9p6b

Cryo-EM structure of full-length human TRPV1 in the presence of alpha-humulene

Method: ELECTRON MICROSCOPY D_max: 145.0 Å Quality: REASONABLE

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	9p6b
沉积日期 deposition_date	2025-06-18
结构标题 title	Cryo-EM structure of full-length human TRPV1 in the presence of alpha-humulene
关键词 keywords	;transient receptor potential V family member 1, TRP, channel, TRPV1, TRP channels, sesquiterpene, alpha-humulene, pain, analgesia, 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	47.48 Å
回转半径 Rg (电子) rg_electron	46.41 Å
零角强度 I(0) i0	1186880000.00
分子量 molecular_weight	322890.0 kDa
排除体积 excluded_volume	419120 Å³
包络体积 envelope_volume	536050 Å³
水化壳体积 shell_volume	92285 Å³
包络直径 envelope_diameter	151.3 Å
壳层 Rg shell_rg	54.61 Å
包络 Rg envelope_rg	45.44 Å
形状 Rg shape_rg	46.43 Å
总 Rg total_rg	46.62 Å
总原子数 total_atoms	22670
残基数 n_residues	2568
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	145.0 Å
Rg (实空间) rg_real	47.60 Å
Rg 误差 (实空间) rg_real_error	0.42 Å
I(0) (实空间) i0_real	1.1600e+09
I(0) 误差 (实空间) i0_real_error	1.6890e+07
Rg (倒空间) rg_reciprocal	47.48 Å
I(0) (倒空间) i0_reciprocal	1187000000.0000
解质量估计 total_estimate	0.7197
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	65.9 Å
偏度 Skewness skewness	0.066
峰度 Kurtosis kurtosis	-0.366
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	1.8320
最高正则化参数 α highest_alpha	58820000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 0.929; Sysdev: 0.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.859

▶

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

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	Transient receptor potential cation channel subfamily V member 1
分子量 formula_weight	124575.3 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	22762

MTSKKWSSTDLGAAADPLQKDTCPDPLDGDPNSRPPPAKPQLSTAKSRTRLFGKGDSEEAFPVDCPHEEGELDSCPTITVSPVITIQRPGDGPTGARLLSQDSVAASTEKTLRLYDRRSIFEAVAQNNCQDLESLLLFLQKSKKHLTDNEFKDPETGKTCLLKAMLNLHDGQNTTIPLLLEIARQTDSLKELVNASYTDSYYKGQTALHIAIERRNMALVTLLVENGADVQAAAHGDFFKKTKGRPGFYFGELPLSLAACTNQLGIVKFLLQNSWQTADISARDSVGNTVLHALVEVADNTADNTKFVTSMYNEILMLGAKLHPTLKLEELTNKKGMTPLALAAGTGKIGVLAYILQREIQEPECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFLVYCLYMIIFTMAAYYRPVDGLPPFKMEKTGDYFRVTGEILSVLGGVYFFFRGIQYFLQRRPSMKTLFVDSYSEMLFFLQSLFMLATVVLYFSHLKEYVASMVFSLALGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYIVFLFGFSTAVVTLIEDGKNDSLPSESTSHRWRGPACRPPDSSYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLLQVGYTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPGNCEGVKRTLSFSLRSSRVSGRHWKNFALVPLLREASARDRQSAQPEEVYLRQFSGSLKPEDAEVFKSPAASGEKLVPRGSAAAAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKSGLRSWSHPQFEK

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	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
分子量 formula_weight	760.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	32

Entity 3 non-polymer

描述 description	(2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate
分子量 formula_weight	867.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	TRIDECANE
分子量 formula_weight	184.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	92

▶

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	2.74 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	226949

fit	/app/data/saxs_computation/p6/9p6b/9p6b.fit
pddf	/app/data/pr_computation/p6/9p6b/9p6b.pr.out
profile	/app/data/saxs_computation/p6/9p6b/9p6b.dat