8jmm

Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution.

Method: ELECTRON MICROSCOPY D_max: 299.1 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	8jmm
沉积日期 deposition_date	2023-06-05
结构标题 title	Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution.
关键词 keywords	Antibody, 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	— Å
回转半径 Rg (电子) rg_electron	109.90 Å
零角强度 I(0) i0	13756200000.00
分子量 molecular_weight	1001800.0 kDa
排除体积 excluded_volume	1253000 Å³
包络体积 envelope_volume	2314600 Å³
水化壳体积 shell_volume	203350 Å³
包络直径 envelope_diameter	423.1 Å
壳层 Rg shell_rg	80.95 Å
包络 Rg envelope_rg	104.00 Å
形状 Rg shape_rg	109.90 Å
总 Rg total_rg	109.70 Å
总原子数 total_atoms	70630
残基数 n_residues	9099
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	299.1 Å
Rg (实空间) rg_real	100.10 Å
Rg 误差 (实空间) rg_real_error	1.42 Å
I(0) (实空间) i0_real	1.3160e+10
I(0) 误差 (实空间) i0_real_error	2.4520e+08
Rg (倒空间) rg_reciprocal	94.64 Å
I(0) (倒空间) i0_reciprocal	13230000000.0000
解质量估计 total_estimate	0.8877
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	85.5 Å
偏度 Skewness skewness	0.478
峰度 Kurtosis kurtosis	-0.664
角度范围 angular_range	— – 0.0700 Å⁻¹
当前正则化参数 α current_alpha	0.8216
最高正则化参数 α highest_alpha	1207000000.0000
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: 0.010; Oscil: 0.874; Stabil: 0.980; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.009

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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
分子量 formula_weight	143147.5 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	A,B,C,D,E,F
原子数 atom_count	70631

MPMGSLQPLATLYLLGMLVASVLAQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGSNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSHHHHHHHH

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 polymer

描述 description	7F3 Fv
分子量 formula_weight	27871.9 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	H,J,N,P,R,L

EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPQYTFGQGTKLEIKGGGGSGGGGSGGGGSEVQLVESGGGLVKPGRSLRLSCTASGFTFGDYAMSWFRQAPGKGLEWVGFIRSKAYGGTTEYAASVKGRFTISRDDSKSIAYLQMNSLKTEDTAVYYCTRDRYARYDILTGLSPAGADYFYYAMDVWGQGTTVTVSS

来源 Source

来源生物 organism	Homo sapiens
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	GW01 Fv
分子量 formula_weight	26330.6 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	I,K,M,O,Q,G

QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNWVFGGGTKLTVLGGGGSGGGGSGGGGSEVQLVESGGGVVQPGGSLRLSCAASGFRFDDHAMHWVRQAPGKGLEWVSVISGDGGSTYYADSVKGRFSISRDDSKNSLYLQMNSLRTEDTALYYCAKDRSYGPPDVFNYEYGMDVWGQGTTVTVSSGS

来源 Source

来源生物 organism	Homo sapiens
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	3.75 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	539055

fit	/app/data/saxs_computation/jm/8jmm/8jmm.fit
pddf	/app/data/pr_computation/jm/8jmm/8jmm.pr.out
profile	/app/data/saxs_computation/jm/8jmm/8jmm.dat

Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution.

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)