SAXSdb — 8epn

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8epn
沉积日期 deposition_date	2022-10-06
结构标题 title	Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD Down conformation
关键词 keywords	Glycoprotein, trimer, 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	51.19 Å
回转半径 Rg (电子) rg_electron	50.82 Å
零角强度 I(0) i0	1777760000.00
分子量 molecular_weight	356230.0 kDa
排除体积 excluded_volume	447270 Å³
包络体积 envelope_volume	681050 Å³
水化壳体积 shell_volume	108680 Å³
包络直径 envelope_diameter	168.8 Å
壳层 Rg shell_rg	56.68 Å
包络 Rg envelope_rg	50.21 Å
形状 Rg shape_rg	50.85 Å
总 Rg total_rg	50.94 Å
总原子数 total_atoms	25077
残基数 n_residues	2991
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	171.5 Å
Rg (实空间) rg_real	51.09 Å
Rg 误差 (实空间) rg_real_error	1.45 Å
I(0) (实空间) i0_real	1.7780e+09
I(0) 误差 (实空间) i0_real_error	3.0900e+07
Rg (倒空间) rg_reciprocal	51.26 Å
I(0) (倒空间) i0_reciprocal	1778000000.0000
解质量估计 total_estimate	0.8758
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	60.9 Å
偏度 Skewness skewness	0.287
峰度 Kurtosis kurtosis	-0.378
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	399700000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.880

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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 (4)

Entity 1 polymer

描述 description	Spike glycoprotein
分子量 formula_weight	123913.3 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	25077

AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGEENSVAYSNNSIAIPTNFTISVTTEIIPVSMQKVSVDCTMYICGDSEECSNLLLQYGSFCTQLNRALHEIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSAIEDLLFNKVTLADAGFIKGYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAAYTSALLAGTITAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNKAIGKIQDGLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLINGRLQALNTYVTQQLIRAAEIRASANLAAEKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPTQYKNFTTAPAICHNGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGDCDVVIGIVNNTVYDPLQPELDS

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Homo sapiens

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	18

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	15

Entity 4 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	15

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	8epnA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

结构域编号 domain_id	8epnB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

结构域编号 domain_id	8epnC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

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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	2.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	33173

fit	/app/data/saxs_computation/ep/8epn/8epn.fit
pddf	/app/data/pr_computation/ep/8epn/8epn.pr.out
profile	/app/data/saxs_computation/ep/8epn/8epn.dat

Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD Down conformation

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution