9nhi

AMC016 v4.2 in complex with Base-C pAb isolated from animal RQk18 at week 43

Method: ELECTRON MICROSCOPY D_max: 142.1 Å Quality: REASONABLE

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	9nhi
沉积日期 deposition_date	2025-02-24
结构标题 title	AMC016 v4.2 in complex with Base-C pAb isolated from animal RQk18 at week 43
关键词 keywords	HIV-1, polyclonal, cryoEMPEM, STRUCTURAL 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	44.04 Å
回转半径 Rg (电子) rg_electron	42.91 Å
零角强度 I(0) i0	714597000.00
分子量 molecular_weight	214500.0 kDa
排除体积 excluded_volume	266020 Å³
包络体积 envelope_volume	377120 Å³
水化壳体积 shell_volume	71265 Å³
包络直径 envelope_diameter	148.0 Å
壳层 Rg shell_rg	49.64 Å
包络 Rg envelope_rg	42.37 Å
形状 Rg shape_rg	42.95 Å
总 Rg total_rg	43.07 Å
总原子数 total_atoms	15028
残基数 n_residues	1844
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	142.1 Å
Rg (实空间) rg_real	43.84 Å
Rg 误差 (实空间) rg_real_error	0.95 Å
I(0) (实空间) i0_real	7.1460e+08
I(0) 误差 (实空间) i0_real_error	1.2180e+07
Rg (倒空间) rg_reciprocal	44.04 Å
I(0) (倒空间) i0_reciprocal	714800000.0000
解质量估计 total_estimate	0.6572
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	59.2 Å
偏度 Skewness skewness	0.142
峰度 Kurtosis kurtosis	-0.386
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	75690000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 0.032; Positv: 1.000; Valcen: 0.991; Smooth: 0.858

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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 (8)

Entity 1 polymer

描述 description	RQk-Base-C pAb heavy chain
分子量 formula_weight	10383.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H
原子数 atom_count	15028

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Entity 2 polymer

描述 description	RQk-Base-C pAb light chain
分子量 formula_weight	8812.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L

XXXXXXXXXXXXXXXXXXCXXXXXXXXXXXWXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCXXXXXXXXFXXXXXXXX

Entity 3 polymer

描述 description	AMC016 v4.2 gp120
分子量 formula_weight	58713.8 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	A,C,D

MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAEEELWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHCCVPTDPSPQEVVLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLGNATDAINRNTTDAPNSTLRTMEEKGEIKNCSFNITTSVRDKMQKEYATFYKLDIVPIDNDNNSYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTDNGKTIIVQLNESVEINCTRPNNNTRKSIHIGPGRAFYTTGQIIGNIRQAHCNISRAKWNNTLHKIVKKLREQFRNKTIVFKQSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWYGNESSDNPGVEGNITLPCRIKQIINLWQEVGKAMYAPPIGGQIRCSSNITGLLLTRDGGNNNITTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQRRRRRR

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI 分类编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Homo sapiens

Entity 4 polymer

描述 description	AMC016 v4.2 gp41
分子量 formula_weight	17192.5 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	B,E,F

AVGIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAPECQQHLLKDTHWGIKQLQARVLAVEHYLKDQQLLGIWGCSGKLICTTAVPWNATWSNKTLDNIWNNMTWMEWEKEISNYTNLIYNLIEESQNQQEKNETENLTLC

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI 分类编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Homo sapiens

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	10

Entity 6 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[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	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 7 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	1

Entity 8 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	42

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7. 引用文献 (2)

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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	3.100 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.10 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	142407

fit	/app/data/saxs_computation/nh/9nhi/9nhi.fit
pddf	/app/data/pr_computation/nh/9nhi/9nhi.pr.out
profile	/app/data/saxs_computation/nh/9nhi/9nhi.dat

AMC016 v4.2 in complex with Base-C pAb isolated from animal RQk18 at week 43

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (8)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

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 branched

Entity 8 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)