SAXSdb — 8rkh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8rkh
沉积日期 deposition_date	2023-12-25
结构标题 title	Crystal structure of the ZP-N2 and ZP-N3 domains of mouse ZP2 (mZP2-N2N3)
关键词 keywords	;Cell adhesion, fertilization, egg-sperm interaction, gamete recognition, sperm receptor, extracellular matrix, egg coat, zona pellucida, glycoprotein, N-glycan, structural protein, ZP-N domain, block to polyspermy, post-fertilization cleavage, ovastacin ;; CELL ADHESION
实验方法 method	X-RAY DIFFRACTION

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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	32.61 Å
回转半径 Rg (电子) rg_electron	32.52 Å
零角强度 I(0) i0	41860800.00
分子量 molecular_weight	51678.0 kDa
排除体积 excluded_volume	65070 Å³
包络体积 envelope_volume	90149 Å³
水化壳体积 shell_volume	26098 Å³
包络直径 envelope_diameter	134.8 Å
壳层 Rg shell_rg	34.49 Å
包络 Rg envelope_rg	33.49 Å
形状 Rg shape_rg	32.52 Å
总 Rg total_rg	32.71 Å
总原子数 total_atoms	7202
残基数 n_residues	438
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	126.8 Å
Rg (实空间) rg_real	33.28 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	4.1860e+07
I(0) 误差 (实空间) i0_real_error	6.7760e+05
Rg (倒空间) rg_reciprocal	33.00 Å
I(0) (倒空间) i0_reciprocal	41850000.0000
解质量估计 total_estimate	0.7330
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.9 Å
偏度 Skewness skewness	0.710
峰度 Kurtosis kurtosis	0.047
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7881000.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.435; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.269; Smooth: 0.951

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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	Zona pellucida sperm-binding protein 2
分子量 formula_weight	26692.3 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
原子数 atom_count	7389

ETGPAIQAETHEISEIVVCRRDLISFSFPQLFSRLADENQNVSEMGWIVKIGNGTRAHILPLKDAIVQGFNLLIDSQKVTLHVPANATGIVHYVQESSYLYTVQLELLFSTTGQKIVFSSHAICAPDLSVACNATHMTLTIPEFPGKLESVDFGQWSIPEDQWHANGIDKEATNGLRLNFRKSLLKTKPSEKCPFYQFYLSSLKLTFYFQGNMLSTVIDPECHCESPVSLEHHHHHH

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	Homo sapiens

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 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	5

Entity 5 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	187

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7. 引用文献 (12)

ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat.

Cell (2024)

PMID: 38490181 · DOI: 10.1016/j.cell.2024.02.013 PRIMARY

Structure of Zona Pellucida Module Proteins.

Curr Top Dev Biol (2018)

PMID: 29853186 · DOI: 10.1016/bs.ctdb.2018.02.007

Structural Basis of Egg Coat-Sperm Recognition at Fertilization.

Cell (2017)

PMID: 28622512 · DOI: 10.1016/j.cell.2017.05.033

;Gamete recognition in mice depends on the cleavage status of an egg's zona pellucida protein. ;

Science (2010)

PMID: 20616279 · DOI: 10.1126/science.1188178

Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats.

Nature (2008)

PMID: 19052627 · DOI: 10.1038/nature07599

Structural characterization of native mouse zona pellucida proteins using mass spectrometry.

J Biol Chem (2003)

PMID: 12799386 · DOI: 10.1074/jbc.M304026200

Fertility and taxon-specific sperm binding persist after replacement of mouse sperm receptors with human homologs.

Dev Cell (2003)

PMID: 12852850 · DOI: 10.1016/s1534-5807(03)00195-3

Defective zonae pellucidae in Zp2-null mice disrupt folliculogenesis, fertility and development.

Development (2001)

PMID: 11245577 · DOI: 10.1242/dev.128.7.1119

Oocyte-specific expression of mouse Zp-2: developmental regulation of the zona pellucida genes.

Mol Cell Biol (1990)

PMID: 1690843 · DOI: 10.1128/mcb.10.4.1507-1515.1990

Biosynthesis of the major zona pellucida glycoprotein secreted by oocytes during mammalian oogenesis.

Cell (1982)

PMID: 6819087 · DOI: 10.1016/0092-8674(82)90329-4

Mammalian sperm-egg interaction: fertilization of mouse eggs triggers modification of the major zona pellucida glycoprotein, ZP2.

Dev Biol (1981)

PMID: 6793422 · DOI: 10.1016/0012-1606(81)90329-8

Synthesis of zona pellucida proteins by denuded and follicle-enclosed mouse oocytes during culture in vitro.

Proc Natl Acad Sci U S A (1980)

PMID: 6928658 · DOI: 10.1073/pnas.77.2.1029

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晶胞边长 a length_a	163.010 Å
晶胞边长 b length_b	54.170 Å
晶胞边长 c length_c	68.660 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.98 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	43.730 Å
R 因子 r_factor	0.2157
R_work r_work	0.2141
R_free r_free	0.2479

fit	/app/data/saxs_computation/rk/8rkh/8rkh.fit
pddf	/app/data/pr_computation/rk/8rkh/8rkh.pr.out
profile	/app/data/saxs_computation/rk/8rkh/8rkh.dat

Crystal structure of the ZP-N2 and ZP-N3 domains of mouse ZP2 (mZP2-N2N3)

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

精修参数 Refinement

衍射实验 Diffraction