8zpp

Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab

Method: ELECTRON MICROSCOPY D_max: 83.6 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	8zpp
沉积日期 deposition_date	2024-05-30
结构标题 title	Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab
关键词 keywords	SARS-CoV-2, antibody, complex, VIRAL PROTEIN; VIRAL PROTEIN
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	24.05 Å
回转半径 Rg (电子) rg_electron	23.36 Å
零角强度 I(0) i0	36161100.00
分子量 molecular_weight	46267.0 kDa
排除体积 excluded_volume	57692 Å³
包络体积 envelope_volume	68025 Å³
水化壳体积 shell_volume	24737 Å³
包络直径 envelope_diameter	87.0 Å
壳层 Rg shell_rg	30.12 Å
包络 Rg envelope_rg	23.90 Å
形状 Rg shape_rg	23.26 Å
总 Rg total_rg	24.46 Å
总原子数 total_atoms	3266
残基数 n_residues	419
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	83.6 Å
Rg (实空间) rg_real	24.10 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	3.6160e+07
I(0) 误差 (实空间) i0_real_error	4.9220e+05
Rg (倒空间) rg_reciprocal	24.09 Å
I(0) (倒空间) i0_reciprocal	36160000.0000
解质量估计 total_estimate	0.7877
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	27.4 Å
偏度 Skewness skewness	0.434
峰度 Kurtosis kurtosis	-0.161
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10440000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.000

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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	Spike glycoprotein,Fibritin
分子量 formula_weight	139437.6 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	A
原子数 atom_count	3266

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGGGGGSGGGGSHHHHHH

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
NCBI 分类编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	variable heavy chain of ORB10 Fab
分子量 formula_weight	13172.4 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

QVQLQQSGAELVRPGSSVKISCKASGYAFSNYWMNWVKQRPGEGLEWIGQIYPGDGDTDYNGKFKGRATLTADKSSSTAYMQLSSLTSEDSAVYFCARGDDGYYVYFDYWGQGTTLTVS

Entity 3 polymer

描述 description	variable light chain of ORB10 Fab
分子量 formula_weight	11486.7 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

EIVLTQSPALMAASPGEKVTITCSVSSSIGSNNLHWYQQKSETSPKPWIYGTSNLASGVPVRFSGSGSGTSYSLTISTMEAEDAATYYCQQWSGYPLTFGGGTKLEIK

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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	3.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	219826

fit	/app/data/saxs_computation/zp/8zpp/8zpp.fit
pddf	/app/data/pr_computation/zp/8zpp/8zpp.pr.out
profile	/app/data/saxs_computation/zp/8zpp/8zpp.dat

Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab

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

Entity 3 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)