9nxy

;Cryo-EM structure of SARS-CoV-2 spike S2' trimer ;

Method: ELECTRON MICROSCOPY D_max: 225.2 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9nxy
沉积日期 deposition_date	2025-03-26
结构标题 title	;Cryo-EM structure of SARS-CoV-2 spike S2' trimer ;
关键词 keywords	SARS-CoV-2, spike protein, postfusion, intermediate, VIRAL PROTEIN; VIRAL 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	78.13 Å
回转半径 Rg (电子) rg_electron	81.26 Å
零角强度 I(0) i0	407723000.00
分子量 molecular_weight	170900.0 kDa
排除体积 excluded_volume	214560 Å³
包络体积 envelope_volume	356530 Å³
水化壳体积 shell_volume	43432 Å³
包络直径 envelope_diameter	263.9 Å
壳层 Rg shell_rg	51.76 Å
包络 Rg envelope_rg	80.69 Å
形状 Rg shape_rg	81.30 Å
总 Rg total_rg	80.46 Å
总原子数 total_atoms	11992
残基数 n_residues	1463
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	225.2 Å
Rg (实空间) rg_real	78.66 Å
Rg 误差 (实空间) rg_real_error	1.85 Å
I(0) (实空间) i0_real	4.0600e+08
I(0) 误差 (实空间) i0_real_error	8.7680e+06
Rg (倒空间) rg_reciprocal	72.49 Å
I(0) (倒空间) i0_reciprocal	401700000.0000
解质量估计 total_estimate	0.6248
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	33.8 Å
偏度 Skewness skewness	0.467
峰度 Kurtosis kurtosis	-1.030
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.0070
最高正则化参数 α highest_alpha	7472000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.111; Stabil: 0.976; Sysdev: 1.000; Positv: 1.000; Valcen: 0.083; Smooth: 0.764

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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	Spike protein S2
分子量 formula_weight	68176.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	11992

SVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYTLESGGGSAWSHPQFEKGGGSGGGSGGSSAWSHPQFEK

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Homo sapiens

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	6

Entity 3 branched

描述 description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	6

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	man
拷贝数 entity_count	9

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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	3.08 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	153848

fit	/app/data/saxs_computation/nx/9nxy/9nxy.fit
pddf	/app/data/pr_computation/nx/9nxy/9nxy.pr.out
profile	/app/data/saxs_computation/nx/9nxy/9nxy.dat