9dgo

;Designed miniproteins potently inhibit and protect against MERS-CoV. Crystal structure of MERS-CoV S RBD in complex with miniprotein cb3 ;

Method: X-RAY DIFFRACTION D_max: 83.7 Å Quality: EXCELLENT

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	9dgo
沉积日期 deposition_date	2024-09-03
最后修订 last_revision	2025-06-18
结构标题 title	;Designed miniproteins potently inhibit and protect against MERS-CoV. Crystal structure of MERS-CoV S RBD in complex with miniprotein cb3 ;
关键词 keywords	;MERS-CoV, miniproteins, neutralization, fusion, cryo-EM, biolayer interferometry, MERS-CoV strains, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, VIRAL PROTEIN ;; VIRAL PROTEIN
实验方法 method	X-RAY DIFFRACTION

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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	27.24 Å
回转半径 Rg (电子) rg_electron	25.89 Å
零角强度 I(0) i0	57673500.00
分子量 molecular_weight	58872.0 kDa
排除体积 excluded_volume	73417 Å³
包络体积 envelope_volume	91903 Å³
水化壳体积 shell_volume	29495 Å³
包络直径 envelope_diameter	91.5 Å
壳层 Rg shell_rg	33.49 Å
包络 Rg envelope_rg	26.01 Å
形状 Rg shape_rg	25.90 Å
总 Rg total_rg	26.71 Å
总原子数 total_atoms	4144
残基数 n_residues	535
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	83.7 Å
Rg (实空间) rg_real	27.09 Å
Rg 误差 (实空间) rg_real_error	0.44 Å
I(0) (实空间) i0_real	5.7670e+07
I(0) 误差 (实空间) i0_real_error	8.1960e+05
Rg (倒空间) rg_reciprocal	27.14 Å
I(0) (倒空间) i0_reciprocal	57680000.0000
解质量估计 total_estimate	0.9089
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.5 Å
偏度 Skewness skewness	0.124
峰度 Kurtosis kurtosis	-0.520
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	14580000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.977

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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	Spike glycoprotein
分子量 formula_weight	28045.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4492

MGILPSPGMPALLSLVSLLSVLLMGCVAETGTECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLGSLVPRGSGGSHHHHHHHH

来源 Source

来源生物 organism	Middle East respiratory syndrome-related coronavirus
NCBI 分类编号 ncbi_taxonomy_id	1335626
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	Designed miniprotein cb_3
分子量 formula_weight	7037.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D

GSPVKRFVREVLEEAEEAYEKGDRRQFEELLWLAEWAARDANDEELEEEIREFEKEVK

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	Escherichia coli

Entity 3 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	1

Entity 4 branched

描述 description	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	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 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	2

Entity 6 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	306

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7. 引用文献 (1)

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晶胞边长 a length_a	61.619 Å
晶胞边长 b length_b	76.291 Å
晶胞边长 c length_c	136.235 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.850 Å
最低分辨率 resolution_low	31.550 Å
R 因子 r_factor	0.1913
R_work r_work	0.1899
R_free r_free	0.2189

fit	/app/data/saxs_computation/dg/9dgo/9dgo.fit
pddf	/app/data/pr_computation/dg/9dgo/9dgo.pr.out
profile	/app/data/saxs_computation/dg/9dgo/9dgo.dat

;Designed miniproteins potently inhibit and protect against MERS-CoV. Crystal structure of MERS-CoV S RBD in complex with miniprotein cb3 ;

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

精修参数 Refinement

衍射实验 Diffraction

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 branched

Entity 4 branched

Entity 5 non-polymer

Entity 6 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)