9dou

Taeniopygia guttata R2 retrotransposon (R2Tg) initiating target-primed reverse transcription

Method: ELECTRON MICROSCOPY D_max: 119.9 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	9dou
沉积日期 deposition_date	2024-09-19
结构标题 title	Taeniopygia guttata R2 retrotransposon (R2Tg) initiating target-primed reverse transcription
关键词 keywords	retrotransposon, LINE, reverse transcriptase, endonuclease, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
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	38.07 Å
回转半径 Rg (电子) rg_electron	37.11 Å
零角强度 I(0) i0	516374000.00
分子量 molecular_weight	152360.0 kDa
排除体积 excluded_volume	177080 Å³
包络体积 envelope_volume	259130 Å³
水化壳体积 shell_volume	57833 Å³
包络直径 envelope_diameter	124.6 Å
壳层 Rg shell_rg	43.74 Å
包络 Rg envelope_rg	36.60 Å
形状 Rg shape_rg	37.07 Å
总 Rg total_rg	37.56 Å
总原子数 total_atoms	10494
残基数 n_residues	1069
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	119.9 Å
Rg (实空间) rg_real	37.86 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	5.1640e+08
I(0) 误差 (实空间) i0_real_error	8.7440e+06
Rg (倒空间) rg_reciprocal	38.00 Å
I(0) (倒空间) i0_reciprocal	516400000.0000
解质量估计 total_estimate	0.9017
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	48.5 Å
偏度 Skewness skewness	0.117
峰度 Kurtosis kurtosis	-0.550
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	34090000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.926

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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	R2Tg retrotransposon ORF
分子量 formula_weight	157228.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	10494

MASCPKPGPPVSAGAMSLESGLTTHSVLAIERGPNSLANSGSDFGGGGLGLPLRLLRVSVGTQTSRSDWVDLVSWSHPGPTSKSQQVDLVSLFPKHRVDLLSKNDQVDLVAQFLPSKFPPNLAENDLALLVNLEFYRSDLHVYECVHFAAHWEGLSGLPEVYEQLAPQPCVGETLHSSLPRDSELFVPEEGSSEKESEDAPKTSPPTPGKHGLEQTGEEKVMVTVPDKNPPCPCCGTRVNSVLNLIEHLKVSHGKRGVCFRCAKCGKENSNYHSVVCHFPKCRGPETEKAPAGEWICEVCNRDFTTKIGLGQHKRLAHPAVRNQERIVASQPKETSNRGAHKRCWTKEEEELLIRLEAQFEGNKNINKLIAEHITTKTAKQISDKRRLLSRKPAEEPREEPGTCHHTRRAAASLRTEPEMSHHAQAEDRDNGPGRRPLPGRAAAGGRTMDEIRRHPDKGNGQQRPTKQKSEEQLQAYYKKTLEERLSAGALNTFPRAFKQVMEGRDIKLVINQTAQDCFGCLESISQIRTATRDKKDTVTREKHPKKPFQKWMKDRAIKKGNYLRFQRLFYLDRGKLAKIILDDIECLSCDIPLSEIYSVFKTRWETTGSFKSLGDFKTYGKADNTAFRELITAKEIEKNVQEMSKGSAPGPDGITLGDVVKMDPEFSRTMEIFNLWLTTGKIPDMVRGCRTVLIPKSSKPDRLKDINNWRPITIGSILLRLFSRIVTARLSKACPLNPRQRGFIRAAGCSENLKLLQTIIWSAKREHRPLGVVFVDIAKAFDTVSHQHIIHALQQREVDPHIVGLVSNMYENISTYITTKRNTHTDKIQIRVGVKQGDPMSPLLFNLAMDPLLCKLEESGKGYHRGQSSITAMAFADDLVLLSDSWENMNTNISILETFCNLTGLKTQGQKCHGFYIKPTKDSYTINDCAAWTINGTPLNMIDPGESEKYLGLQFDPWIGIARSGLSTKLDFWLQRIDQAPLKPLQKTDILKTYTIPRLIYIADHSEVKTALLETLDQKIRTAVKEWLHLPPCTCDAILYSSTRDGGLGITKLAGLIPSVQARRLHRIAQSSDDTMKCFMEKEKMEQLHKKLWIQAGGDRENIPSIWEAPPSSEPPNNVSTNSEWEAPTQKDKFPKPCNWRKNEFKKWTKLASQGRGIVNFERDKISNHWIQYYRRIPHRKLLTALQLRANVYPTREFLARGRQDQYIKACRHCDADIESCAHIIGNCPVTQDARIKRHNYICELLLEEAKKKDWVVFKEPHIRDSNKELYKPDLIFVKDARALVVDVTVRYEAAKSSLEEAAAEKVRKYKHLETEVRHLTNAKDVTFVGFPLGARGKWHQDNFKLLTELGLSKSRQVKMAETFSTVALFSSVDIVHMFASRARKSMVM

来源 Source

来源生物 organism	Taeniopygia guttata
通用名 common_name	zebra finch
NCBI 分类编号 ncbi_taxonomy_id	59729
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 polymer

描述 description	;28S DNA bottom strand, 3' side ;
分子量 formula_weight	65051.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	B

TTCCCTTGGCTGTGGTTTCGCTAGATAGTAGATAGGGACAGTGGGAATCTCGTTAATCCATTCATGCGCGTCACTAATTAGATGACGAGGCATTTGGCTACCTTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCTTCATTGAATTTCTTCACTTTGACATTCAGAGCACTGGGCAGAAATCACATCGCGTCAACCAGCTGAAAAA

Entity 3 polymer

描述 description	;28S DNA bottom strand, 5' side (priming strand) ;
分子量 formula_weight	3997.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	P

GGCATTTGGCTAT

Entity 4 polymer

描述 description	;R2Tg 3'UTR RNA ;
分子量 formula_weight	106656.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	R

UUCAGGUUAUUUAGAUGCUUAGUUUUUGUACCUUUCUUGUUUUGUUUAGGAUUUUGAUAGUGUUAGUAUUUUUAUAUUUUUGUACGAUUGCAUAAUGUUCUUUUUUAUACAGUUCUGUUUUAAUAAAAUAGACGAUAGCUAGAGACGUUAGGGCAGCCACAAGCCAGUUAGGUAGCGGAUAGUAGGUAGGAACAGACUUUUACUAUUUCAUAACGCGUCAAUUACCACCUGAUUUGGACCAAUUCACGGGAUUUGUCCAAGGUGGACGGGCCACCUUUACUUAACCCGGAAAAGGAACAUAUAUAAUUUAUGUGUGUUCGAUAAAUAGCCAAA

Entity 5 polymer

描述 description	28S DNA top strand
分子量 formula_weight	65225.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	T

TTTTTCAGCTGGTTGACGCGATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAATGAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTATCTACTATCTAGCGAAACCACAGCCAAGGGAA

Entity 6 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	THYMIDINE-5'-TRIPHOSPHATE
分子量 formula_weight	482.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	4

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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	—

分辨率 resolution	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	30612

fit	/app/data/saxs_computation/do/9dou/9dou.fit
pddf	/app/data/pr_computation/do/9dou/9dou.pr.out
profile	/app/data/saxs_computation/do/9dou/9dou.dat

Taeniopygia guttata R2 retrotransposon (R2Tg) initiating target-primed reverse transcription

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

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)