SAXSdb — 8g1u

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8g1u
沉积日期 deposition_date	2023-02-03
结构标题 title	Structure of the methylosome-Lsm10/11 complex
关键词 keywords	Methylation, GENE REGULATION, TRANSFERASE; TRANSFERASE
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	50.58 Å
回转半径 Rg (电子) rg_electron	50.19 Å
零角强度 I(0) i0	2434680000.00
分子量 molecular_weight	411930.0 kDa
排除体积 excluded_volume	514540 Å³
包络体积 envelope_volume	658100 Å³
水化壳体积 shell_volume	106280 Å³
包络直径 envelope_diameter	158.8 Å
壳层 Rg shell_rg	56.00 Å
包络 Rg envelope_rg	49.44 Å
形状 Rg shape_rg	50.19 Å
总 Rg total_rg	50.40 Å
总原子数 total_atoms	29100
残基数 n_residues	3651
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	163.2 Å
Rg (实空间) rg_real	50.38 Å
Rg 误差 (实空间) rg_real_error	1.36 Å
I(0) (实空间) i0_real	2.4350e+09
I(0) 误差 (实空间) i0_real_error	5.0890e+07
Rg (倒空间) rg_reciprocal	50.73 Å
I(0) (倒空间) i0_reciprocal	2436000000.0000
解质量估计 total_estimate	0.8937
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	63.2 Å
偏度 Skewness skewness	0.110
峰度 Kurtosis kurtosis	-0.575
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	168900000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.925

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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 (5)

Entity 1 polymer

描述 description	Protein arginine N-methyltransferase 5
分子量 formula_weight	72766.7 kDa
EC 编号 ec_number	2.1.1.320
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,E,I,M
原子数 atom_count	29100

MAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL

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

Entity 2 polymer

描述 description	Methylosome protein 50
分子量 formula_weight	36757.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,F,J,N

MRKETPPPLVPPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVPTEPLPAPGPASVTE

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

Entity 3 polymer

描述 description	Methylosome subunit pICln
分子量 formula_weight	26039.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,G,K,O

MSFLKSFPPPGSADGLRLQQPDTEAVLNGKGLGTGTLYIAESRLSWLDGSGLGFSLEYPTISLHAVSRDPNAYPQEHLYVMVNAKLGEESKEPPSDEDEEDNDDIEPISEFRFVPSDKSALEAMFTAMCECQALHPDPEDEDSDDYDGEEYDVEAHEQGQGDIPTFYTYEEGLSHLTAEGQATLERLEGMLSQSVSSQYNMAGVRTEDSVRNYEDGMEVETTPTVAGQFEDADVDH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

描述 description	U7 snRNA-associated Sm-like protein LSm11
分子量 formula_weight	39572.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,H,L,P

MEERERGARSAGAGSPARPPSPRLDVSSDSFDPLLALYAPRLPPIPYPNAPCFNNVAEYESFLRTGVRGGGRGRGRARGAAAGSGVPAAPGPSGRTRRRPDAPAPDPERIQRLRRLMVAKEEGDGAAGAGRRGPGRSRKAPRNVLTRMPLHEGSPLGELHRCIREGVKVNVHIRTFKGLRGVCTGFLVAFDKFWNMALTDVDETYRKPVLGKAYERDSSLTLTRLFDRLKLQDSSKKEADSKSAVEDSTLSRYSQTSTWKLASVWGRADTGRGSHKRSRSVPSSLQASAREESRSELSGRTTRTDGSSVGGTFSRATTLSRGQSRKKKRKPKVDYQQVFTRHINQIFIRGENVLLVHLAQ

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

Entity 5 non-polymer

描述 description	ADENOSINE
分子量 formula_weight	267.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

结构域编号 domain_id	8g1uA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

结构域编号 domain_id	8g1uA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	8g1uA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	160 — Hnrnp arginine n-methyltransferase1
同源超家族 H-superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

结构域编号 domain_id	8g1uE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

结构域编号 domain_id	8g1uE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	8g1uE03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	160 — Hnrnp arginine n-methyltransferase1
同源超家族 H-superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

结构域编号 domain_id	8g1uI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

结构域编号 domain_id	8g1uI02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	160 — Hnrnp arginine n-methyltransferase1
同源超家族 H-superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

结构域编号 domain_id	8g1uI03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	8g1uM01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	150 — Divalent-metal-dependent TIM barrel enzymes

结构域编号 domain_id	8g1uM02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

结构域编号 domain_id	8g1uM03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	160 — Hnrnp arginine n-methyltransferase1
同源超家族 H-superfamily homologous superfamily	11 — Hnrnp arginine n-methyltransferase1

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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	2.83 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	754047

fit	/app/data/saxs_computation/g1/8g1u/8g1u.fit
pddf	/app/data/pr_computation/g1/8g1u/8g1u.pr.out
profile	/app/data/saxs_computation/g1/8g1u/8g1u.dat

Structure of the methylosome-Lsm10/11 complex

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 (5)

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 non-polymer

6. 折叠分类 (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)