1zc8

Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex

Method: ELECTRON MICROSCOPY D_max: 215.5 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	1zc8
沉积日期 deposition_date	2005-04-11
结构标题 title	Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex
关键词 keywords	SmpB, tmRNA, EF-Tu, h44, 30S, 16s rRNA, Cryo-EM, trans-translation, 70S, RNA binding protein-RNA COMPLEX; RNA binding protein/RNA
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	60.34 Å
回转半径 Rg (电子) rg_electron	50.29 Å
零角强度 I(0) i0	161773000.00
分子量 molecular_weight	72626.0 kDa
排除体积 excluded_volume	76103 Å³
包络体积 envelope_volume	269700 Å³
水化壳体积 shell_volume	38867 Å³
包络直径 envelope_diameter	231.1 Å
壳层 Rg shell_rg	54.21 Å
包络 Rg envelope_rg	64.62 Å
形状 Rg shape_rg	60.95 Å
总 Rg total_rg	49.70 Å
总原子数 total_atoms	416
残基数 n_residues	416
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	215.5 Å
Rg (实空间) rg_real	61.19 Å
Rg 误差 (实空间) rg_real_error	3.10 Å
I(0) (实空间) i0_real	1.6180e+08
I(0) 误差 (实空间) i0_real_error	3.3970e+06
Rg (倒空间) rg_reciprocal	59.57 Å
I(0) (倒空间) i0_reciprocal	161300000.0000
解质量估计 total_estimate	0.7360
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	33.2 Å
偏度 Skewness skewness	0.423
峰度 Kurtosis kurtosis	-0.612
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	7704000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.440; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.559; Smooth: 0.687

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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 (11)

Entity 1 polymer

描述 description	TLD 16S ribosomal RNA
分子量 formula_weight	18951.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	A
原子数 atom_count	951

GGGGCUGAUUCUGGAUUCGACGGGAUAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCC

Entity 2 polymer

描述 description	H2 16S rRNA
分子量 formula_weight	5162.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B

UUGCGAAACAUGUAGG

Entity 3 polymer

描述 description	H2b d mRNA
分子量 formula_weight	10013.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	C

CCCAAGGUGCAUGCGCAUGUAGUACCGAGGA

Entity 4 polymer

描述 description	protein kinase 4 mRNA
分子量 formula_weight	9738.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	G

CGAGGGGCGGUUGGCCUCGUAAAAAGCCGC

Entity 5 polymer

描述 description	H5 16S ribosomal RNA
分子量 formula_weight	9206.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	F

CUUUAGCAGCUUAAUAACCUGCUUAGAGC

Entity 6 polymer

描述 description	protein kinase 2 mRNA
分子量 formula_weight	18915.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	H

CCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAG

Entity 7 polymer

描述 description	protein kinase 3
分子量 formula_weight	15808.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	I

AUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGC

Entity 8 polymer

描述 description	protein kinase 4 mRNA
分子量 formula_weight	16782.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	J

GUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGAC

Entity 9 polymer

描述 description	H44 16S ribosomal RNA
分子量 formula_weight	29593.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	Z

GCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUC

Entity 10 polymer

描述 description	SsrA-binding protein
分子量 formula_weight	15087.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K

GKSDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKL

Entity 11 polymer

描述 description	Elongation factor Tu
分子量 formula_weight	44743.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	Y

AKGEFIRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEEMHKNPKTKRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGLLLRGVSREEVERGQVLAKPGSITPHTKFEASVYILKKEEGGRHTGFFTGYRPQFYFRTTDVTGVVRLPQGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1zc8k1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.111 — Small protein B (SmpB)
超家族 Superfamily superfamily	b.111.1 — Small protein B (SmpB)
家族 Family family	b.111.1.1 — Small protein B (SmpB)

结构域编号 domain_id	d1zc8y1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.1 — Elongation factors

结构域编号 domain_id	d1zc8y2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
超家族 Superfamily superfamily	b.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
家族 Family family	b.44.1.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain

结构域编号 domain_id	d1zc8y3
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.37.1.8 — G proteins

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7. 引用文献 (6)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	13.00 Å
分辨率测定方法 resolution_method	3D projection matching: conjugate gradients with regularization
颗粒数 num_particles	27644

fit	/app/data/saxs_computation/zc/1zc8/1zc8.fit
pddf	/app/data/pr_computation/zc/1zc8/1zc8.pr.out
profile	/app/data/saxs_computation/zc/1zc8/1zc8.dat

Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (11)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)