SAXSdb — 9h4r

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9h4r
沉积日期 deposition_date	2024-10-21
结构标题 title	Structure of fertilization-blocking monoclonal antibody IE-3 VHVL bound to the ZP-N1 domain of mouse ZP2 (crystal form I)
关键词 keywords	;Zona pellucida, ZP2, ZP-N domain, ZP-N1 domain, ZP module, ZP domain, egg-sperm recognition, gamete interaction, immunocontraception, monoclonal antibody, IE-3, IE3, heavy chain variable domain, light chain variable domain, cell adhesion ;; 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	28.72 Å
回转半径 Rg (电子) rg_electron	28.21 Å
零角强度 I(0) i0	89818100.00
分子量 molecular_weight	73235.0 kDa
排除体积 excluded_volume	90951 Å³
包络体积 envelope_volume	113290 Å³
水化壳体积 shell_volume	33432 Å³
包络直径 envelope_diameter	104.6 Å
壳层 Rg shell_rg	35.37 Å
包络 Rg envelope_rg	28.16 Å
形状 Rg shape_rg	28.15 Å
总 Rg total_rg	29.08 Å
总原子数 total_atoms	5152
残基数 n_residues	663
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	96.9 Å
Rg (实空间) rg_real	28.64 Å
Rg 误差 (实空间) rg_real_error	0.80 Å
I(0) (实空间) i0_real	8.9820e+07
I(0) 误差 (实空间) i0_real_error	1.4250e+06
Rg (倒空间) rg_reciprocal	28.67 Å
I(0) (倒空间) i0_reciprocal	89820000.0000
解质量估计 total_estimate	0.8897
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	95.1 Å
偏度 Skewness skewness	0.195
峰度 Kurtosis kurtosis	-0.512
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18420000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.998

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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	Zona pellucida sperm-binding protein 2
分子量 formula_weight	12994.6 kDa
突变 mutation	N83S
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	5768

VSLPQSENPAFPGTLICDKDEVRIEFSSRFDMEKWNPSVVDTLGSEILSCTYALDLERFVLKFPYETCTIKVVGGYQVNIRVGDTTTDVRYKDDMYHFFCPAIQLEHHHHHH

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 polymer

描述 description	Heavy chain variable (VH) domain of anti-ZP2 monoclonal antibody IE-3
分子量 formula_weight	13290.5 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	H,X

ETGQVQLQQSGAELVKPGSSVKISCKASGYTFTSDDMHWIKQQPGNGLEWIGWIYPGNDDTKYNQKFNGKATLTADKSSSTVYMQLSSLTSEDSAVYFCARGDLNYGGSMDAWGQGTSVTVSS

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	Light chain variable (VL) domain of anti-ZP2 monoclonal antibody IE-3
分子量 formula_weight	12847.2 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	L,Y

ETGDTVMTQSPSSLAVSAGETLTINCKSSQNLFSSRNQKNYLAWFQQKPGQSPTLLIHWASTRQSGVPDRFIGSGSGTDFTLTISSVQAEDLAIYYCQQYYNSPLTFGSGTKLEIKR

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

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	616

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7. 引用文献 (13)

Structural basis of ZP2-targeted female nonhormonal contraception.

Proc.Natl.Acad.Sci.USA (2025)

PMID: 40215272 · DOI: 10.1073/pnas.2426057122 PRIMARY

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

Cell (2024)

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

Structural Basis of Egg Coat-Sperm Recognition at Fertilization.

Cell (2017)

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

Vectored antibody gene delivery mediates long-term contraception.

Curr Biol (2015)

PMID: 26439332 · DOI: 10.1016/j.cub.2015.08.002

A single domain of the ZP2 zona pellucida protein mediates gamete recognition in mice and humans.

J Cell Biol (2014)

PMID: 24934154 · DOI: 10.1128/MCB.22.9.3111-3120.2002

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

A contraceptive peptide vaccine targeting sulfated glycoprotein ZP2 of the mouse zona pellucida.

Biol Reprod (1999)

PMID: 10084964 · DOI: 10.1095/biolreprod60.4.900

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

;Monoclonal antibodies to the murine zona pellucida protein with sperm receptor activity: effects on fertilization and early development. ;

Dev Biol (1985)

PMID: 3996750 · DOI: 10.1016/0012-1606(85)90454-3

Monoclonal antibodies to the major protein of the murine zona pellucida: effects on fertilization and early development.

Dev Biol (1984)

PMID: 6376213 · DOI: 10.1016/0012-1606(84)90035-6

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	91.640 Å
晶胞边长 b length_b	92.290 Å
晶胞边长 c length_c	91.170 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.530 Å
最低分辨率 resolution_low	29.160 Å
R 因子 r_factor	0.2095
R_work r_work	0.2058
R_free r_free	0.2329

fit	/app/data/saxs_computation/h4/9h4r/9h4r.fit
pddf	/app/data/pr_computation/h4/9h4r/9h4r.pr.out
profile	/app/data/saxs_computation/h4/9h4r/9h4r.dat

Structure of fertilization-blocking monoclonal antibody IE-3 VHVL bound to the ZP-N1 domain of mouse ZP2 (crystal form I)

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

5. 实体与聚合体信息 (4)

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 water

7. 引用文献 (13)

8. 文件与曲线 (10)

Files (7)

Curves (3)