SAXSdb — 8dmh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8dmh
沉积日期 deposition_date	2022-07-08
结构标题 title	Lymphocytic choriomeningitis virus glycoprotein in complex with neutralizing antibody M28
关键词 keywords	Viral glycoprotein, arenavirus, LCMV, GP, antibody, neutralization, 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	38.59 Å
回转半径 Rg (电子) rg_electron	37.97 Å
零角强度 I(0) i0	636546000.00
分子量 molecular_weight	203170.0 kDa
排除体积 excluded_volume	252840 Å³
包络体积 envelope_volume	326280 Å³
水化壳体积 shell_volume	69660 Å³
包络直径 envelope_diameter	125.2 Å
壳层 Rg shell_rg	45.29 Å
包络 Rg envelope_rg	37.83 Å
形状 Rg shape_rg	37.98 Å
总 Rg total_rg	38.37 Å
总原子数 total_atoms	14259
残基数 n_residues	1725
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	119.5 Å
Rg (实空间) rg_real	38.35 Å
Rg 误差 (实空间) rg_real_error	0.79 Å
I(0) (实空间) i0_real	6.3650e+08
I(0) 误差 (实空间) i0_real_error	1.1260e+07
Rg (倒空间) rg_reciprocal	38.50 Å
I(0) (倒空间) i0_reciprocal	636600000.0000
解质量估计 total_estimate	0.9026
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	49.5 Å
偏度 Skewness skewness	0.140
峰度 Kurtosis kurtosis	-0.550
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	118700000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.934

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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	Glycoprotein G1
分子量 formula_weight	25521.2 kDa
突变 mutation	G207C, L264R, A265R
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	14259

MKLCILLAVVAFVGLSLGMYGLKGPDIYKGVYQFKSVEFDMSHLNLTMPNACSANNSHHYISMGTSGLELTFTNDSIISHNFCNLTSAFNKKTFDHTLMSIVSSLHLSIRGNSNYKAVSCDFNNGITIQYNLTFSDAQSAQSQCRTFRGRVLDMFRTAFGGKYMRSCWGWTGSDGKTTWCSQTSYQYLIIQNRTWENHCTYAGPFGMSRILLSQEKTKFLTRRRR

来源 Source

来源生物 organism	Lymphocytic choriomeningitis virus
NCBI 分类编号 ncbi_taxonomy_id	11623
宿主生物 host_organism	Drosophila melanogaster

Entity 2 polymer

描述 description	18.5C-M28 Fab Light Chain
分子量 formula_weight	23306.8 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	E,G,I

DIVLTQSPGTLSLSPGERATLSCRASQSVISYYVAWYQHKGGQAPRLLIYGASSRATGVPDRFSGSGSGTDFTLTISSLEPEDFALYYCQYYGSSPLWAFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

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	Cricetulus griseus

Entity 3 polymer

描述 description	18.5C-M28 Fab Heavy Chain
分子量 formula_weight	23610.7 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	F,H,J

DEVQLVQSGGGLVRPGGSLRLSCAAAGFTFKRYSMNWVRQAPGRGLEWVSSITSRGGSKTYYADVVKGRFTVSRDNAKQSLYLQMNSLRAEDTAIYFCARSLHSTSQPSYMDVWGRKITVIVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

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	Cricetulus griseus

Entity 4 polymer

描述 description	Glycoprotein G2,Cobalamin adenosyltransferase-like domain-containing protein trimerization tag
分子量 formula_weight	42166.8 kDa
突变 mutation	E334P,G366C,S398A
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

GTFTWTLSDSSGVENPGGYCLTKWMILAAELKCFGNTAVAKCNVNHDEEFCDMLRLIDYNKAALSKFKPDVESALHLFKTTVNSLISDQLLMRNHLRDLMCVPYCNYSKFWYLEHAKTGETSVPKCWLVTNGAYLNETHFSDQIEQEADNMITEMLRKDYIKRQGLEGGSPVVEVQGTIDELNSFIGYALVLSRWDDIRNDLFRIQNDLFVLGEDVSTGGKGRTVTREMIDYLEARVKEMKAEIGKIELFVVPGGSVESASLHMARAVSRRLERRIVAASKLTEINKNVLIYANRLSSILFMHALISNKRLNIPEKIWALEVDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEKGSGGLNDIFEAQKIEWHE

来源 Source

来源生物 organism	Lymphocytic choriomeningitis virus
NCBI 分类编号 ncbi_taxonomy_id	11623
宿主生物 host_organism	Drosophila melanogaster

Entity 5 branched

描述 description	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	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 6 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	15

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	syn
拷贝数 entity_count	6

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6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id	8dmhE01
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	8dmhF01
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	8dmhG01
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	8dmhH01
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	8dmhI01
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	8dmhJ01
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	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

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

分辨率 resolution	3.19 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	34783

fit	/app/data/saxs_computation/dm/8dmh/8dmh.fit
pddf	/app/data/pr_computation/dm/8dmh/8dmh.pr.out
profile	/app/data/saxs_computation/dm/8dmh/8dmh.dat

Lymphocytic choriomeningitis virus glycoprotein in complex with neutralizing antibody M28

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

冷冻电镜 EM 3D

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 polymer

聚合体 Polymer

来源 Source

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)