2hyi

Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA

Method: X-RAY DIFFRACTION D_max: 132.6 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	2hyi
沉积日期 deposition_date	2006-08-06
结构标题 title	Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA
关键词 keywords	;exon junction, splicing, mRNA processing, translation, DEAD-box ATPase, nonsense mediated decay, hydrolase-RNA binding protein-RNA COMPLEX ;; hydrolase/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	40.45 Å
回转半径 Rg (电子) rg_electron	40.13 Å
零角强度 I(0) i0	403939000.00
分子量 molecular_weight	161890.0 kDa
排除体积 excluded_volume	201490 Å³
包络体积 envelope_volume	260140 Å³
水化壳体积 shell_volume	53548 Å³
包络直径 envelope_diameter	139.6 Å
壳层 Rg shell_rg	46.04 Å
包络 Rg envelope_rg	39.53 Å
形状 Rg shape_rg	40.18 Å
总 Rg total_rg	40.27 Å
总原子数 total_atoms	11373
残基数 n_residues	1373
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	132.6 Å
Rg (实空间) rg_real	40.49 Å
Rg 误差 (实空间) rg_real_error	1.16 Å
I(0) (实空间) i0_real	4.0390e+08
I(0) 误差 (实空间) i0_real_error	6.3250e+06
Rg (倒空间) rg_reciprocal	40.45 Å
I(0) (倒空间) i0_reciprocal	403900000.0000
解质量估计 total_estimate	0.6749
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	40.8 Å
偏度 Skewness skewness	0.302
峰度 Kurtosis kurtosis	-0.564
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	77120000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 0.107; Positv: 1.000; Valcen: 0.941; Smooth: 0.794

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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 (8)

Entity 1 polymer

描述 description	5'-R(UPUPUPUPUPU)-3'
分子量 formula_weight	1792.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	F,L
原子数 atom_count	12033

UUUUUU

Entity 2 polymer

描述 description	Protein mago nashi homolog
分子量 formula_weight	17189.6 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,G

MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI

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	Escherichia coli

Entity 3 polymer

描述 description	RNA-binding protein 8A
分子量 formula_weight	10370.5 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	B,H

PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP

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	Escherichia coli

Entity 4 polymer

描述 description	Probable ATP-dependent RNA helicase DDX48
分子量 formula_weight	47173.2 kDa
EC 编号 ec_number	3.6.1.-
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	C,I

MATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE

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	Escherichia coli

Entity 5 polymer

描述 description	Protein CASC3
分子量 formula_weight	9435.4 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	D,J

LDDDEDRKNPAYIPRKGLFFEHDLRGQTQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRS

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	Escherichia coli

Entity 6 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	2

Entity 7 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
分子量 formula_weight	506.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 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	660

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d2hyia_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.232 — Mago nashi protein
超家族 Superfamily superfamily	d.232.1 — Mago nashi protein
家族 Family family	d.232.1.1 — Mago nashi protein

结构域编号 domain_id	d2hyib_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
家族 Family family	d.58.7.1 — Canonical RBD

结构域编号 domain_id	d2hyic1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.19 — Tandem AAA-ATPase domain

结构域编号 domain_id	d2hyic2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.19 — Tandem AAA-ATPase domain

结构域编号 domain_id	d2hyic3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2hyig_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.232 — Mago nashi protein
超家族 Superfamily superfamily	d.232.1 — Mago nashi protein
家族 Family family	d.232.1.1 — Mago nashi protein

结构域编号 domain_id	d2hyih_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
家族 Family family	d.58.7.1 — Canonical RBD

结构域编号 domain_id	d2hyii1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.19 — Tandem AAA-ATPase domain

结构域编号 domain_id	d2hyii2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.19 — Tandem AAA-ATPase domain

结构域编号 domain_id	d2hyii3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

结构域编号 domain_id	2hyiA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1560 — Mago nashi protein
同源超家族 H-superfamily homologous superfamily	10 — Mago nashi

结构域编号 domain_id	2hyiB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

结构域编号 domain_id	2hyiC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	2hyiC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	2hyiG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1560 — Mago nashi protein
同源超家族 H-superfamily homologous superfamily	10 — Mago nashi

结构域编号 domain_id	2hyiH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

结构域编号 domain_id	2hyiI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	2hyiI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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7. 引用文献 (1)

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晶胞边长 a length_a	185.830 Å
晶胞边长 b length_b	88.260 Å
晶胞边长 c length_c	145.770 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.77 °
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	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2130
R_work r_work	0.2120
R_free r_free	0.2310

fit	/app/data/saxs_computation/hy/2hyi/2hyi.fit
pddf	/app/data/pr_computation/hy/2hyi/2hyi.pr.out
profile	/app/data/saxs_computation/hy/2hyi/2hyi.dat

Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNA

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 (8)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)