9c1h

Rhesus rotavirus (upright structure at 2.88 Angstrom resolution)

Method: ELECTRON MICROSCOPY D_max: 211.2 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9c1h
沉积日期 deposition_date	2024-05-29
结构标题 title	Rhesus rotavirus (upright structure at 2.88 Angstrom resolution)
关键词 keywords	Rotavirus, non-enveloped virus, viral particle, VIRAL PROTEIN; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	83.14 Å
回转半径 Rg (电子) rg_electron	82.85 Å
零角强度 I(0) i0	47236200000.00
分子量 molecular_weight	1857000.0 kDa
排除体积 excluded_volume	2321000 Å³
包络体积 envelope_volume	3344800 Å³
水化壳体积 shell_volume	314810 Å³
包络直径 envelope_diameter	301.9 Å
壳层 Rg shell_rg	93.51 Å
包络 Rg envelope_rg	82.43 Å
形状 Rg shape_rg	82.86 Å
总 Rg total_rg	82.89 Å
总原子数 total_atoms	258079
残基数 n_residues	16309
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	211.2 Å
Rg (实空间) rg_real	80.18 Å
Rg 误差 (实空间) rg_real_error	0.40 Å
I(0) (实空间) i0_real	4.5570e+10
I(0) 误差 (实空间) i0_real_error	7.6720e+08
Rg (倒空间) rg_reciprocal	84.17 Å
I(0) (倒空间) i0_reciprocal	47380000000.0000
解质量估计 total_estimate	0.9033
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	100.1 Å
偏度 Skewness skewness	0.089
峰度 Kurtosis kurtosis	-0.521
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.1671
最高正则化参数 α highest_alpha	3038000000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 0.982; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.000

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (9)

Entity 1 polymer

描述 description	Outer capsid glycoprotein VP7
分子量 formula_weight	37136.5 kDa
来源方法 src_method	man
拷贝数 entity_count	19

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	0,1,P,Q,R,S,T,U,V,W,X,Y,Z,t,u,v,w,x,y
原子数 atom_count	258079

MYGIEYTTVLTFLISLILLNYILKSLTRMMDFIIYRFLFIVVILSPLLKAQNYGINLPITGSMDTAYANSTQEETFLTSTLCLYYPTEAATEINDNSWKDTLSQLFLTKGWPTGSVYFKEYTDIASFSVDPQLYCDYNVVLMKYDATLQLDMSELADLILNEWLCNPMDITLYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTDTATFEEVATAEKLVITDVVDGVNHKLDVTTATCTIRNCKKLGPRENVAVIQVGGSDVLDITADPTTAPQTERMMRINWKKWWQVFYTVVDYVNQIIQAMSKRSRSLNSAAFYYRI

来源 Source

来源生物 organism	Simian rotavirus A strain RRV
NCBI 分类编号 ncbi_taxonomy_id	444185
宿主生物 host_organism	Simian rotavirus A strain RRV

Entity 2 polymer

描述 description	Outer capsid protein VP4
分子量 formula_weight	86655.6 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	2,3,4

MASLIYRQLLTNSYTVDLSDEIQEIGSTKTQNVTINLGPFAQTGYAPVNWGPGETNDSTTVEPVLDGPYQPTTFNPPVDYWMLLAPTAAGVVVEGTNNTDRWLATILVEPNVTSETRSYTLFGTQEQITIANASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTYNGETPNVTTKYYSTTNYDSVNMTAFCDFYIIPREEESTCTEYINNGLPPIQNTRNIVPLALSARNIISHRAQANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEEVTAHTTCSVNGMNDFNFNGGSLPTDFVISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSLNSLRFRFRLTVEEPSFSITRTRVSRLYGLPAANPNNGKEYYEVAGRFSLISLVPSNDDYQTPITNSVTVRQDLERQLGELREEFNALSQEIAMSQLIDLALLPLDMFSMFSGIKSTIDAAKSMATSVMKKFKKSGLANSVSTLTDSLSDAASSISRGASIRSVGSSASAWTDVSTQITDVSSSVSSISTQTSTISRRLRLKEMATQTEGMNFDDISAAVLKTKIDRSTQISPNTLPDIVTEASEKFIPNRAYRVINNDEVFEAGTDGRFFAYRVETFDEIPFDVQKFADLVTDSPVISAIIDFKTLKNLNDNYGISRQQAFNLLRSDPRVLREFINQDNPIIRNRIEQLIMQCRL

来源 Source

来源生物 organism	Simian rotavirus A strain RRV
NCBI 分类编号 ncbi_taxonomy_id	444185
宿主生物 host_organism	Simian rotavirus A strain RRV

Entity 3 polymer

描述 description	Inner capsid protein VP2
分子量 formula_weight	103426.0 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

MAYRKRGARRETNLKQDDRMQEKEENKNVNTNSENKNATKPQLSEKVLSQKEEVITDNQEEIKIADEVKKSNKEESKQLLEVLKTKEEHQKEVQYEILQKTIPTFEPKESILKKLEDIKPEQVKKQTKLFRIFEPRQLPVYRANGEKELRNRWYWKLKRDTLPDGDYDVREYFLNLYDQVLTEMPDYLLLKDMAVENKNSRDAGKVVDSETAAICDAIFQDEETEGVVRRFIAEMRQRVQADRNVVNYPSILHPIDHAFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVNYILNMDRNLPSTARYIRPNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQLEALTIQSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTNYMSLISGMWLLTVVPNDMFIRESLVACQLAIINTIIYPAFGMQRMHYRNGDPQTPFQIAEQQIQNFQVANWLHFVNNNQFRQVVIDGVLNQVLNDNIRNGHVVNQLMEALMQLSRQQFPTMPVDYKRSIQRGILLLSNRLGQLVDLTRLLAYNYETLMACITMNMQHVQTLTTEKLQLTSVTSLCMLIGNATVIPSPQTLFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKSIVEDFLKRLQIFDISRVPDDQMYRLRDRLRLLPVEIRRLDIFNLILMNMEQIERASDKIAQGVIIAYRDMQLERDEMYGYVNIARNLDGFQQINLEELMRTGDYAQITNMLLNNQPVALVGALPFITDSSVISLVAKLDATVFAQIVKLRKVDTLKPILYKINSDSNDFYLVANYDWVPTSTTKVYKQIPQQFDFRASMHMLTSNLTFTVYSDLLAFVSADTVEPINAVAFDNMRIMNEL

来源 Source

来源生物 organism	Simian rotavirus A strain RRV
NCBI 分类编号 ncbi_taxonomy_id	444185
宿主生物 host_organism	Simian rotavirus A strain RRV

Entity 4 polymer

描述 description	Intermediate capsid protein VP6
分子量 formula_weight	44962.8 kDa
来源方法 src_method	man
拷贝数 entity_count	19

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D,E,F,G,H,I,J,K,L,M,N,O,f,g,h,i,j,k

MDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLRKLSGIKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANIQQFEHIVQLRRVLTTATITLLPDAERFSFPRVINSADGATTWYFNPVILRPNNVEVEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASKTMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK

来源 Source

来源生物 organism	Simian rotavirus A strain RRV
NCBI 分类编号 ncbi_taxonomy_id	444185
宿主生物 host_organism	Simian rotavirus A strain RRV

Entity 5 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	1

Entity 6 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	17

Entity 7 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	76

Entity 8 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	26

Entity 9 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	triclinic

分辨率 resolution	2.88 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	542965

fit	/app/data/saxs_computation/c1/9c1h/9c1h.fit
pddf	/app/data/pr_computation/c1/9c1h/9c1h.pr.out
profile	/app/data/saxs_computation/c1/9c1h/9c1h.dat

Rhesus rotavirus (upright structure at 2.88 Angstrom 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

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (9)

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

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)