8vq9

Prefusion stabilized structure of the SARS-CoV-2 fusion machinery

Method: ELECTRON MICROSCOPY D_max: 119.5 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	8vq9
沉积日期 deposition_date	2024-01-18
结构标题 title	Prefusion stabilized structure of the SARS-CoV-2 fusion machinery
关键词 keywords	;Sarbecoviruses, Spike glycoprotein, fusion protein, prefusion-stabilized, Seattle Structural Genomics Center for Infectious Disease, SSGCID, 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	35.81 Å
回转半径 Rg (电子) rg_electron	34.99 Å
零角强度 I(0) i0	277721000.00
分子量 molecular_weight	135030.0 kDa
排除体积 excluded_volume	169150 Å³
包络体积 envelope_volume	228910 Å³
水化壳体积 shell_volume	53441 Å³
包络直径 envelope_diameter	127.7 Å
壳层 Rg shell_rg	42.05 Å
包络 Rg envelope_rg	34.92 Å
形状 Rg shape_rg	34.98 Å
总 Rg total_rg	35.55 Å
总原子数 total_atoms	9513
残基数 n_residues	1278
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	119.5 Å
Rg (实空间) rg_real	35.80 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	2.7770e+08
I(0) 误差 (实空间) i0_real_error	4.6450e+06
Rg (倒空间) rg_reciprocal	35.81 Å
I(0) (倒空间) i0_reciprocal	277700000.0000
解质量估计 total_estimate	0.8779
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	40.8 Å
偏度 Skewness skewness	0.390
峰度 Kurtosis kurtosis	-0.230
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	89240000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.924

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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 (3)

Entity 1 polymer

描述 description	Spike protein S2
分子量 formula_weight	68224.2 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	9513

MGILPSPGMPALLSLVSLLSVLLMGCVAETGTSVASQSIIAYTMSLGAENSVACSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNFLVKQLSSNCGAISSVLNDILSRLDKPEAEVQIDRLITCRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGSGGLNDIFEAQKIEWHEGSGHHHHHHHH

来源 Source

来源生物 organism	Sarbecovirus
NCBI 分类编号 ncbi_taxonomy_id	2509511
宿主生物 host_organism	Homo sapiens

Entity 2 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	9

Entity 3 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	9

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7. 引用文献 (1)

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分辨率 resolution	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	671707

fit	/app/data/saxs_computation/vq/8vq9/8vq9.fit
pddf	/app/data/pr_computation/vq/8vq9/8vq9.pr.out
profile	/app/data/saxs_computation/vq/8vq9/8vq9.dat