9dbz

;Molecular basis of pathogenicity of the recently emerged FCoV-23 coronavirus. FCoV-23 S long with Do in mixed conformations (global refinement). ;

Method: ELECTRON MICROSCOPY D_max: 170.5 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	9dbz
沉积日期 deposition_date	2024-08-24
结构标题 title	;Molecular basis of pathogenicity of the recently emerged FCoV-23 coronavirus. FCoV-23 S long with Do in mixed conformations (global refinement). ;
关键词 keywords	;Coronavirus, alphacoronavirus, feline coronavirus, cryo-EM, neutralization assays, binding assays, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, 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	52.45 Å
回转半径 Rg (电子) rg_electron	51.96 Å
零角强度 I(0) i0	2078900000.00
分子量 molecular_weight	384380.0 kDa
排除体积 excluded_volume	481360 Å³
包络体积 envelope_volume	719400 Å³
水化壳体积 shell_volume	112640 Å³
包络直径 envelope_diameter	180.5 Å
壳层 Rg shell_rg	57.10 Å
包络 Rg envelope_rg	51.51 Å
形状 Rg shape_rg	52.05 Å
总 Rg total_rg	51.83 Å
总原子数 total_atoms	27100
残基数 n_residues	3428
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	170.5 Å
Rg (实空间) rg_real	52.28 Å
Rg 误差 (实空间) rg_real_error	1.19 Å
I(0) (实空间) i0_real	2.0790e+09
I(0) 误差 (实空间) i0_real_error	3.8810e+07
Rg (倒空间) rg_reciprocal	52.57 Å
I(0) (倒空间) i0_reciprocal	2080000000.0000
解质量估计 total_estimate	0.8915
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	62.5 Å
偏度 Skewness skewness	0.174
峰度 Kurtosis kurtosis	-0.558
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	293000000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.903

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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 (7)

Entity 1 polymer

描述 description	Spike glycoprotein
分子量 formula_weight	162599.6 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	27176

MGILPSPGMPALLSLVSLLSVLLMGCVAETGTIKPNNDCRQVNVTQLDGNENLIRDFLFQNFKEEGTVVVGGYYPTEVWYNCSKTLTTTAYAYFNNIHAFYFDMEAMENSTGNARGKPLLFHVHGEPVSVIIYISAYGDDVQHRPLLKHGLVCITKTRNVDYNSFTSSQWNSICTGNDRKVPFSVIPTDNGTKIYGLEWNDELVTAYISGRSYNWNINNNWFNNVTLMYSRSSTATWLHSAAYVYQGVSNFTYYKLNNTNGLKTYEFCEDYEYCTGYATNVFAPTVGGYIPDGFSFNNWFLLTNDSTFVSGRFVTNQPLLVNCLWPVPSFGVAAQEFCFEGAQFSQCNGVSLNNTVDVIRFNLNFTADVQSGMGATVFSLNTTGGVILEISCYNDTVRESSFYSYGEIPFGITDGPKYCYVLYNGTALKYLGTLPPSVKEIAISKWGHFYINGYNFFSTFPIDCISFNLTTSTSGAFWTIAYTSYTEALVQVENTAIKKVTYCNSHINNIKCSQLTANLQNGFYPVASSEVGLVNKSVVLLPSFYSHTSVNITIDLGMKLSGYGQPIASALSNITLPMQDNNTDVYCIRSNQFSVYVHSTCKSSLWDNVFNSDCTDVLHATAVIKTGTCPFSFDKLNNYLTFNKFCLSLHPVGANCKFDVAARTRTNEQVVRSLYVIYEEGDNIAGVPSDNSGLHDLSVLHLDSCTDYNIYGKTGIGIIRQTNSTLLSGLYYTSLSGDLLGFKNVTDGVVYSVTPCDVSAQAAVIDGTIVGAMTSINSELLGLTHWTTTPNFYYYSIYNYTNERTRGTAIDSNDVDCEPIITYSNIGVCKNGALVFINVTHSDGDVQPISTGNVTIPTNFTISVQVEYIQVYTTPVSIDCSRYVCNGNPRCNKLLTQYVSACQTIEQALAMGARLENMEVDSMLFVSENALKLASVEAFNSTEHLDPIYKEWPNIGGSWLGGLKDILPSHNSKRKYRSAIEDLLFDKVVTSGLGTVDEDYKRCTGGYDIADLVCAQYYNGIMVLPGVANDDKMTMYTASLAGGITLGALGGGAVAIPFAVAVQARLNYVALQTDVLNKNQQILANAFNQAIGNITQAFGKVNDAIHQTSKGLATVAKALAKVQDVVNTQGQALSHLTVQLQNNFQAISSSISDIYNRLDPPSADAQVDRLITGRLTALNAFVSQTLTRQAEVRASRQLAKDKVNECVRSQSQRFGFCGNGTHLFSLANAAPNGMIFFHTVLLPTAYETVTAWSGICASDGDHTFGLVVKDVQLTLFRNLDDKFYLTPRTMYQPRVATISDFVQIEGCDVLFVNATVIELPGIIPDYIDINQTVQDILENYRPNWTVPELTLDIFNSTYLNLTGEINDLEFRSEKLHNTTVELAVLIDNINNTLVNLEWLNRIETYVKSGGYIPEAPRDGQAYVRKDGEWVLLSTFLVPRGSGGSGGSGLNDIFEAQKIEWHEGGSHHHHHHHH

来源 Source

来源生物 organism	Feline coronavirus
NCBI 分类编号 ncbi_taxonomy_id	12663
宿主生物 host_organism	Mammalia

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	26

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	7

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	3

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	40

Entity 6 non-polymer

描述 description	PALMITOLEIC ACID
分子量 formula_weight	254.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 7 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	76

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7. 引用文献 (1)

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分辨率 resolution	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	213214

fit	/app/data/saxs_computation/db/9dbz/9dbz.fit
pddf	/app/data/pr_computation/db/9dbz/9dbz.pr.out
profile	/app/data/saxs_computation/db/9dbz/9dbz.dat