2c35

Subunits Rpb4 and Rpb7 of human RNA polymerase II

Method: X-RAY DIFFRACTION D_max: 151.0 Å Quality: GOOD

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	2c35
沉积日期 deposition_date	2005-10-04
结构标题 title	Subunits Rpb4 and Rpb7 of human RNA polymerase II
关键词 keywords	TRANSCRIPTION, RNA POLYMERASE II, POLYMERASE, NUCLEOTIDYLTRANSFERASE, TRANSFERASE; TRANSFERASE
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	45.12 Å
回转半径 Rg (电子) rg_electron	45.67 Å
零角强度 I(0) i0	242960000.00
分子量 molecular_weight	131120.0 kDa
排除体积 excluded_volume	165470 Å³
包络体积 envelope_volume	234490 Å³
水化壳体积 shell_volume	46404 Å³
包络直径 envelope_diameter	161.5 Å
壳层 Rg shell_rg	44.84 Å
包络 Rg envelope_rg	45.56 Å
形状 Rg shape_rg	45.68 Å
总 Rg total_rg	45.59 Å
总原子数 total_atoms	9236
残基数 n_residues	1194
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	151.0 Å
Rg (实空间) rg_real	45.57 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	2.4300e+08
I(0) 误差 (实空间) i0_real_error	4.9030e+06
Rg (倒空间) rg_reciprocal	45.13 Å
I(0) (倒空间) i0_reciprocal	242800000.0000
解质量估计 total_estimate	0.8276
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	38.8 Å
偏度 Skewness skewness	0.486
峰度 Kurtosis kurtosis	-0.448
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	25320000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.720; Smooth: 0.618

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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 (3)

Entity 1 polymer

描述 description	DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
分子量 formula_weight	17319.3 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G
原子数 atom_count	9290

GSRRASVGSQMAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY

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 2 polymer

描述 description	DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE
分子量 formula_weight	19314.3 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F,H

MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS

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 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	54

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2c35a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.8 — HRDC-like
家族 Family family	a.60.8.2 — RNA polymerase II subunit RBP4 (RpoF)

结构域编号 domain_id	d2c35b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.5 — Cold shock DNA-binding domain-like

结构域编号 domain_id	d2c35b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
家族 Family family	d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)

结构域编号 domain_id	d2c35c_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.8 — HRDC-like
家族 Family family	a.60.8.2 — RNA polymerase II subunit RBP4 (RpoF)

结构域编号 domain_id	d2c35d1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.5 — Cold shock DNA-binding domain-like

结构域编号 domain_id	d2c35d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
家族 Family family	d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)

结构域编号 domain_id	d2c35e_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.8 — HRDC-like
家族 Family family	a.60.8.2 — RNA polymerase II subunit RBP4 (RpoF)

结构域编号 domain_id	d2c35f1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.5 — Cold shock DNA-binding domain-like

结构域编号 domain_id	d2c35f2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
家族 Family family	d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)

结构域编号 domain_id	d2c35g_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.60 — SAM domain-like
超家族 Superfamily superfamily	a.60.8 — HRDC-like
家族 Family family	a.60.8.2 — RNA polymerase II subunit RBP4 (RpoF)

结构域编号 domain_id	d2c35h1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.40 — OB-fold
超家族 Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
家族 Family family	b.40.4.5 — Cold shock DNA-binding domain-like

结构域编号 domain_id	d2c35h2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.230 — Dodecin subunit-like
超家族 Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
家族 Family family	d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)

CATH v4.4 (12 domains)

结构域编号 domain_id	2c35A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	40 — RNA Polymerase II, Rpb4 subunit

结构域编号 domain_id	2c35B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

结构域编号 domain_id	2c35B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	2c35C00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	40 — RNA Polymerase II, Rpb4 subunit

结构域编号 domain_id	2c35D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

结构域编号 domain_id	2c35D02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	2c35E00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	40 — RNA Polymerase II, Rpb4 subunit

结构域编号 domain_id	2c35F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

结构域编号 domain_id	2c35F02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

结构域编号 domain_id	2c35G00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily	40 — RNA Polymerase II, Rpb4 subunit

结构域编号 domain_id	2c35H01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

结构域编号 domain_id	2c35H02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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7. 引用文献 (1)

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晶胞边长 a length_a	45.690 Å
晶胞边长 b length_b	83.190 Å
晶胞边长 c length_c	99.310 Å
晶胞夹角 α angle_alpha	85.53 °
晶胞夹角 β angle_beta	81.80 °
晶胞夹角 γ angle_gamma	81.77 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	43.260 Å
R 因子 r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2660

fit	/app/data/saxs_computation/c3/2c35/2c35.fit
pddf	/app/data/pr_computation/c3/2c35/2c35.pr.out
profile	/app/data/saxs_computation/c3/2c35/2c35.dat

Subunits Rpb4 and Rpb7 of human RNA polymerase II

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)