9b6g

Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist AMTB

Method: ELECTRON MICROSCOPY D_max: 159.2 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9b6g
沉积日期 deposition_date	2024-03-25
结构标题 title	Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist AMTB
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

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	52.54 Å
回转半径 Rg (电子) rg_electron	51.67 Å
零角强度 I(0) i0	1963920000.00
分子量 molecular_weight	401660.0 kDa
排除体积 excluded_volume	513950 Å³
包络体积 envelope_volume	781170 Å³
水化壳体积 shell_volume	121540 Å³
包络直径 envelope_diameter	154.6 Å
壳层 Rg shell_rg	59.74 Å
包络 Rg envelope_rg	49.44 Å
形状 Rg shape_rg	51.71 Å
总 Rg total_rg	51.78 Å
总原子数 total_atoms	55292
残基数 n_residues	3660
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	159.2 Å
Rg (实空间) rg_real	52.24 Å
Rg 误差 (实空间) rg_real_error	0.87 Å
I(0) (实空间) i0_real	1.9640e+09
I(0) 误差 (实空间) i0_real_error	3.5450e+07
Rg (倒空间) rg_reciprocal	52.77 Å
I(0) (倒空间) i0_reciprocal	1965000000.0000
解质量估计 total_estimate	0.8732
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	69.0 Å
偏度 Skewness skewness	0.050
峰度 Kurtosis kurtosis	-0.516
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	220300000.0000
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: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.606

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

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	55292

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	CHOLESTEROL HEMISUCCINATE
分子量 formula_weight	486.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

Entity 3 non-polymer

描述 description	N-(3-aminopropyl)-2-[(3-methylphenyl)methoxy]-N-[(thiophen-2-yl)methyl]benzamide
分子量 formula_weight	394.5 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 4 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

▶

7. 引用文献 (1)

▶

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

fit	/app/data/saxs_computation/b6/9b6g/9b6g.fit
pddf	/app/data/pr_computation/b6/9b6g/9b6g.pr.out
profile	/app/data/saxs_computation/b6/9b6g/9b6g.dat