1un6

THE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO MODES OF MOLECULAR RECOGNITION

Method: X-RAY DIFFRACTION D_max: 108.0 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	1un6
沉积日期 deposition_date	2003-09-04
结构标题 title	THE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO MODES OF MOLECULAR RECOGNITION
关键词 keywords	;RNA-BINDING PROTEIN/RNA, COMPLEX(ZINC FINGER-RNA), TFIIIA, 5S RIBOSOMAL RNA, ZINC FINGER, RNA-PROTEIN COMPLEX, X. LAEVIS, TRANSCRIPTION REGULATION, RNA-BINDING, DNA-BINDING, NUCLEAR PROTEIN, RNA-BINDING PROTEIN-RNA complex ;; RNA-BINDING PROTEIN/RNA
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	33.48 Å
回转半径 Rg (电子) rg_electron	33.22 Å
零角强度 I(0) i0	152567000.00
分子量 molecular_weight	67567.0 kDa
排除体积 excluded_volume	70984 Å³
包络体积 envelope_volume	112280 Å³
水化壳体积 shell_volume	29749 Å³
包络直径 envelope_diameter	115.0 Å
壳层 Rg shell_rg	37.79 Å
包络 Rg envelope_rg	32.41 Å
形状 Rg shape_rg	33.18 Å
总 Rg total_rg	33.55 Å
总原子数 total_atoms	4538
残基数 n_residues	354
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	108.0 Å
Rg (实空间) rg_real	33.54 Å
Rg 误差 (实空间) rg_real_error	0.89 Å
I(0) (实空间) i0_real	1.5260e+08
I(0) 误差 (实空间) i0_real_error	2.4230e+06
Rg (倒空间) rg_reciprocal	33.51 Å
I(0) (倒空间) i0_reciprocal	152600000.0000
解质量估计 total_estimate	0.6764
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	36.8 Å
偏度 Skewness skewness	0.303
峰度 Kurtosis kurtosis	-0.475
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3942000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.936; Smooth: 0.735

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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	TRANSCRIPTION FACTOR IIIA
分子量 formula_weight	10299.8 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,C,D
原子数 atom_count	4554

MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD

来源 Source

来源生物 organism	XENOPUS LAEVIS
通用名 common_name	AFRICAN CLAWED FROG
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	5S RIBOSOMAL RNA
分子量 formula_weight	19708.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	E,F

GCCGGCCACACCUACGGGGCCUGGUUAGUACCUGGGAAACCUGGGAAUACCAGGUGCCGGC

Entity 3 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	8

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	13

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	16

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1un6b1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1un6b2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1un6b3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1un6c1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1un6c2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1un6c3
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1un6d1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

结构域编号 domain_id	d1un6d2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.37 — beta-beta-alpha zinc fingers
超家族 Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
家族 Family family	g.37.1.1 — Classic zinc finger, C2H2

CATH v4.4 (8 domains)

结构域编号 domain_id	1un6B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1un6B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1un6B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1un6C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1un6C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1un6C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1un6D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

结构域编号 domain_id	1un6D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	60 — Classic Zinc Finger

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7. 引用文献 (2)

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晶胞边长 a length_a	58.598 Å
晶胞边长 b length_b	191.593 Å
晶胞边长 c length_c	79.770 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.51 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	35.190 Å
R 因子 r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2590

fit	/app/data/saxs_computation/un/1un6/1un6.fit
pddf	/app/data/pr_computation/un/1un6/1un6.pr.out
profile	/app/data/saxs_computation/un/1un6/1un6.dat

THE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO MODES OF MOLECULAR RECOGNITION

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

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

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)