8w25

Cryo-EM structure of human tankyrase 2 SAM-PARP filament bound to compound, TDI-2804 (focused refinement map).

Method: ELECTRON MICROSCOPY D_max: 100.5 Å Quality: GOOD

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	8w25
沉积日期 deposition_date	2024-02-20
最后修订 last_revision	2025-07-09
结构标题 title	Cryo-EM structure of human tankyrase 2 SAM-PARP filament bound to compound, TDI-2804 (focused refinement map).
关键词 keywords	NAD+ ADP-ribosyltransferase, WNT signaling, inhibitor, SIGNALING PROTEIN, SIGNALING PROTEIN-INHIBITOR complex; SIGNALING PROTEIN/INHIBITOR
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	30.91 Å
回转半径 Rg (电子) rg_electron	30.48 Å
零角强度 I(0) i0	131279000.00
分子量 molecular_weight	60265.0 kDa
排除体积 excluded_volume	57980 Å³
包络体积 envelope_volume	111570 Å³
水化壳体积 shell_volume	31734 Å³
包络直径 envelope_diameter	97.4 Å
壳层 Rg shell_rg	36.18 Å
包络 Rg envelope_rg	30.25 Å
形状 Rg shape_rg	30.46 Å
总 Rg total_rg	30.92 Å
总原子数 total_atoms	4560
残基数 n_residues	568
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	100.5 Å
Rg (实空间) rg_real	30.93 Å
Rg 误差 (实空间) rg_real_error	0.91 Å
I(0) (实空间) i0_real	1.3130e+08
I(0) 误差 (实空间) i0_real_error	2.1250e+06
Rg (倒空间) rg_reciprocal	30.92 Å
I(0) (倒空间) i0_reciprocal	131300000.0000
解质量估计 total_estimate	0.8921
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	29.6 Å
偏度 Skewness skewness	0.239
峰度 Kurtosis kurtosis	-0.674
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11500000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.940

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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 (4)

Entity 1 polymer

描述 description	Maltose/maltodextrin-binding periplasmic protein,Poly [ADP-ribose] polymerase tankyrase-2
分子量 formula_weight	80614.0 kDa
EC 编号 ec_number	2.4.2.30,2.4.2.-
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,Q
原子数 atom_count	4600

MSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKTGSMGIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTELELEVLFQGPELSSVVSSSGTEGASSLEKKEVPGVDFSITQFVRNLGLEHLMDIFEREQITLDVLVEMGHKELKEIGINAYGHRHKLIKGVERLISGQQGLNPYLTLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEGMVDG

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	Spodoptera frugiperda

Entity 2 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	2

Entity 3 non-polymer

描述 description	N-{2-[4-(2-hydroxypropan-2-yl)phenyl]-4-oxo-1,4-dihydroquinazolin-7-yl}-4-methoxy-6-phenylpyridine-3-carboxamide
分子量 formula_weight	506.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	40

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7. 引用文献 (1)

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分辨率 resolution	2.42 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	1310954

fit	/app/data/saxs_computation/w2/8w25/8w25.fit
pddf	/app/data/pr_computation/w2/8w25/8w25.pr.out
profile	/app/data/saxs_computation/w2/8w25/8w25.dat