9mxj

Human Vault Cage in complex with ADP-ribose

Method: ELECTRON MICROSCOPY D_max: 386.8 Å Quality: REASONABLE

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	9mxj
沉积日期 deposition_date	2025-01-20
最后修订 last_revision	2025-08-06
结构标题 title	Human Vault Cage in complex with ADP-ribose
关键词 keywords	;Vault, Vault Cage, MVP, Major Vault Protein, SPFH, PARP4, Poly(ADP-ribose)Polymerase 4, MINT, NAD+, NAD, Poly(ADP-ribose)Polymerase, Ribonucleoprotein, Megadalton complex, TEP1, vault RNA, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT
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	— Å
回转半径 Rg (电子) rg_electron	171.60 Å
零角强度 I(0) i0	440654000.00
分子量 molecular_weight	177330.0 kDa
排除体积 excluded_volume	221690 Å³
包络体积 envelope_volume	1107800 Å³
水化壳体积 shell_volume	57653 Å³
包络直径 envelope_diameter	663.1 Å
壳层 Rg shell_rg	99.57 Å
包络 Rg envelope_rg	195.50 Å
形状 Rg shape_rg	171.30 Å
总 Rg total_rg	172.00 Å
总原子数 total_atoms	12506
残基数 n_residues	1568
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	386.8 Å
Rg (实空间) rg_real	142.10 Å
Rg 误差 (实空间) rg_real_error	2.72 Å
I(0) (实空间) i0_real	4.0600e+08
I(0) 误差 (实空间) i0_real_error	1.0770e+07
Rg (倒空间) rg_reciprocal	104.90 Å
I(0) (倒空间) i0_reciprocal	362800000.0000
解质量估计 total_estimate	0.6467
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	43.0 Å
偏度 Skewness skewness	0.211
峰度 Kurtosis kurtosis	-1.231
角度范围 angular_range	— – 0.0450 Å⁻¹
当前正则化参数 α current_alpha	0.1366
最高正则化参数 α highest_alpha	107300000.0000
实空间数据点数 n_real_points	10
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.415; Oscil: 0.043; Stabil: 0.921; Sysdev: 1.000; Positv: 1.000; Valcen: 0.760; Smooth: 0.642

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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 (2)

Entity 1 polymer

描述 description	Major vault protein
分子量 formula_weight	99452.8 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	12506

MATEEFIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPMRMVTVPPRHYCTVANPVSRDAQGLVLFDVTGQVRLRHADLEIRLAQDPFPLYPGEVLEKDITPLQVVLPNTALHLKALLDFEDKDGDKVVAGDEWLFEGPGTYIPRKEVEVVEIIQATIIRQNQALRLRARKECWDRDGKERVTGEEWLVTTVGAYLPAVFEEVLDLVDAVILTEKTALHLRARRNFRDFRGVSRRTGEEWLVTVQDTEAHVPDVHEEVLGVVPITTLGPHNYCVILDPVGPDGKNQLGQKRVVKGEKSFFLQPGEQLEQGIQDVYVLSEQQGLLLRALQPLEEGEDEEKVSHQAGDHWLIRGPLEYVPSAKVEVVEERQAIPLDENEGIYVQDVKTGKVRAVIGSTYMLTQDEVLWEKELPPGVEELLNKGQDPLADRGEKDTAKSLQPLAPRNKTRVVSYRVPHNAAVQVYDYREKRARVVFGPELVSLGPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVITIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASRVRGAVASVTFDDFHKNSARIIRTAVFGFETSEAKGPDGMALPRPRDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEALSMAVESTGTAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELQRVQKVRELELVYARAQLELEVSKAQQLAEVEVKKFKQMTEAIGPSTIRDLAVAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTAFGLLGMGPEGQPLGRRVASGPSPGEGISPQSAQAPQAPGDNHVVPVLR

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 non-polymer

描述 description	ADENOSINE-5-DIPHOSPHORIBOSE
分子量 formula_weight	559.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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7. 引用文献 (1)

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分辨率 resolution	3.49 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	155096

fit	/app/data/saxs_computation/mx/9mxj/9mxj.fit
pddf	/app/data/pr_computation/mx/9mxj/9mxj.pr.out
profile	/app/data/saxs_computation/mx/9mxj/9mxj.dat