9b6h

Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist TC-I 2014 and the cooling agonist C3

Method: ELECTRON MICROSCOPY D_max: 155.0 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	9b6h
沉积日期 deposition_date	2024-03-25
最后修订 last_revision	2024-08-21
结构标题 title	Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist TC-I 2014 and the cooling agonist C3
关键词 keywords	;TRPM8, menthol receptor, cold receptor, PI(4, 5)P2, cooling agonists, temperature sensing, ion channel, sensory transduction, transient receptor potential ion channel, TRPM8 activation, TRPM8 inhibition, TRPM8 desensitization, TRPM8 antagonists, 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	52.78 Å
回转半径 Rg (电子) rg_electron	52.03 Å
零角强度 I(0) i0	2055330000.00
分子量 molecular_weight	409480.0 kDa
排除体积 excluded_volume	523530 Å³
包络体积 envelope_volume	794450 Å³
水化壳体积 shell_volume	122510 Å³
包络直径 envelope_diameter	155.2 Å
壳层 Rg shell_rg	60.35 Å
包络 Rg envelope_rg	49.82 Å
形状 Rg shape_rg	52.04 Å
总 Rg total_rg	52.23 Å
总原子数 total_atoms	55880
残基数 n_residues	3736
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	155.0 Å
Rg (实空间) rg_real	52.48 Å
Rg 误差 (实空间) rg_real_error	0.84 Å
I(0) (实空间) i0_real	2.0550e+09
I(0) 误差 (实空间) i0_real_error	3.3730e+07
Rg (倒空间) rg_reciprocal	53.03 Å
I(0) (倒空间) i0_reciprocal	2057000000.0000
解质量估计 total_estimate	0.8343
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	72.3 Å
偏度 Skewness skewness	0.045
峰度 Kurtosis kurtosis	-0.519
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	222800000.0000
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: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; 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 (5)

Entity 1 polymer

描述 description	Transient receptor potential cation channel subfamily M member 8
分子量 formula_weight	131548.3 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	55880

MASFEGARLSMRSRRNGTMGSTRTLYSSVSRSTDVSYSDSDLVNFIQANFKKRECVFFTRDSKAMENICKCGYAQSQHIEGTQINQNEKWNYKKHTKEFPTDAFGDIQFETLGKKGKYLRLSCDTDSETLYELLTQHWHLKTPNLVISVTGGAKNFALKPRMRKIFSRLIYIAQSKGAWILTGGTHYGLMKYIGEVVRDNTISRNSEENIVAIGIAAWGMVSNRDTLIRSCDDEGHFSAQYIMDDFTRDPLYILDNNHTHLLLVDNGCHGHPTVEAKLRNQLEKYISERTSQDSNYGGKIPIVCFAQGGGRETLKAINTSVKSKIPCVVVEGSGQIADVIASLVEVEDVLTSSMVKEKLVRFLPRTVSRLPEEEIESWIKWLKEILESSHLLTVIKMEEAGDEIVSNAISYALYKAFSTNEQDKDNWNGQLKLLLEWNQLDLASDEIFTNDRRWESADLQEVMFTALIKDRPKFVRLFLENGLNLQKFLTNEVLTELFSTHFSTLVYRNLQIAKNSYNDALLTFVWKLVANFRRSFWKEDRSSREDLDVELHDASLTTRHPLQALFIWAILQNKKELSKVIWEQTKGCTLAALGASKLLKTLAKVKNDINAAGESEELANEYETRAVELFTECYSNDEDLAEQLLVYSCEAWGGSNCLELAVEATDQHFIAQPGVQNFLSKQWYGEISRDTKNWKIILCLFIIPLVGCGLVSFRKKPIDKHKKLLWYYVAFFTSPFVVFSWNVVFYIAFLLLFAYVLLMDFHSVPHTPELILYALVFVLFCDEVRQWYMNGVNYFTDLWNVMDTLGLFYFIAGIVFRLHSSNKSSLYSGRVIFCLDYIIFTLRLIHIFTVSRNLGPKIIMLQRMLIDVFFFLFLFAVWMVAFGVARQGILRQNEQRWRWIFRSVIYEPYLAMFGQVPSDVDSTTYDFSHCTFSGNESKPLCVELDEHNLPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGIVQENNDQVWKFQRYFLVQEYCNRLNIPFPFVVFAYFYMVVKKCFKCCCKEKNMESNACCFRNEDNETLAWEGVMKENYLVKINTKANDNSEEMRHRFRQLDSKLNDLKSLLKEIANNIKSNSLEVLFQGPDYKDDDDKAHHHHHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 non-polymer

描述 description	3-{7-(trifluoromethyl)-5-[2-(trifluoromethyl)phenyl]-1H-benzimidazol-2-yl}-1-oxa-2-azaspiro[4.5]dec-2-ene
分子量 formula_weight	467.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 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 4 non-polymer

描述 description	nonyl(oxo)di(propan-2-yl)-lambda~5~-phosphane
分子量 formula_weight	260.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 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	2.76 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	112062

fit	/app/data/saxs_computation/b6/9b6h/9b6h.fit
pddf	/app/data/pr_computation/b6/9b6h/9b6h.pr.out
profile	/app/data/saxs_computation/b6/9b6h/9b6h.dat