SAXSdb — 8w4f

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8w4f
沉积日期 deposition_date	2023-08-24
结构标题 title	SARS-CoV-2 spike protein in complex with a trivalent nanobody
关键词 keywords	trivalent nanobody, viral neutralization, all-RBD-down spike, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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	50.35 Å
回转半径 Rg (电子) rg_electron	49.91 Å
零角强度 I(0) i0	2670720000.00
分子量 molecular_weight	433940.0 kDa
排除体积 excluded_volume	543080 Å³
包络体积 envelope_volume	709760 Å³
水化壳体积 shell_volume	114330 Å³
包络直径 envelope_diameter	173.5 Å
壳层 Rg shell_rg	56.68 Å
包络 Rg envelope_rg	49.52 Å
形状 Rg shape_rg	49.94 Å
总 Rg total_rg	50.01 Å
总原子数 total_atoms	60429
残基数 n_residues	3951
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	168.7 Å
Rg (实空间) rg_real	50.26 Å
Rg 误差 (实空间) rg_real_error	1.25 Å
I(0) (实空间) i0_real	2.6710e+09
I(0) 误差 (实空间) i0_real_error	5.0600e+07
Rg (倒空间) rg_reciprocal	50.41 Å
I(0) (倒空间) i0_reciprocal	2671000000.0000
解质量估计 total_estimate	0.8717
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	59.9 Å
偏度 Skewness skewness	0.310
峰度 Kurtosis kurtosis	-0.332
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	349200000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.865

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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	Spike glycoprotein
分子量 formula_weight	123893.2 kDa
突变 mutation	R683A/R685A/F817P/A892P/A899P/A942P/R986P/V987P
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	60429

AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD

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 polymer

描述 description	Tribody
分子量 formula_weight	20878.4 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	D,E,F

QVQLVESGGGLVQAGGSLRLSCAASGIIFGRNAMGWYRQAPGKERELVAGITRRGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADPASPAPGDYWGQGTQVTVSSGAGGSGGSSGSDGASGSRVTAFSNMDDMLQKAHLVIEGTFIYLRDSTEFFIRVRDGWKKLQLGELIPIPADSPPPPAL

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli BL21(DE3)

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7. 引用文献 (1)

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分辨率 resolution	4.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	262855

fit	/app/data/saxs_computation/w4/8w4f/8w4f.fit
pddf	/app/data/pr_computation/w4/8w4f/8w4f.pr.out
profile	/app/data/saxs_computation/w4/8w4f/8w4f.dat

SARS-CoV-2 spike protein in complex with a trivalent nanobody

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

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 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)