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1y1w

Complete RNA Polymerase II elongation complex

Method: X-RAY DIFFRACTION Dmax: 165.7 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1y1w

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1y1w
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1y1w
沉积日期 deposition_date2004-11-19
结构标题 titleComplete RNA Polymerase II elongation complex
关键词 keywordsRNA Polymerase II, transcription bubble, transcription, elongation complex, TRANSFERASE-DNA-RNA HYBRID COMPLEX; TRANSCRIPTION,TRANSFERASE/DNA-RNA HYBRID
实验方法 methodX-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_guinier50.62 Å
回转半径 Rg (电子) rg_electron50.45 Å
零角强度 I(0) i03047900000.00
分子量 molecular_weight453930.0 kDa
排除体积 excluded_volume564920 ų
包络体积 envelope_volume795890 ų
水化壳体积 shell_volume124100 ų
包络直径 envelope_diameter169.5 Å
壳层 Rg shell_rg59.11 Å
包络 Rg envelope_rg50.31 Å
形状 Rg shape_rg50.46 Å
总 Rg total_rg50.64 Å
总原子数 total_atoms31802
残基数 n_residues3953
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 Å−1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3
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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax165.7 Å
Rg (实空间) rg_real50.45 Å
Rg 误差 (实空间) rg_real_error1.51 Å
I(0) (实空间) i0_real3.0480e+09
I(0) 误差 (实空间) i0_real_error6.3060e+07
Rg (倒空间) rg_reciprocal50.75 Å
I(0) (倒空间) i0_reciprocal3049000000.0000
解质量估计 total_estimate0.8761
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary64.2 Å
偏度 Skewness skewness0.222
峰度 Kurtosis kurtosis-0.375
角度范围 angular_range— – 0.1550 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha647200000.0000
实空间数据点数 n_real_points32
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.863
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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 (17)

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

结构域编号 domain_idd1y1wa_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wb_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wc_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wd_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1we_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wf_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wg_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wh_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wi_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wj_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wk_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase
结构域编号 domain_idd1y1wl_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.8 — RNA polymerase
超家族 Superfamily superfamilyi.8.1 — RNA polymerase
家族 Family familyi.8.1.1 — RNA polymerase

CATH v4.4 (24 domains)

结构域编号 domain_id1y1wA03
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily20 —
结构域编号 domain_id1y1wA04
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily180 — RNA polymerase ii
结构域编号 domain_id1y1wA05
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily100 — RNA polymerase Rpb1, domain 3
结构域编号 domain_id1y1wA06
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology132 — Topoisomerase I; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily30 — RNA polymerase Rpb1 funnel domain
结构域编号 domain_id1y1wA09
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily140 —
结构域编号 domain_id1y1wB04
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
同源超家族 H-superfamily homologous superfamily10 — RNA polymerase Rpb2, domain 2
结构域编号 domain_id1y1wB05
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1070 — Hypothetical Protein Ta0175; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily20 —
结构域编号 domain_id1y1wB06
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
同源超家族 H-superfamily homologous superfamily10 — DNA-directed RNA polymerase, subunit 2, domain 6
结构域编号 domain_id1y1wB07
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily150 — RNA polymerase II, Rpb2 subunit, wall domain
结构域编号 domain_id1y1wB08
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology1800 — DCoH-like
同源超家族 H-superfamily homologous superfamily10 — RNA polymerase alpha subunit dimerisation domain
结构域编号 domain_id1y1wC01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
结构域编号 domain_id1y1wC02
类 Class class2 — Mainly Beta
架构 Architecture architecture170 — Beta Complex
拓扑 Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
结构域编号 domain_id1y1wD02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1250 — Growth Hormone; Chain: A;
同源超家族 H-superfamily homologous superfamily40 — RNA Polymerase II, Rpb4 subunit
结构域编号 domain_id1y1wE01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology1340 — Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
同源超家族 H-superfamily homologous superfamily10 — RNA polymerase, Rpb5, N-terminal domain
结构域编号 domain_id1y1wE02
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology940 — Eukaryotic RPB6 RNA polymerase subunit
同源超家族 H-superfamily homologous superfamily20 — RPB5-like RNA polymerase subunit
结构域编号 domain_id1y1wF00
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology940 — Eukaryotic RPB6 RNA polymerase subunit
同源超家族 H-superfamily homologous superfamily10 — RNA polymerase subunit, RPB6/omega
结构域编号 domain_id1y1wG01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1490 — Dna Ligase; domain 1
同源超家族 H-superfamily homologous superfamily120 — RNA polymerase Rpb7-like, N-terminal domain
结构域编号 domain_id1y1wG02
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily140 — Nucleic acid-binding proteins
结构域编号 domain_id1y1wH00
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily140 — Nucleic acid-binding proteins
结构域编号 domain_id1y1wI01
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id1y1wI02
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology25 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id1y1wJ00
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily60 — Homeodomain-like
结构域编号 domain_id1y1wK00
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
结构域编号 domain_id1y1wL00
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily30 — RNA polymerase ii, chain L
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7. 引用文献 (1)

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8. 文件与曲线 (10)