SAXSdb — 8z4t

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8z4t
沉积日期 deposition_date	2024-04-17
结构标题 title	MERS-CoV S ectodomain trimer in complex with receptor DPP4-750E
关键词 keywords	MERS-CoV, spike, DPP4, 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	72.27 Å
回转半径 Rg (电子) rg_electron	72.48 Å
零角强度 I(0) i0	3741610000.00
分子量 molecular_weight	516400.0 kDa
排除体积 excluded_volume	643840 Å³
包络体积 envelope_volume	1004000 Å³
水化壳体积 shell_volume	118690 Å³
包络直径 envelope_diameter	240.1 Å
壳层 Rg shell_rg	70.13 Å
包络 Rg envelope_rg	69.67 Å
形状 Rg shape_rg	72.52 Å
总 Rg total_rg	72.28 Å
总原子数 total_atoms	36433
残基数 n_residues	4687
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	263.1 Å
Rg (实空间) rg_real	72.31 Å
Rg 误差 (实空间) rg_real_error	3.01 Å
I(0) (实空间) i0_real	3.7420e+09
I(0) 误差 (实空间) i0_real_error	7.6100e+07
Rg (倒空间) rg_reciprocal	71.96 Å
I(0) (倒空间) i0_reciprocal	3739000000.0000
解质量估计 total_estimate	0.7892
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	95.7 Å
偏度 Skewness skewness	0.224
峰度 Kurtosis kurtosis	-0.574
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0004
最高正则化参数 α highest_alpha	210400000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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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 (2)

Entity 1 polymer

描述 description	Spike glycoprotein
分子量 formula_weight	132301.2 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	36433

VDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQGRTYSNITITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFVVRIGAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHTLVLLPDGCGTLLRAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDGNYNRNASLNSFKEYFNLRNCTFMYTYNITEDEILEWFGITQTAQGVHLFSSRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSIRSIQSDRKAWAAFYVYKLQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGVYSVSSFEAKPSGSVVEQAEGVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLEFANDTKIASQLGNCVEYSLYGVSGRGVFQNCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVSVIYDKETKTHATLFGSVACEHISSTMSQYSRSTRSMLKRRDSTYGPLQTPVGCVLGLVNSSLFVEDCKLPLGQSLCALPDTPSTLTPSSVGSVPGEMRLASIAFNHPIQVDQLNSSYFKLSIPTNFSFGVTQEYIQTTIQKVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHGANLRQDDSVRNLFASVKSSQSSPIIPGFGGDFNLTLLEPVSISTGSRSARSAIEDLLFDKVTIADPGYMQGYDDCMQQGPASARDLICAQYVAGYKVLPPLMDVNMEAAYTSSLLGSIAGVGWTAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKLIANKFNQALGAMQTGFTTTNEAFQKVQDAVNNNAQALSKLASELSNTFGAISASIGDIIQRLDPPEQDAQIDRLINGRLTTLNAFVAQQLVRSESAALSAQLAKDKVNECVKAQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVGYYPSNHIEVVSAYGLCDAANPTNCIAPVNGYFIKTNNTRIVDEWSYTGSSFYAPEPITSLNTKYVAPQVTYQNISTNLPPPLLG

来源 Source

来源生物 organism	Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)
通用名 common_name	MERS-CoV, Betacoronavirus England 1
NCBI 分类编号 ncbi_taxonomy_id	1263720
宿主生物 host_organism	Trichoplusia ni

Entity 2 polymer

描述 description	Dipeptidyl peptidase 4 soluble form
分子量 formula_weight	84453.6 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	D,I

SRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQEIYTHMSHFIKQCFSLP

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	Trichoplusia ni

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7. 引用文献 (1)

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分辨率 resolution	3.93 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	397140

fit	/app/data/saxs_computation/z4/8z4t/8z4t.fit
pddf	/app/data/pr_computation/z4/8z4t/8z4t.pr.out
profile	/app/data/saxs_computation/z4/8z4t/8z4t.dat

MERS-CoV S ectodomain trimer in complex with receptor DPP4-750E

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 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)