9n1n

Cryo-EM structure of rabbit TRPM3 in complex with CIM0216 in activated state at 18 degrees Celsius

Method: ELECTRON MICROSCOPY D_max: 163.5 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	9n1n
沉积日期 deposition_date	2025-01-26
结构标题 title	Cryo-EM structure of rabbit TRPM3 in complex with CIM0216 in activated state at 18 degrees Celsius
关键词 keywords	TRPM3, ion 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	52.33 Å
回转半径 Rg (电子) rg_electron	52.02 Å
零角强度 I(0) i0	5098480000.00
分子量 molecular_weight	405340.0 kDa
排除体积 excluded_volume	396700 Å³
包络体积 envelope_volume	850890 Å³
水化壳体积 shell_volume	130000 Å³
包络直径 envelope_diameter	167.6 Å
壳层 Rg shell_rg	61.13 Å
包络 Rg envelope_rg	50.11 Å
形状 Rg shape_rg	52.05 Å
总 Rg total_rg	52.16 Å
总原子数 total_atoms	30764
残基数 n_residues	4072
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	163.5 Å
Rg (实空间) rg_real	52.02 Å
Rg 误差 (实空间) rg_real_error	1.14 Å
I(0) (实空间) i0_real	5.0980e+09
I(0) 误差 (实空间) i0_real_error	9.3440e+07
Rg (倒空间) rg_reciprocal	52.58 Å
I(0) (倒空间) i0_reciprocal	5102000000.0000
解质量估计 total_estimate	0.8782
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	70.9 Å
偏度 Skewness skewness	0.060
峰度 Kurtosis kurtosis	-0.457
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	403800000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.869

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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	rabbit TRPM3
分子量 formula_weight	150840.3 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	30764

MCWKGVIPGELVDPVAGREGTQRRFRAQKSWIERAFYKRECVHIIPSTKDPHRCCCGRLIGQHVGLTPSISVLQNEKNESRLSRNDIQSEKWSISKHTQLSPTDAFGTIEFQGGGHSNKAMYVRVSFDTKPDLLLHLMTKEWQLELPKLLISVHGGLQNFELQPKLKQVFGKGLIKAAMTTGAWIFTGGVNTGVIRHVGDALKDHASKSRGKICTIGIAPWGIVENQEDLIGRDVVRPYQTMSNPMSKLTVLNSMHSHFILADNGTTGKYGAEVKLRRQLEKHISLQKINTRIGQGVPVVALIVEGGPNVISIVLEYLRDTPPVPVVVCDGSGRASDILAFGHKYSEEGGLINESLRDQLLVTIQKTFTYTRTQAQHLFIILMECMKKKELITVFRMGSEGHQDIDLAILTALLKGANASAPDQLSLALAWNRVDIARSQIFIYGQQWPVGSLEQAMLDALVLDRVDFVKLLIENGVSMHRFLTISRLEELYNTRHGPSNTLYHLVRDVKKREYPGFGWIYFKGNLPPDYRISLIDIGLVIEYLMGGAYRCNYTRKRFRTLYHNLFGPKRPKALKLLGMEDDIPLRRGRKTTKKREEEVDIDLDDPEINHFPFPFHELMVWAVLMKRQKMALFFWQHGEEAMAKALVACKLCKAMAHEASENDMVDDISQELNHNSRDFGQLAVELLDQSYKQDEQLAMKLLTYELKNWSNATCLQLAVAAKHRDFIAHTCSQMLLTDMWMGRLRMRKNSGLKVILGILLPPSILSLEFKNKDDMPYMTQAQEIHLQEKEPEEPEKPTKEKDEEDMELTAMLGRNNGESSRKKDEEEVQSRHRLIPLGRKIYEFYNAPIVKFWFYTLAYIGYLMLFNYIVLVKMERWPSTQEWIVISYIFTLGIEKMREILMSEPGKLLQKVKVWLQEYWNVTDLIAILLFSVGMILRLQDQPFRSDGRVIYCVNIIYWYIRLLDIFGVNKYLGPYVMMIGKMMIDMMYFVIIMLVVLMSFGVARQAILFPNEEPSWKLAKNIFYMPYWMIYGEVFADQIDPPCGQNETREDGKIIQLPPCKTGAWIVPAIMACYLLVANILLVNLLIAVFNNTFFEVKSISNQVWKFQRYQLIMTFHERPVLPPPLIIFSHMTMIFQHLCCRWRKHESDPDERDYGLKLFITDDELKKVHDFEEQCIEEYFREKDDRFNSSNDERIRVTSERVENMSMRLEEVNEREHSMKASLQTVDIRLAQLEDLIGRMATALERLTGVERAESNKIRSRTSSDCTDAAYIVRQSSFNSQEGNTFKLQESIDPAEHPFYSVFE

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI 分类编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Homo sapiens

Entity 2 non-polymer

描述 description	CHOLESTEROL HEMISUCCINATE
分子量 formula_weight	486.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 non-polymer

描述 description	(2S)-2-(3,4-dihydroquinolin-1(2H)-yl)-N-(5-methyl-1,2-oxazol-3-yl)-2-phenylacetamide
分子量 formula_weight	347.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.200 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	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	563237

fit	/app/data/saxs_computation/n1/9n1n/9n1n.fit
pddf	/app/data/pr_computation/n1/9n1n/9n1n.pr.out
profile	/app/data/saxs_computation/n1/9n1n/9n1n.dat

Cryo-EM structure of rabbit TRPM3 in complex with CIM0216 in activated state at 18 degrees Celsius

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

冷冻电镜 EM 3D