2f66
Structure of the ESCRT-I endosomal trafficking 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
| 条目编号 entry_id | 2f66 |
| 沉积日期 deposition_date | 2005-11-28 |
| 结构标题 title | Structure of the ESCRT-I endosomal trafficking complex |
| 关键词 keywords | ;Endosome, Trafficking complex, Vps23, Vps28, Vps37, Vacuolar Protein Sorting, ESCRT protein complexes, Endosomal Sorting Complex Required for Transport, ESCRT-I, ubiquitin, Tsg101, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 25.38 Å |
| 回转半径 Rg (电子) rg_electron | 24.33 Å |
| 零角强度 I(0) i0 | 52592800.00 |
| 分子量 molecular_weight | 56067.0 kDa |
| 排除体积 excluded_volume | 70116 ų |
| 包络体积 envelope_volume | 86862 ų |
| 水化壳体积 shell_volume | 29443 ų |
| 包络直径 envelope_diameter | 93.0 Å |
| 壳层 Rg shell_rg | 31.88 Å |
| 包络 Rg envelope_rg | 24.69 Å |
| 形状 Rg shape_rg | 24.29 Å |
| 总 Rg total_rg | 25.29 Å |
| 总原子数 total_atoms | 3953 |
| 残基数 n_residues | 480 |
| 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/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 87.0 Å |
| Rg (实空间) rg_real | 25.27 Å |
| Rg 误差 (实空间) rg_real_error | 0.56 Å |
| I(0) (实空间) i0_real | 5.2590e+07 |
| I(0) 误差 (实空间) i0_real_error | 7.4190e+05 |
| Rg (倒空间) rg_reciprocal | 25.31 Å |
| I(0) (倒空间) i0_reciprocal | 52590000.0000 |
| 解质量估计 total_estimate | 0.8769 |
| 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 | 31.8 Å |
| 偏度 Skewness skewness | 0.190 |
| 峰度 Kurtosis kurtosis | -0.425 |
| 角度范围 angular_range | — – 0.3150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9079000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.999 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d2f66a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.17 — Endosomal sorting complex assembly domain |
| 家族 Family family | a.2.17.1 — VPS23 C-terminal domain |
| 结构域编号 domain_id | d2f66a2 |
| 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 | d2f66b1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.17 — Endosomal sorting complex assembly domain |
| 家族 Family family | a.2.17.2 — VPS28 N-terminal domain |
| 结构域编号 domain_id | d2f66c1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.17 — Endosomal sorting complex assembly domain |
| 家族 Family family | a.2.17.3 — VPS37 C-terminal domain-like |
| 结构域编号 domain_id | d2f66d2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.17 — Endosomal sorting complex assembly domain |
| 家族 Family family | a.2.17.1 — VPS23 C-terminal domain |
| 结构域编号 domain_id | d2f66d3 |
| 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 | d2f66e_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.17 — Endosomal sorting complex assembly domain |
| 家族 Family family | a.2.17.2 — VPS28 N-terminal domain |
| 结构域编号 domain_id | d2f66f_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.17 — Endosomal sorting complex assembly domain |
| 家族 Family family | a.2.17.3 — VPS37 C-terminal domain-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2f66A00 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 140 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 820 — |
| 结构域编号 domain_id | 2f66B00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1440 — de novo design (two linked rop proteins) |
| 同源超家族 H-superfamily homologous superfamily | 200 — Vps28 N-terminal domain |
| 结构域编号 domain_id | 2f66C00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 660 — Helix hairpin bin |
| 结构域编号 domain_id | 2f66D00 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 140 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 820 — |
| 结构域编号 domain_id | 2f66E00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1440 — de novo design (two linked rop proteins) |
| 同源超家族 H-superfamily homologous superfamily | 200 — Vps28 N-terminal domain |
| 结构域编号 domain_id | 2f66F00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 660 — Helix hairpin bin |