8dwx

Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)

Method: ELECTRON MICROSCOPY D_max: 286.2 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	8dwx
沉积日期 deposition_date	2022-08-02
结构标题 title	Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)
关键词 keywords	Antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex, CSGID, Structural Genomics, Center for Structural Genomics of Infectious Diseases; 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	78.66 Å
回转半径 Rg (电子) rg_electron	78.85 Å
零角强度 I(0) i0	4256490000.00
分子量 molecular_weight	544360.0 kDa
排除体积 excluded_volume	678210 Å³
包络体积 envelope_volume	1382500 Å³
水化壳体积 shell_volume	154710 Å³
包络直径 envelope_diameter	256.2 Å
壳层 Rg shell_rg	71.29 Å
包络 Rg envelope_rg	75.19 Å
形状 Rg shape_rg	78.84 Å
总 Rg total_rg	78.75 Å
总原子数 total_atoms	38228
残基数 n_residues	4956
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	286.2 Å
Rg (实空间) rg_real	79.43 Å
Rg 误差 (实空间) rg_real_error	2.60 Å
I(0) (实空间) i0_real	4.2640e+09
I(0) 误差 (实空间) i0_real_error	1.0070e+08
Rg (倒空间) rg_reciprocal	78.69 Å
I(0) (倒空间) i0_reciprocal	4257000000.0000
解质量估计 total_estimate	0.8504
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	100.2 Å
偏度 Skewness skewness	0.337
峰度 Kurtosis kurtosis	-0.201
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.1405
最高正则化参数 α highest_alpha	219100000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.841

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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 (6)

Entity 1 polymer

描述 description	E1 glycoprotein
分子量 formula_weight	47346.7 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	A,B,C,D
原子数 atom_count	38228

YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTRVVDAPSVTDMSCEVPACTHSSDFGGVAIIKYTASKKGKCAVHSMTNAVTIREADVEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAACHPPKDHIVNYPASHTTLGVQDISTTAMSWVQKITGGVGLIVAVAALILIVVLCVSFSRH

来源 Source

来源生物 organism	Chikungunya virus strain Senegal 37997
NCBI 分类编号 ncbi_taxonomy_id	371095
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	E2 glycoprotein
分子量 formula_weight	46858.3 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	M,N,O,P

NFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHTCTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEPNYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

来源 Source

来源生物 organism	Chikungunya virus strain Senegal 37997
NCBI 分类编号 ncbi_taxonomy_id	371095
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	Capsid protein
分子量 formula_weight	16458.7 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	Q,R,S,T

NDCIFEVKHEGKVMGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVHMKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGARTALSVVTWNKDIVTKITPEGAEEW

来源 Source

来源生物 organism	Chikungunya virus strain Senegal 37997
NCBI 分类编号 ncbi_taxonomy_id	371095
宿主生物 host_organism	Homo sapiens

Entity 4 polymer

描述 description	506.C01 light chain
分子量 formula_weight	11486.8 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,U,W,Y

DIQMTQSPSSVSASVGDRVTITCRASQGISSWLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPRTFGQGTKVEIK

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 5 polymer

描述 description	506.C01 heavy chain
分子量 formula_weight	14082.7 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,V,X,Z

QVQLQESGPGLVKPSQTLSLTCTVSGGSISSDDYYWTWIRLPPGKGLEWIGYIFYTGGTYYNPSLKSRVTISLDRSKNQFSLKLSSVTAADTAVYFCARAPETYCSTTNCYKGYFDSWGQGTLVTVSS

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 6 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	12

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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	8dwxA01
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	350 —

结构域编号 domain_id	8dwxB01
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	350 —

结构域编号 domain_id	8dwxC01
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	350 —

结构域编号 domain_id	8dwxD01
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	350 —

结构域编号 domain_id	8dwxH01
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	8dwxL01
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	8dwxM01
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	3200 — Alphavirus E2 glycoprotein, A domain

结构域编号 domain_id	8dwxN01
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	3200 — Alphavirus E2 glycoprotein, A domain

结构域编号 domain_id	8dwxO01
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	3200 — Alphavirus E2 glycoprotein, A domain

结构域编号 domain_id	8dwxP01
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	3200 — Alphavirus E2 glycoprotein, A domain

结构域编号 domain_id	8dwxU01
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	8dwxV01
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	8dwxW01
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	8dwxX01
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	8dwxY01
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	8dwxZ01
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	3.27 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	866369

fit	/app/data/saxs_computation/dw/8dwx/8dwx.fit
pddf	/app/data/pr_computation/dw/8dwx/8dwx.pr.out
profile	/app/data/saxs_computation/dw/8dwx/8dwx.dat

Chikungunya VLP in complex with neutralizing Fab 506.C01 (asymmetric unit)

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 (6)

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 polymer

聚合体 Polymer

来源 Source

Entity 6 non-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)