SAXSdb — 8z6u

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8z6u
沉积日期 deposition_date	2024-04-19
最后修订 last_revision	2025-02-12
结构标题 title	SARS-CoV-2 EG.5.1 Spike in complex with CYFN1006-2(S-CYFN1006-2 dimer trimer).
关键词 keywords	antibody, viral protein, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; 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	— Å
回转半径 Rg (电子) rg_electron	112.00 Å
零角强度 I(0) i0	13242500000.00
分子量 molecular_weight	991690.0 kDa
排除体积 excluded_volume	1243100 Å³
包络体积 envelope_volume	2149300 Å³
水化壳体积 shell_volume	178740 Å³
包络直径 envelope_diameter	412.8 Å
壳层 Rg shell_rg	88.15 Å
包络 Rg envelope_rg	106.20 Å
形状 Rg shape_rg	112.00 Å
总 Rg total_rg	111.80 Å
总原子数 total_atoms	69900
残基数 n_residues	9042
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	301.5 Å
Rg (实空间) rg_real	102.80 Å
Rg 误差 (实空间) rg_real_error	1.42 Å
I(0) (实空间) i0_real	1.2670e+10
I(0) 误差 (实空间) i0_real_error	2.6670e+08
Rg (倒空间) rg_reciprocal	95.63 Å
I(0) (倒空间) i0_reciprocal	12660000000.0000
解质量估计 total_estimate	0.8755
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	64.6 Å
偏度 Skewness skewness	0.411
峰度 Kurtosis kurtosis	-0.845
角度范围 angular_range	— – 0.0700 Å⁻¹
当前正则化参数 α current_alpha	0.8534
最高正则化参数 α highest_alpha	462700000.0000
实空间数据点数 n_real_points	15
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.008; Oscil: 0.852; Stabil: 0.977; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.002

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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,Expression Tag
分子量 formula_weight	143147.6 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,A,C,E,D,F
原子数 atom_count	69900

MPMGSLQPLATLYLLGMLVASVLAQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTHDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPVDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLLRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSHHHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	CYFN1006-2 light chain
分子量 formula_weight	22673.1 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J,K,L,P,Q,R

QSALTQPPSASGSPGQSVTISCTGASSDVGGYNYVSWYQQHPGKAPKLMIYEVNKRPSGVPDRFSGSKSGNTASLTISGLQADDEADYYCCSYALSRVVFGGGTMLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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 3 polymer

描述 description	CYFN1006-2 heavy chain
分子量 formula_weight	23388.4 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,H,I,M,N,O

QMQLVQSGAEVKKPGESLKISCKGSGYTFSYYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLHWSSLKASDTAMYYCARQGDLGDWILLGYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV

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

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7. 引用文献 (1)

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分辨率 resolution	3.83 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	66958

fit	/app/data/saxs_computation/z6/8z6u/8z6u.fit
pddf	/app/data/pr_computation/z6/8z6u/8z6u.pr.out
profile	/app/data/saxs_computation/z6/8z6u/8z6u.dat

SARS-CoV-2 EG.5.1 Spike in complex with CYFN1006-2(S-CYFN1006-2 dimer trimer).

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

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)