SAXSdb — 8f0h

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8f0h
沉积日期 deposition_date	2022-11-02
结构标题 title	Structure of SARS-CoV-2 spike with antibody Fabs 2A10 and 1H2 (Local refinement of the RBD and Fabs 1H2 and 2A10)
关键词 keywords	VIRAL PROTEIN, glycoprotein, immune system, antibody, SARS-CoV-2, COVID, VIRAL PROTEIN-Immune System complex, coronavirus; 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	28.96 Å
回转半径 Rg (电子) rg_electron	28.48 Å
零角强度 I(0) i0	82405300.00
分子量 molecular_weight	70322.0 kDa
排除体积 excluded_volume	87385 Å³
包络体积 envelope_volume	106280 Å³
水化壳体积 shell_volume	32096 Å³
包络直径 envelope_diameter	112.4 Å
壳层 Rg shell_rg	34.64 Å
包络 Rg envelope_rg	28.67 Å
形状 Rg shape_rg	28.42 Å
总 Rg total_rg	29.27 Å
总原子数 total_atoms	4957
残基数 n_residues	634
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	104.3 Å
Rg (实空间) rg_real	29.02 Å
Rg 误差 (实空间) rg_real_error	1.04 Å
I(0) (实空间) i0_real	8.2410e+07
I(0) 误差 (实空间) i0_real_error	1.3290e+06
Rg (倒空间) rg_reciprocal	29.00 Å
I(0) (倒空间) i0_reciprocal	82400000.0000
解质量估计 total_estimate	0.6307
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.2 Å
偏度 Skewness skewness	0.424
峰度 Kurtosis kurtosis	-0.194
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15820000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.832; Smooth: 0.955

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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	Antibody Fab 1H2 heavy chain
分子量 formula_weight	13783.5 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	B
原子数 atom_count	4959

QVQLQQSGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGITWNSGTIGYADSVKGRFTISRDNAKNSLYLQMRSLRAEDTALYYCAKDSGRKLLWGREDYYMGVWGKGTTVTV

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 2 polymer

描述 description	Spike glycoprotein
分子量 formula_weight	134065.7 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	C

MGVKVLFALICIAVAEAQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQ

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
通用名 common_name	2019-nCoV, SARS-CoV-2
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Cricetulus griseus

Entity 3 polymer

描述 description	Antibody Fab 1H2 light chain
分子量 formula_weight	10796.7 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	D

SYELTQPPSVSVAPGKTARITCGGSNIGSKSVHWYQQKPGQAPVLVIYYDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHVVFGG

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	Antibody Fab 2A10 heavy chain
分子量 formula_weight	12750.3 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	H

QVQLVESGGGLIQPGGSLRLSCAASEFIVSSNYMSWVRQAPGKGLEWVSLLYSGGTTYYADSVKGRFTISRDNSKNTLFLQMNSLRAEDTAMYYCARDRGPWLHDYWGQGTLVTV

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 5 polymer

描述 description	Antibody Fab 2A10 light chain
分子量 formula_weight	11920.2 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	L

DIVMTQSPSSLSASVGDRVTITCQASQDINKYCNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTINSLQPEDIATYYCQQYDNLPPTFGGGTKVEIKRT

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 6 branched

描述 description	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	570.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	8f0hB01
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	8f0hD01
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	8f0hH01
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	8f0hL01
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	3.18 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	204842

fit	/app/data/saxs_computation/f0/8f0h/8f0h.fit
pddf	/app/data/pr_computation/f0/8f0h/8f0h.pr.out
profile	/app/data/saxs_computation/f0/8f0h/8f0h.dat

Structure of SARS-CoV-2 spike with antibody Fabs 2A10 and 1H2 (Local refinement of the RBD and Fabs 1H2 and 2A10)

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 branched

6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)