9lev

Cryo-EM structure of human ZAC in nanodisc in apo state

Method: ELECTRON MICROSCOPY D_max: 122.5 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	9lev
沉积日期 deposition_date	2025-01-07
结构标题 title	Cryo-EM structure of human ZAC in nanodisc in apo state
关键词 keywords	Cys-loop receptor, homopentamer, cation channel, MEMBRANE PROTEIN; MEMBRANE 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	37.68 Å
回转半径 Rg (电子) rg_electron	36.87 Å
零角强度 I(0) i0	426994000.00
分子量 molecular_weight	179860.0 kDa
排除体积 excluded_volume	230060 Å³
包络体积 envelope_volume	294500 Å³
水化壳体积 shell_volume	64983 Å³
包络直径 envelope_diameter	123.7 Å
壳层 Rg shell_rg	44.47 Å
包络 Rg envelope_rg	36.48 Å
形状 Rg shape_rg	36.88 Å
总 Rg total_rg	37.35 Å
总原子数 total_atoms	12685
残基数 n_residues	1555
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	122.5 Å
Rg (实空间) rg_real	37.58 Å
Rg 误差 (实空间) rg_real_error	0.98 Å
I(0) (实空间) i0_real	4.2700e+08
I(0) 误差 (实空间) i0_real_error	6.7740e+06
Rg (倒空间) rg_reciprocal	37.64 Å
I(0) (倒空间) i0_reciprocal	427000000.0000
解质量估计 total_estimate	0.8736
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	46.6 Å
偏度 Skewness skewness	0.333
峰度 Kurtosis kurtosis	-0.274
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	74840000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.893

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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 (3)

Entity 1 polymer

描述 description	Ligand-gated cation channel ZACN,Genome polyprotein
分子量 formula_weight	78830.9 kDa
EC 编号 ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
突变 mutation	A152T
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,A,B,D,E
原子数 atom_count	12685

MMALWSLLHLTFLGFSITLLLVHGQGFQGTAAIWPSLFNVNLSKKVQESIQIPNNGSAPLLVDVRVFVSNVFNVDILRYTMSSMLLLRLSWLDTRLAWNTSAHPRHAITLPWESLWTPRLTILEALWVDWRDQSPQARVDQDGHVKLNLALTTETNCNFELLHFPRDHSNCSLSFYALSNTAMELEFQAHVVNEIVSVKREYVVYDLKTQVPPQQLVPCFQVTLRLKNTALKSIIALLVPAEALLLADVCGGLLPLRAIERIGYKVTLLLSYLVLHSSLVQALPSSSSCNPLLIYYFTILLLLLFLSTIETVLLAGLLARGNLGAKSGPSPAPRGEQREHGNPGPHPAEEPSRGVKGSQRSWPETADRIFFLVYVVGVLCTQFVFAGIWMWAACKSDAAPGEAAPHGRRPRLSDLEVLFQGPEFWSHPQFEKGGGSGGGSGGSAWSHPQFEKEFDIDYKDDDDKSRMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK

来源 Source

来源生物 organism	Enterovirus A71
NCBI 分类编号 ncbi_taxonomy_id	39054
宿主生物 host_organism	Homo sapiens

Entity 2 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	5

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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7. 引用文献 (1)

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分辨率 resolution	3.350 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.35 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	16419

fit	/app/data/saxs_computation/le/9lev/9lev.fit
pddf	/app/data/pr_computation/le/9lev/9lev.pr.out
profile	/app/data/saxs_computation/le/9lev/9lev.dat