SAXSdb — 8yww

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8yww
沉积日期 deposition_date	2024-04-01
结构标题 title	The structure of HKU1-B S protein with bsAb1
关键词 keywords	SARS-CoV-2, Antibody, VIRAL PROTEIN/IMMUNE SYSTEM, 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	67.75 Å
回转半径 Rg (电子) rg_electron	67.61 Å
零角强度 I(0) i0	2785730000.00
分子量 molecular_weight	448510.0 kDa
排除体积 excluded_volume	561870 Å³
包络体积 envelope_volume	950440 Å³
水化壳体积 shell_volume	121310 Å³
包络直径 envelope_diameter	240.9 Å
壳层 Rg shell_rg	66.41 Å
包络 Rg envelope_rg	64.69 Å
形状 Rg shape_rg	67.62 Å
总 Rg total_rg	67.53 Å
总原子数 total_atoms	31649
残基数 n_residues	4177
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	226.2 Å
Rg (实空间) rg_real	67.88 Å
Rg 误差 (实空间) rg_real_error	3.36 Å
I(0) (实空间) i0_real	2.7860e+09
I(0) 误差 (实空间) i0_real_error	6.3400e+07
Rg (倒空间) rg_reciprocal	67.22 Å
I(0) (倒空间) i0_reciprocal	2782000000.0000
解质量估计 total_estimate	0.8394
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	78.7 Å
偏度 Skewness skewness	0.439
峰度 Kurtosis kurtosis	-0.172
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	114100000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.369

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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 (4)

Entity 1 polymer

描述 description	Spike glycoprotein
分子量 formula_weight	134104.0 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	31649

MFVFLVLLPLVSSQCVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKHVDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNSSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGS

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
通用名 common_name	2019-nCoV, SARS-CoV-2
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	H4B6 heavy chain
分子量 formula_weight	23023.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,G

EVQLVESGGDLVQPGGSLRLSCAASGFIVSRNYMSWVRQAPGKGLEWVSSIYSGGSTFYAGSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARDIPRHGGDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

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 3 polymer

描述 description	H4B6 light chain
分子量 formula_weight	23399.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,F

IRMTQSPASLSASIGDRVTITCQASQDINKYLNWYQQKPGKAPRLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

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 4 polymer

描述 description	the scfv of H4D12
分子量 formula_weight	26383.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

EVQLVESGGGLVQPGWSLRLSCVVSGLKFDDFAMHWVRQVPGKGLEWVSGLNWNGDNVAFADSVKGRFTISRDNAENSLYLQMNNLRPEDTAFYYCAKDSYYDILTGYSGAFDMWGQGTMVTVSSGGGGSGGGGSGGGGAIRMTQSPATLSLSPGERATLSCRASQSVHNYLAWYQQKPGQAPRLLFYDASNRATGIPARFSASASGTDSTLTISSLEPEDFAVYYCQQRRNGYSFGQGTKVEIK

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

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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	368678

fit	/app/data/saxs_computation/yw/8yww/8yww.fit
pddf	/app/data/pr_computation/yw/8yww/8yww.pr.out
profile	/app/data/saxs_computation/yw/8yww/8yww.dat

The structure of HKU1-B S protein with bsAb1

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 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)