8hc8

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB13-292 Fab, focused refinement of Fab region

Method: ELECTRON MICROSCOPY D_max: 111.0 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	8hc8
沉积日期 deposition_date	2022-11-01
结构标题 title	SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB13-292 Fab, focused refinement of Fab region
关键词 keywords	Spike protein, RBD, antibody, Fab, 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	33.16 Å
回转半径 Rg (电子) rg_electron	33.39 Å
零角强度 I(0) i0	75954000.00
分子量 molecular_weight	68577.0 kDa
排除体积 excluded_volume	85487 Å³
包络体积 envelope_volume	118680 Å³
水化壳体积 shell_volume	32213 Å³
包络直径 envelope_diameter	117.8 Å
壳层 Rg shell_rg	36.99 Å
包络 Rg envelope_rg	33.21 Å
形状 Rg shape_rg	33.37 Å
总 Rg total_rg	33.77 Å
总原子数 total_atoms	4832
残基数 n_residues	628
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	111.0 Å
Rg (实空间) rg_real	33.57 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	7.5950e+07
I(0) 误差 (实空间) i0_real_error	1.2100e+06
Rg (倒空间) rg_reciprocal	33.40 Å
I(0) (倒空间) i0_reciprocal	75940000.0000
解质量估计 total_estimate	0.8176
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	30.1 Å
偏度 Skewness skewness	0.565
峰度 Kurtosis kurtosis	-0.235
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21390000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.765; Smooth: 0.417

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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 protein S1
分子量 formula_weight	21332.1 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	C
原子数 atom_count	4832

ITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFEL

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	Heavy chain of YB13-292 Fab
分子量 formula_weight	25283.4 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

EVQLVESGGGLVKPGGSLRLSCAASGFSFITYNMNWVRQAPGKGLEWVSSISSNILSSTSYIYYADSVKGRFTISRDDAANSLFLQMNSLRVEDTAQYYCARTRSRSVRNCTSATCPVDAFDLWGQGTMVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	Light chain of YB13-292 Fab
分子量 formula_weight	23976.6 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	L

DIVLTQSPLSLPVTPGEPASISCRSSQSLLRSNGYNYLDWYLQKPGQSPHLLIYLGSNRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQALQTPYTFGQGTNLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 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	1

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	8hc8H01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8hc8H02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8hc8L01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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分辨率 resolution	3.95 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	210698

fit	/app/data/saxs_computation/hc/8hc8/8hc8.fit
pddf	/app/data/pr_computation/hc/8hc8/8hc8.pr.out
profile	/app/data/saxs_computation/hc/8hc8/8hc8.dat

SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB13-292 Fab, focused refinement of Fab region

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 non-polymer

6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)