8w0v

Crystal structure of broadly neutralizing antibody hcab55 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain

Method: X-RAY DIFFRACTION D_max: 118.9 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	8w0v
沉积日期 deposition_date	2024-02-14
结构标题 title	Crystal structure of broadly neutralizing antibody hcab55 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
关键词 keywords	HCV glycoprotein, broadly neutralizing antibodies, IMMUNE SYSTEM, IMMUNE SYSTEM-VIRAL PROTEIN complex; IMMUNE SYSTEM/VIRAL PROTEIN
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	34.11 Å
回转半径 Rg (电子) rg_electron	34.06 Å
零角强度 I(0) i0	89409100.00
分子量 molecular_weight	74019.0 kDa
排除体积 excluded_volume	91992 Å³
包络体积 envelope_volume	124020 Å³
水化壳体积 shell_volume	32715 Å³
包络直径 envelope_diameter	120.9 Å
壳层 Rg shell_rg	37.74 Å
包络 Rg envelope_rg	33.66 Å
形状 Rg shape_rg	34.04 Å
总 Rg total_rg	34.39 Å
总原子数 total_atoms	5203
残基数 n_residues	643
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	118.9 Å
Rg (实空间) rg_real	34.40 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	8.9410e+07
I(0) 误差 (实空间) i0_real_error	1.5800e+06
Rg (倒空间) rg_reciprocal	34.22 Å
I(0) (倒空间) i0_reciprocal	89390000.0000
解质量估计 total_estimate	0.8331
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	31.0 Å
偏度 Skewness skewness	0.533
峰度 Kurtosis kurtosis	-0.349
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9410000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.795

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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 (7)

Entity 1 polymer

描述 description	Envelope glycoprotein E2
分子量 formula_weight	28946.5 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	C
原子数 atom_count	5203

STHVTGGTASHTTRHFASLFSSGASQRVQLINTNGSWHINRTALNCNDSLHTGFLAALFYTHKFNASGCPERMAHCRPIDEFAQGWGPITYAEGHGSDQRPYCWHYAPRQCGTIPASQVCGPVYCFTPSPVVVGTTDRFGAPTYTWGENETDVLILNNTRPPQGNWFGCTWMNSTGFTKTCGGPPCNIGGVGNNTLTCPTDCFRKHPEATYTKCGSGPWLTPRCLVDYPYRLWHYPCTVNFTIFKVRMYVGGVEHRLNAACN

来源 Source

来源生物 organism	Hepacivirus hominis
NCBI 分类编号 ncbi_taxonomy_id	3052230
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	hcab55 Fab Heavy Chain
分子量 formula_weight	25447.6 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	H

QVQLVQSGAEIKKPGASVKVSCKASGYTFISNYFHWVRQAPGQGLEWMGIINPSSGSTTYGQKFQGRVTLTSDTSASIVYLELSRLRSEDTAVYYCVSPRIAHCRGGRCYETLDWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

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	hcab55 Fab Light Chain
分子量 formula_weight	23528.2 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

EIVLTQSPVSLSLSPGERATLSCRASQSVSSNYLAWYQLKPGRAPRLLIYGASSRAPGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGISSWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 branched

描述 description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 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	man
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	67.019 Å
晶胞边长 b length_b	88.840 Å
晶胞边长 c length_c	175.400 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	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.590 Å
最低分辨率 resolution_low	45.670 Å
R 因子 r_factor	0.2049
R_work r_work	0.2023
R_free r_free	0.2574

fit	/app/data/saxs_computation/w0/8w0v/8w0v.fit
pddf	/app/data/pr_computation/w0/8w0v/8w0v.pr.out
profile	/app/data/saxs_computation/w0/8w0v/8w0v.dat

Crystal structure of broadly neutralizing antibody hcab55 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain

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 (7)

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 branched

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)