.1 Å
壳层 Rg shell_rg	28.04 Å
包络 Rg envelope_rg	20.91 Å
形状 Rg shape_rg	20.54 Å
总 Rg total_rg	21.25 Å
总原子数 total_atoms	3037
残基数 n_residues	403
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	67.0 Å
Rg (实空间) rg_real	21.31 Å
Rg 误差 (实空间) rg_real_error	0.31 Å
I(0) (实空间) i0_real	5.2910e+07
I(0) 误差 (实空间) i0_real_error	6.0350e+05
Rg (倒空间) rg_reciprocal	21.34 Å
I(0) (倒空间) i0_reciprocal	52910000.0000
解质量估计 total_estimate	0.9022
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.6 Å
偏度 Skewness skewness	0.209
峰度 Kurtosis kurtosis	-0.424
角度范围 angular_range	— – 0.3700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8334000.0000
实空间数据点数 n_real_points	69
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.996

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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	Soluble cytochrome b562,Vesicular acetylcholine transporter
分子量 formula_weight	69325.8 kDa
突变 mutation	M8W,H103I,R107L
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3037

MADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLLQEPRRQRRLVLVIVCVALLLDNMLYMVIVPIVPDYIAHMRGGGEGPTRTPEVWEPTLPLPTPANASAYTANTSASPTAAWPAGSALRPRYPTESEDVKIGVLFASKAILQLLVNPLSGPFIDRMSYDVPLLIGLGVMFASTVLFAFAEDYATLFAARSLQGLGSAFADTSGIAMIADKYPEEPERSRALGVALAFISFGSLVAPPFGGILYEFAGKRVPFLVLAAVSLFDALLLLAVAKPFSAAARARANLPVGTPIHRLMLDPYIAVVAGALTTCNIPLAFLEPTIATWMKHTMAASEWEMGMAWLPAFVPHVLGVYLTVRLAARYPHLQWLYGALGLAVIGASSCIVPACRSFAPLVVSLCGLCFGIALVDTALLPTLAFLVDVRHVSVYGSVYAIADISYSVAYALGPIVAGHIVHSLGFEQLSLGMGLANLLYAPVLLLLRNVGLLTRSRSERDVLLDEPPQGLYDAVRLRERPVSGQDGEPRSPPGPFDACEDDYNYYYTRSHHHHHHHHHHGSVEDYKDDDDK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 non-polymer

描述 description	(1R,2R)-2-(4-phenylpiperidin-1-yl)cyclohexan-1-ol
分子量 formula_weight	259.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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分辨率 resolution	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	172916

fit	/app/data/saxs_computation/kq/9kqm/9kqm.fit
pddf	/app/data/pr_computation/kq/9kqm/9kqm.pr.out
profile	/app/data/saxs_computation/kq/9kqm/9kqm.dat