8xc4

Nipah virus attachment glycoprotein head domain in complex with a broadly neutralizing antibody 1E5

Method: X-RAY DIFFRACTION D_max: 157.8 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8xc4
沉积日期 deposition_date	2023-12-08
结构标题 title	Nipah virus attachment glycoprotein head domain in complex with a broadly neutralizing antibody 1E5
关键词 keywords	Henipavirus, Glycoprotein, Head domain, Antibody, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex; ANTIVIRAL PROTEIN/IMMUNE SYSTEM
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	43.24 Å
回转半径 Rg (电子) rg_electron	43.24 Å
零角强度 I(0) i0	569098000.00
分子量 molecular_weight	195840.0 kDa
排除体积 excluded_volume	244940 Å³
包络体积 envelope_volume	324390 Å³
水化壳体积 shell_volume	63684 Å³
包络直径 envelope_diameter	172.6 Å
壳层 Rg shell_rg	46.45 Å
包络 Rg envelope_rg	43.74 Å
形状 Rg shape_rg	43.21 Å
总 Rg total_rg	43.49 Å
总原子数 total_atoms	13778
残基数 n_residues	1736
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	157.8 Å
Rg (实空间) rg_real	43.48 Å
Rg 误差 (实空间) rg_real_error	1.94 Å
I(0) (实空间) i0_real	5.6910e+08
I(0) 误差 (实空间) i0_real_error	1.0300e+07
Rg (倒空间) rg_reciprocal	43.24 Å
I(0) (倒空间) i0_reciprocal	568900000.0000
解质量估计 total_estimate	0.8303
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	51.2 Å
偏度 Skewness skewness	0.564
峰度 Kurtosis kurtosis	0.228
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	134800000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.754

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (8)

Entity 1 polymer

描述 description	Glycoprotein
分子量 formula_weight	49310.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	13778

HHHHHHGSGGGSEGVSNLVGLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLEKIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPSNPNTVYHCSAVYNNEFYYVLCAVSVVGDPILNSTYWSGSLMMTRLAVKPKNNGESYNQHQFALRNIEKGKYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPIAECQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDEENSKIVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVQTVNPLVVNWRDNTVISRPGQSQCPRFNKCPEVCWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEVLYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCT

来源 Source

来源生物 organism	Henipavirus nipahense
NCBI 分类编号 ncbi_taxonomy_id	3052225
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	1E5-VH
分子量 formula_weight	26120.0 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

QVQLQESGPGVVKPSETLSLTCAVSGGSISDTYRWSWIRQPPGKGLEWIGYIYGSATSTYYNPSLSSRVTISKDMSKNQFSLNLNSVTAADTAVYYCARDYQYYYSGSYPTPHNWFDVWGPGVLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSGLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHHH

来源 Source

来源生物 organism	Macaca mulatta
NCBI 分类编号 ncbi_taxonomy_id	9544
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	1E5-VL
分子量 formula_weight	23235.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

DIQMTQSPSSLSASVGDRVTITCRASQGIIDYLSWYQQKPGKAPKLLISTASNLESGVPSRFSGSGSGTEFTLTISSLQPEDFATYSCLQGYTTPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Macaca mulatta
NCBI 分类编号 ncbi_taxonomy_id	9544
宿主生物 host_organism	Homo sapiens

Entity 4 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	732.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 branched

描述 description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	894.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	syn
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)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	878.8 kDa
来源方法 src_method	syn
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	2

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	193.422 Å
晶胞边长 b length_b	193.422 Å
晶胞边长 c length_c	198.111 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	16

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	3.240 Å
最低分辨率 resolution_low	33.690 Å
R 因子 r_factor	0.2190
R_work r_work	0.2180
R_free r_free	0.2468

fit	/app/data/saxs_computation/xc/8xc4/8xc4.fit
pddf	/app/data/pr_computation/xc/8xc4/8xc4.pr.out
profile	/app/data/saxs_computation/xc/8xc4/8xc4.dat

Nipah virus attachment glycoprotein head domain in complex with a broadly neutralizing antibody 1E5

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 (8)

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 branched

Entity 8 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)