8dyy

Cryo-EM structure of 334 Fab in complex with recombinant shortened Plasmodium falciparum circumsporozoite protein (rsCSP)

Method: ELECTRON MICROSCOPY D_max: 141.6 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	8dyy
沉积日期 deposition_date	2022-08-05
结构标题 title	Cryo-EM structure of 334 Fab in complex with recombinant shortened Plasmodium falciparum circumsporozoite protein (rsCSP)
关键词 keywords	malaria antibody, PfCSP, IMMUNE SYSTEM; 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	42.86 Å
回转半径 Rg (电子) rg_electron	42.73 Å
零角强度 I(0) i0	844574000.00
分子量 molecular_weight	233890.0 kDa
排除体积 excluded_volume	290050 Å³
包络体积 envelope_volume	387240 Å³
水化壳体积 shell_volume	74725 Å³
包络直径 envelope_diameter	147.3 Å
壳层 Rg shell_rg	48.26 Å
包络 Rg envelope_rg	42.19 Å
形状 Rg shape_rg	42.68 Å
总 Rg total_rg	43.17 Å
总原子数 total_atoms	16499
残基数 n_residues	2034
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	141.6 Å
Rg (实空间) rg_real	42.81 Å
Rg 误差 (实空间) rg_real_error	0.86 Å
I(0) (实空间) i0_real	8.4460e+08
I(0) 误差 (实空间) i0_real_error	1.2750e+07
Rg (倒空间) rg_reciprocal	42.86 Å
I(0) (倒空间) i0_reciprocal	844600000.0000
解质量估计 total_estimate	0.8609
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	49.7 Å
偏度 Skewness skewness	0.353
峰度 Kurtosis kurtosis	-0.246
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	65080000.0000
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: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.834

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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 (3)

Entity 1 polymer

描述 description	Circumsporozoite protein
分子量 formula_weight	30232.2 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	I
原子数 atom_count	16499

YGSSSNTRVLNELNYDNAGTNLYNELEMNYYGKQENWYSLKKNSRSLGENDDGNNEDNEKLRKPKHKKLKQPADGNPDPNANPNVDPNANPNVDPNANPNVDPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNANPNKNNQGNGQGHNMPNDPNRNVDENANANSAVKNNNNEEPSDKHIKEYLNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKICKMEKCSSVFNVVNS

来源 Source

来源生物 organism	Plasmodium falciparum
NCBI 分类编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	334 Fab heavy chain
分子量 formula_weight	24292.2 kDa
来源方法 src_method	man
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,A,C,E,M,O,Q,S,U

QVQLVESGGGVVQPGRSLTLSCAASGFTFSNYGMHWVRQTPGKGLAWVAIIWYDGSKTYYEDSVKGRFTISRDNSKNTLYLQMNSLRVDDTAVYYCARVRHSSSRHGSAFDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

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	334 Fab light chain
分子量 formula_weight	23621.1 kDa
来源方法 src_method	man
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L,B,D,F,N,P,R,T,V

VIQMTQSPSTLSASVGDRVTITCRASQSVSTWLAWYQQKPGQGPKLLIYEASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNSYSFWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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

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6. 折叠分类 (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

结构域编号 domain_id	8dyyA01
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	8dyyB01
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	8dyyC01
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	8dyyD01
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	8dyyE01
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	8dyyF01
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	8dyyH01
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	8dyyL01
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	8dyyM01
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	8dyyN01
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	8dyyO01
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	8dyyP01
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	8dyyQ01
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	8dyyR01
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	8dyyS01
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	8dyyT01
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	8dyyU01
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	8dyyV01
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	3.62 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	458706

fit	/app/data/saxs_computation/dy/8dyy/8dyy.fit
pddf	/app/data/pr_computation/dy/8dyy/8dyy.pr.out
profile	/app/data/saxs_computation/dy/8dyy/8dyy.dat

Cryo-EM structure of 334 Fab in complex with recombinant shortened Plasmodium falciparum circumsporozoite protein (rsCSP)

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 (3)

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

6. 折叠分类 (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)