8sli

Cryo-EM structure of the rat TRPM5 channel in 2mM calcium, high-1

Method: ELECTRON MICROSCOPY D_max: 167.9 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	8sli
沉积日期 deposition_date	2023-04-21
结构标题 title	Cryo-EM structure of the rat TRPM5 channel in 2mM calcium, high-1
关键词 keywords	;ion channel, Transient Receptor Potential, TRP, Transient Receptor Potential Melastatin 5, TRPM5, MEMBRANE PROTEIN, TRANSPORT PROTEIN ;; TRANSPORT 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	54.15 Å
回转半径 Rg (电子) rg_electron	53.24 Å
零角强度 I(0) i0	1491040000.00
分子量 molecular_weight	294620.0 kDa
排除体积 excluded_volume	355580 Å³
包络体积 envelope_volume	745420 Å³
水化壳体积 shell_volume	115030 Å³
包络直径 envelope_diameter	160.0 Å
壳层 Rg shell_rg	59.77 Å
包络 Rg envelope_rg	50.08 Å
形状 Rg shape_rg	53.27 Å
总 Rg total_rg	53.39 Å
总原子数 total_atoms	20996
残基数 n_residues	3576
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	167.9 Å
Rg (实空间) rg_real	53.79 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	1.4910e+09
I(0) 误差 (实空间) i0_real_error	2.4790e+07
Rg (倒空间) rg_reciprocal	54.44 Å
I(0) (倒空间) i0_reciprocal	1492000000.0000
解质量估计 total_estimate	0.8152
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	69.5 Å
偏度 Skewness skewness	0.002
峰度 Kurtosis kurtosis	-0.511
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	185200000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; 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 (2)

Entity 1 polymer

描述 description	Transient receptor potential cation channel subfamily M member 5
分子量 formula_weight	132351.7 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,D,C,B
原子数 atom_count	20996

MDYKDDDDKLEMPMAQSSCPGSPPDTGDGWEPVLCKGEVNFGGSGKKRSKFVKVPSNVAPSMLFELLLTEWHLPAPNLVVSLVGEERLFAMKSWLRDVLRKGLVKAAQSTGAWILTSALHVGLARHVGQAVRDHSLASTSTKVRVVAIGMASLDRILHRQLLDGVQAQEDTPIHYPADEGSTQGPLCPLDSNLSHFILVEPGTLGSGNDGLAELQLSLEKHISQQRTGYGGTSSIQIPVLCLLVNGDPSTLERMSRAVEQAAPWLILAGSGGIADVLAALVGQPHLLVPQVTEKQFREKFPSECFSWEAIVHWTELLQNIAAHPHLLTVYDFEQEGSEDLDTVILKALVKACKSHSRDAQDYLDELKLAVAWDRVDIAKSEIFNGDVEWKSCDLEEVMTDALVSNKPDFVRLFVDSGADMAEFLTYGRLQQLYHSVSPKSLLFELLERKHEEGRLTLAGLGAQQTRELPVGLPAFSLHEVSRVLKDFLHDACRGFYQDGRRMEERGPPKRPAGQKWLPDLSRKSEDPWRDLFLWAVLQNRYEMATYFWAMGREGVAAALAACKIIKEMSHLEKEAEVARTMREAKYEQLALDLFSECYSNSEDRAFALLVRRNHSWSRTTCLHLATEADAKAFFAHDGVQAFLTKIWWGDMATGTPILRLLGAFTCPALIYTNLISFSEDAPQRMDLEDLQEPDSLDMEKSFLCSHGGQLEKLTEAPRAPGDLGPQAAFLLTRWRKFWGAPVTVFLGNVVMYFAFLFLFSYVLLVDFRPPPQGPSGSEVTLYFWVFTLVLEEIRQGFFTNEDTRLVKKFTLYVEDNWNKCDMVAIFLFIVGVTCRMVPSVFEAGRTVLAIDFMVFTLRLIHIFAIHKQLGPKIIIVERMMKDVFFFLFFLSVWLVAYGVTTQALLHPHDGRLEWIFRRVLYRPYLQIFGQIPLDEIDEARVNCSLHPLLLDSSASCPNLYANWLVILLLVTFLLVTNVLLMNLLIAMFSYTFQVVQGNADMFWKFQRYHLIVEYHGRPALAPPFILLSHLSLVLKQVFRKEAQHKQQHLERDLPDPVDQKIITWETVQKENFLSTMEKRRRDSEEEVLRKTAHRVDLIAKYIGGLREQEKRIKCLESQANYCMLLLSSMTDTLAPGGTYSSSQNCGRRSQPASARDREYLEAGLPHSDT

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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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	triclinic

分辨率 resolution	4.90 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	29977

fit	/app/data/saxs_computation/sl/8sli/8sli.fit
pddf	/app/data/pr_computation/sl/8sli/8sli.pr.out
profile	/app/data/saxs_computation/sl/8sli/8sli.dat

Cryo-EM structure of the rat TRPM5 channel in 2mM calcium, high-1

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)