8dgu

;Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC25.106 isolated from a vaccinated COVID-19 convalescent ;

Method: X-RAY DIFFRACTION D_max: 80.2 Å Quality: EXCELLENT

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	8dgu
沉积日期 deposition_date	2022-06-24
结构标题 title	;Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC25.106 isolated from a vaccinated COVID-19 convalescent ;
关键词 keywords	;broadly neutralizing antibody, pan-betacoronavirus, S2 stem helix, spike, SARS-CoV-2, MERS-CoV, HCoV-HKU1, sarbecovirus, cross-reactive, cross-neutralizing, IMMUNE SYSTEM ;; IMMUNE SYSTEM
实验方法 method	X-RAY DIFFRACTION

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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	25.23 Å
回转半径 Rg (电子) rg_electron	24.25 Å
零角强度 I(0) i0	38047100.00
分子量 molecular_weight	47112.0 kDa
排除体积 excluded_volume	58651 Å³
包络体积 envelope_volume	71887 Å³
水化壳体积 shell_volume	24960 Å³
包络直径 envelope_diameter	81.0 Å
壳层 Rg shell_rg	31.30 Å
包络 Rg envelope_rg	24.01 Å
形状 Rg shape_rg	24.23 Å
总 Rg total_rg	25.10 Å
总原子数 total_atoms	3318
残基数 n_residues	437
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	80.2 Å
Rg (实空间) rg_real	25.22 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	3.8050e+07
I(0) 误差 (实空间) i0_real_error	4.6800e+05
Rg (倒空间) rg_reciprocal	25.22 Å
I(0) (倒空间) i0_reciprocal	38050000.0000
解质量估计 total_estimate	0.9050
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.0 Å
偏度 Skewness skewness	0.301
峰度 Kurtosis kurtosis	-0.477
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5931000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.964

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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	2981.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3508

PLQPELDSFKEELDKYFKNHTSPDV

Entity 2 polymer

描述 description	Antibody CC25.106 Fab heavy chain
分子量 formula_weight	23477.5 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

EVQLVQSGAEVKKPGASLKVSCKASGYTFTDYYMHWVRQAPGQGLEWMGIIKPSAGNTRNAQKFQGRVTMTRDTSTSTVYMELSALRFEDTAVYYCARGGVHGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

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	Antibody CC25.106 Fab light chain
分子量 formula_weight	22830.2 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	L

QSVLTQPPSVSAPPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIHENNQRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDTNLGAFVFGAATRVTVLGQPKANPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	190

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6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	8dguH01
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	8dguH02
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	8dguL01
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	8dguL02
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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晶胞边长 a length_a	40.934 Å
晶胞边长 b length_b	70.719 Å
晶胞边长 c length_c	76.551 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	95.31 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.890 Å
最低分辨率 resolution_low	40.760 Å
R 因子 r_factor	0.2159
R_work r_work	0.2144
R_free r_free	0.2451

fit	/app/data/saxs_computation/dg/8dgu/8dgu.fit
pddf	/app/data/pr_computation/dg/8dgu/8dgu.pr.out
profile	/app/data/saxs_computation/dg/8dgu/8dgu.dat

;Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC25.106 isolated from a vaccinated COVID-19 convalescent ;

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)