8dgw

;Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 isolated from a vaccinated COVID-19 convalescent ;

Method: X-RAY DIFFRACTION D_max: 158.8 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	8dgw
沉积日期 deposition_date	2022-06-24
结构标题 title	;Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 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	46.33 Å
回转半径 Rg (电子) rg_electron	46.59 Å
零角强度 I(0) i0	516633000.00
分子量 molecular_weight	185090.0 kDa
排除体积 excluded_volume	230210 Å³
包络体积 envelope_volume	322520 Å³
水化壳体积 shell_volume	58080 Å³
包络直径 envelope_diameter	159.3 Å
壳层 Rg shell_rg	50.01 Å
包络 Rg envelope_rg	46.28 Å
形状 Rg shape_rg	46.58 Å
总 Rg total_rg	46.76 Å
总原子数 total_atoms	13052
残基数 n_residues	1740
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	158.8 Å
Rg (实空间) rg_real	46.52 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	5.1660e+08
I(0) 误差 (实空间) i0_real_error	9.3530e+06
Rg (倒空间) rg_reciprocal	46.33 Å
I(0) (倒空间) i0_reciprocal	516500000.0000
解质量估计 total_estimate	0.8719
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	51.4 Å
偏度 Skewness skewness	0.387
峰度 Kurtosis kurtosis	-0.414
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35250000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.727

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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	Antibody CC95.108 Fab heavy chain
分子量 formula_weight	23503.3 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,A,C,E
原子数 atom_count	13052

QVQLVQSGTEVRQPGASVRVSCKASGYTFTDSYIHWVRQAPGQGLEWMGIIKPSGGNTRYAQRFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDSRGPGIFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

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 2 polymer

描述 description	Antibody CC95.108 Fab light chain
分子量 formula_weight	22841.3 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

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

QSVLTQPPSVSAAPERKVTISCSGSSSNIGTNFVSWYQQLPGTAPKLLIYENNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGAWDSTPGTWVFGGGTRLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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	;Spike protein S2' ;
分子量 formula_weight	2889.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,I,J,K

HSVPKLSDFESELSHWFKNQTSIAP

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6. 折叠分类 (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

结构域编号 domain_id	8dgwA01
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	8dgwA02
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	8dgwB01
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	8dgwB02
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	8dgwC01
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	8dgwC02
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	8dgwD01
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	8dgwD02
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	8dgwE01
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	8dgwE02
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	8dgwF01
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	8dgwF02
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	8dgwH01
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	8dgwH02
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	8dgwL01
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	8dgwL02
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	157.422 Å
晶胞边长 b length_b	157.422 Å
晶胞边长 c length_c	205.095 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	H 3
空间群编号 int_tables_number	146
晶系 crystal_system	—

分辨率 resolution	2.810 Å
最低分辨率 resolution_low	39.360 Å
R 因子 r_factor	0.2183
R_work r_work	0.2167
R_free r_free	0.2481

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

;Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 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 (3)

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

6. 折叠分类 (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)