8vwi

The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised reconstruction)

Method: ELECTRON MICROSCOPY D_max: 221.1 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	8vwi
沉积日期 deposition_date	2024-02-01
结构标题 title	The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised reconstruction)
关键词 keywords	Nucleocapsid, Base, baculovirus, virus, AcMNPV, VP39, 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	84.99 Å
回转半径 Rg (电子) rg_electron	84.57 Å
零角强度 I(0) i0	16768500000.00
分子量 molecular_weight	1118500.0 kDa
排除体积 excluded_volume	1405200 Å³
包络体积 envelope_volume	2523400 Å³
水化壳体积 shell_volume	247520 Å³
包络直径 envelope_diameter	281.6 Å
壳层 Rg shell_rg	83.49 Å
包络 Rg envelope_rg	82.07 Å
形状 Rg shape_rg	84.55 Å
总 Rg total_rg	84.60 Å
总原子数 total_atoms	156266
残基数 n_residues	9602
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	221.1 Å
Rg (实空间) rg_real	82.35 Å
Rg 误差 (实空间) rg_real_error	0.41 Å
I(0) (实空间) i0_real	1.6040e+10
I(0) 误差 (实空间) i0_real_error	2.8000e+08
Rg (倒空间) rg_reciprocal	85.50 Å
I(0) (倒空间) i0_reciprocal	16790000000.0000
解质量估计 total_estimate	0.9107
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	98.2 Å
偏度 Skewness skewness	0.163
峰度 Kurtosis kurtosis	-0.550
角度范围 angular_range	— – 0.0900 Å⁻¹
当前正则化参数 α current_alpha	1.0540
最高正则化参数 α highest_alpha	932200000.0000
实空间数据点数 n_real_points	19
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 1.000; Stabil: 0.967; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.001

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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 (8)

Entity 1 polymer

描述 description	Major capsid protein
分子量 formula_weight	38991.1 kDa
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,V,W,X,Y,Z,a
原子数 atom_count	156266

MALVPVGMAPRQMRVNRCIFASIVSFDACITYKSPCSPDAYHDDGWFICNNHLIKRFKMSKMVLPIFDEDDNQFKMTIARHLVGNKERGIKRILIPSATNYQDVFNLNSMMQAEQLIFHLIYNNENAVNTICDNLKYTEGFTSNTQRVIHSVYATTKSILDTTNPNTFCSRVSRDELRFFDVTNARALRGGAGDQLFNNYSGFLQNLIRRAVAPEYLQIDTEELRFRNCATCIIDETGLVASVPDGPELYNPIRSSDIMRSQPNRLQIRNVLKFEGDTRELDRTLSGYEEYPTYVPLFLGYQIINSENNFLRNDFIPRANPNATLGGGAVAGPAPGVAGEAGGGIAV

来源 Source

来源生物 organism	Autographa californica multiple nucleopolyhedrovirus
NCBI 分类编号 ncbi_taxonomy_id	307456
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	Capsid-associated protein VP80
分子量 formula_weight	79974.5 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	G,H,I,b,c,d

MNDSNSLLITRLAAQILSRNMQTVDVIVDDKTLSLEEKIDTLTSMVLAVNSPPQSPPRVTSSDLAASIIKNNSKMVGNDFEMRYNVLRMAVVFVKHYPKYYNETTAGLVAEIESNLLQYQNYVNQGNYQNIEGYDSLLNKAEECYVKIDRLFKESIKKIMDDTEAFEREQEAERLRAEQTAANALLERRAQTSADDVVNRADANIPTAFSDPLPGPSAPRYMYESSESDTYMETARRTAEHYTDQDKDYNAAYTADEYNSLVKTVLLRLIEKALATLKNRLHITTIDQLKKFRDYLNSDADAGEFQIFLNQEDCVILKNLSNLASKFFNVRCVADTLEVMLEALRNNIELVQPESDAVRRIVIKMTQEIKDSSTPLYNIAMYKSDYDAIKNKNIKTLFDLYNDRLPINFLDTSATSPVRKTSGKRSAEDDLLPTRSSKRANRPEINVISSEDEQEDDDVEDVDYEKESKRRKLEDEDFLKLKALEFSKDIVNEKLQKIIVVTDGMKRLYEYCNCKNSLETLPSAANYGSLLKRLNLYNLDHIEMNVNFYELLFPLTLYNDNDNSDKTLSHQLVNYIFLASNYFQNCAKNFNYMRETFNVFGPFKQIDFMVMFVIKFNFLCDMRNFAKLIDELVPNKQPNMRIHSVLVMRDKIVKLAFSNLQFQTFSKKDKSRNTKHLQRLIMLMNANYNVI

来源 Source

来源生物 organism	Autographa californica multiple nucleopolyhedrovirus
NCBI 分类编号 ncbi_taxonomy_id	307456
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 polymer

描述 description	Occlusion-derived virus envelope protein E27
分子量 formula_weight	33568.2 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	J,M,Q,S,e,h

MKRIKCNKVRTVTEIVNSDEKIQKTYELAEFDLKNLSSLESYETLKIKLALSKYMAMLSTLEMTQPLLEIFRNKADTRQIAAVVFSTLAFIHNRFHPLVTNFTNKMEFVVTETNDTSIPGEPILFTENEGVLLCSVDRPSIVKMLSREFDTEALVNFENDNCNVRIAKTFGASKRKNTTRSDDYESNKQPNYDMDLSDFSITEVEATQYLTLLLTVEHAYLHYYIFKNYGVFEYCKSLTDHSLFTNKLRSTMSTKTSNLLLSKFKFTIEDFDKINSNSVTSGFNIYNFNK

来源 Source

来源生物 organism	Autographa californica multiple nucleopolyhedrovirus
NCBI 分类编号 ncbi_taxonomy_id	307456
宿主生物 host_organism	Spodoptera frugiperda

Entity 4 polymer

描述 description	Protein C42
分子量 formula_weight	41583.6 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	K,L,R,T,f,g

MSAIALYLEINKLRLKIDEPMQLAIWPQLFPLLCDEHQSVQLNTDVLINFMMHVARKSQNTILNNNAAIASQYAAGNADVVAAPASAQPTPRPVINLFARANAAAPAQPSEELINMRRYRNAARKLIHHYSLNSTSSTEYKISDVVMTMIFLLRSEKYHSLFKLLETTFDDYTCRPQMTQVQTDTLLDAVRSLLEMPSTTIDLTTVDIMRSSFARCFNSPIMRYAKIVLLQNVALQRDKRTTLEELLIERGEKIQMLQPQQYINSGTEIPFCDDAEFLNRLLKHIDPYPLSRMYYNAANTMFYTTMENYAVSNCKFNIEDYNNIFKVMENIRKHSNKNSNDQDELNIYLGVQSSNAKRKKY

来源 Source

来源生物 organism	Autographa californica multiple nucleopolyhedrovirus
NCBI 分类编号 ncbi_taxonomy_id	307456
宿主生物 host_organism	Spodoptera frugiperda

Entity 5 polymer

描述 description	Protein AC109
分子量 formula_weight	44851.4 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	N,i

MECPFQIQVCISDRFFAFPHNLVEPQSDVGNKLIENLIVYVPTDDDRLYIDKKQFPKFNSVLVYRHEHDVNIDSRSPKKTASATIVYWNPLVPITEIGAGETRVFSVLLTNNLFYCNTMIVHHENPKCPIEFTYPETDMQSACSALLKNRNGQSVPPPIKSNLRPIACEIPLSHFKELVESNDFLLCFNLETSTMVKILSLKRIFCIFQYRKQPARYVINLPHEEIDNLYNKLNWERTRRLMKGDVPSNCATVNRSSLKYIKQAQSLLGIPDYSQTVVDFVKMFQKIIFPYQLVPNVIIKLNNFDQMVSSAPNKAEPYKKIRLFCKNDSIAISSSGIVPINMPDFSPPNTFDYSDYANRTNINFVTQRVLTDGGFSSGITVTPVKYNYYL

来源 Source

来源生物 organism	Autographa californica multiple nucleopolyhedrovirus
NCBI 分类编号 ncbi_taxonomy_id	307456
宿主生物 host_organism	Spodoptera frugiperda

Entity 6 polymer

描述 description	Protein AC142
分子量 formula_weight	55480.9 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	O,j

MSGGGNLLTLERDHFKYLFLTSYFDLKDNEHVPSEPMAFIRNYLNCTFDLLDDAVLMNYFNYLQSMQLKHLVGSTSTNIFKFVKPQFRFVCDRTTVDILEFDTRMYIKPGTPVYATNLFTSNPRKMMAFLYAEFGKVFKNKIFVNINNYGCVLAGSAGFLFDDAYVDWNGVRMCAAPRLDNNMHPFRLYLLGEDMAKHFVDNNILPPHPSNAKTRKINNSMFMLKNFYKGLPLFKSKYTVVNSTKIVTRKPNDIFNEIDKELNGNCPFIKFIQRDYIFDAQFPPDLLDLLNEYMTKSSIMKIITKFVIEENPAMSGEMSREIILDRYSVDNYRKLYIKMEITNQFPVMYDHESSYIFVSKDFLQLKGTMNAFYAPKQRILSILAVNRLFGATETIDFHPNLLVYRQSSPPVRLTGDVYVVDKNEKVFLVKHVFSNTVPAYLLIRGDYESSSDLKSLRDLNPWVQNTLLKLLIPDSVQ

来源 Source

来源生物 organism	Autographa californica multiple nucleopolyhedrovirus
NCBI 分类编号 ncbi_taxonomy_id	307456
宿主生物 host_organism	Spodoptera frugiperda

Entity 7 polymer

描述 description	38K (AC98) protein in P143-LEF5 intergenic region
分子量 formula_weight	38070.5 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	P,k

MASSLQSKWICLRLNDAIIKRHVLVLSEYADLKYLGFEKYKFFEYVIFQFCNDPQLCKIIENNYNYCMQIFKAPADDMRDIRHNIKRAFKTPVLGHMCVLSNKPPMYSFLKEWFLLPHYKVVSLKSESLTWGFPHVVVFDLDSTLITEEEQVEIRDPFVYDSLQELHEMGCVLVLWSYGSRDHVAHSMRDVDLEGYFDIIISEGSTVQEERSDLVQNSHNAIVDYNLKKRFIENKFVFDIHNHRSDNNIPKSPKIVIKYLSDKNVNFFKSITLVDDLPTNNYAYDFYVKVKRCPTPVQDWEHYHNEIIQNIMDYEQYFIK

来源 Source

来源生物 organism	Autographa californica multiple nucleopolyhedrovirus
NCBI 分类编号 ncbi_taxonomy_id	307456
宿主生物 host_organism	Spodoptera frugiperda

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	12

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7. 引用文献 (1)

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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	4.71 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	53750

fit	/app/data/saxs_computation/vw/8vwi/8vwi.fit
pddf	/app/data/pr_computation/vw/8vwi/8vwi.pr.out
profile	/app/data/saxs_computation/vw/8vwi/8vwi.dat

The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised reconstruction)

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 (8)

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 polymer

聚合体 Polymer

来源 Source

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 polymer

聚合体 Polymer

来源 Source

Entity 8 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)