4ujd

mammalian 80S HCV-IRES initiation complex with eIF5B PRE-like state

Method: ELECTRON MICROSCOPY Dmax: 247.8 Å Quality: EXCELLENT

1. 蛋白身份与相关结构 Protein Identity & Related Structures

EIF5B

物种未注明

UniProt G1TRL5

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白–RNA 异源复合物 蛋白 × 77 RNA 6 PDB 声明:83-meric(83) 与全部聚合物数一致 链 BB; UniProt 583–1209 未记录 28S Ribosomal RNA × 1 5.8S Ribosomal RNA × 1 5S Ribosomal RNA × 1 60S RIBOSOMAL PROTEIN L8 × 1 60S RIBOSOMAL PROTEIN L3 × 1 60S RIBOSOMAL PROTEIN L4 × 1 60S RIBOSOMAL PROTEIN L5 × 1 60S RIBOSOMAL PROTEIN L6 × 1 60S RIBOSOMAL PROTEIN L7 × 1 60S RIBOSOMAL PROTEIN L7A × 1 60S RIBOSOMAL PROTEIN L9 × 1 60S RIBOSOMAL PROTEIN L10 × 1 60S RIBOSOMAL PROTEIN L11 × 1 60S RIBOSOMAL PROTEIN L13 × 1 60S RIBOSOMAL PROTEIN L14 × 1 60S RIBOSOMAL PROTEIN L15 × 1 60S RIBOSOMAL PROTEIN L13A × 1 60S RIBOSOMAL PROTEIN L17 × 1 60S RIBOSOMAL PROTEIN L18 × 1 60S RIBOSOMAL PROTEIN L19 × 1 60S RIBOSOMAL PROTEIN L18A × 1 60S RIBOSOMAL PROTEIN L21 × 1 60S RIBOSOMAL PROTEIN L22 × 1 60S RIBOSOMAL PROTEIN L23 × 1 60S RIBOSOMAL PROTEIN L24 × 1 60S RIBOSOMAL PROTEIN L23A × 1 60S RIBOSOMAL PROTEIN L26 × 1 60S RIBOSOMAL PROTEIN L27 × 1 60S RIBOSOMAL PROTEIN L27A × 1 60S RIBOSOMAL PROTEIN L29 × 1 60S RIBOSOMAL PROTEIN L30 × 1 60S RIBOSOMAL PROTEIN L31 × 1 60S RIBOSOMAL PROTEIN L32 × 1 60S RIBOSOMAL PROTEIN L35A × 1 60S RIBOSOMAL PROTEIN L34 × 1 60S RIBOSOMAL PROTEIN L35 × 1 60S RIBOSOMAL PROTEIN L36 × 1 60S RIBOSOMAL PROTEIN L37 × 1 60S RIBOSOMAL PROTEIN L38 × 1 60S RIBOSOMAL PROTEIN L39 × 1 UBIQUITIN-60S RIBOSOMAL PROTEIN L40 × 1 60S RIBOSOMAL PROTEIN L41 × 1 60S RIBOSOMAL PROTEIN L36A × 1 60S RIBOSOMAL PROTEIN L37A × 1 60S RIBOSOMAL PROTEIN L28 × 1 60S RIBOSOMAL PROTEIN L10A × 1 TRNA × 1 HCV-IRES × 1 18S Ribosomal RNA × 1 40S RIBOSOMAL PROTEIN US2 × 1 40S RIBOSOMAL PROTEIN ES1 × 1 40S RIBOSOMAL PROTEIN US5 × 1 40S RIBOSOMAL PROTEIN US3 × 1 40S RIBOSOMAL PROTEIN ES4 × 1 40S RIBOSOMAL PROTEIN US7 × 1 40S RIBOSOMAL PROTEIN ES6 × 1 40S RIBOSOMAL PROTEIN ES7 × 1 40S RIBOSOMAL PROTEIN ES8 × 1 40S RIBOSOMAL PROTEIN US4 × 1 40S RIBOSOMAL PROTEIN ES10 × 1 40S RIBOSOMAL PROTEIN US17 × 1 40S RIBOSOMAL PROTEIN ES12 × 1 40S RIBOSOMAL PROTEIN ES15 × 1 40S RIBOSOMAL PROTEIN ES11 × 1 40S RIBOSOMAL PROTEIN US19 × 1 40S RIBOSOMAL PROTEIN US9 × 1 40S RIBOSOMAL PROTEIN ES17 × 1 40S RIBOSOMAL PROTEIN US13 × 1 40S RIBOSOMAL PROTEIN ES19 × 1 40S RIBOSOMAL PROTEIN US10 × 1 40S RIBOSOMAL PROTEIN ES21 × 1 40S RIBOSOMAL PROTEIN US8 × 1 40S RIBOSOMAL PROTEIN US12 × 1 40S RIBOSOMAL PROTEIN ES24 × 1 40S RIBOSOMAL PROTEIN ES25 × 1 40S RIBOSOMAL PROTEIN ES26 × 1 40S RIBOSOMAL PROTEIN ES27 × 1 40S RIBOSOMAL PROTEIN ES28 × 1 40S RIBOSOMAL PROTEIN US14 × 1 40S RIBOSOMAL PROTEIN ES30 × 1 40S RIBOSOMAL PROTEIN ES31 × 1 40S RIBOSOMAL PROTEIN RACK1 × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM缓冲液:20MM TRIS-HCL, 5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT;pH 7.6;20MM TRIS-HCL, 5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT cryo-EM玻璃化条件:冷冻剂 ETHANE;VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING, 分辨率 8.90 Å

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 4 个其他 PDB 条目、4 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 G1TRL5_RABIT
Isoform
PDB实体 48
链与序列区间 作者链 BB; PDB构建体 1–627; UniProt 583–1209

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中;数据库内部编号、导入时间和 assembly 操作表达式仅用于维护,因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

SAXS profile for 4ujd

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4ujd
下载 Download

2. 结构基本信息 2. Structure Basics

条目编号 entry_id4ujd
沉积日期 deposition_date2014-06-18
结构标题 titlemammalian 80S HCV-IRES initiation complex with eIF5B PRE-like state
关键词 keywordsRIBOSOME, TRANSLATION INITIATION, HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE, EUKARYOTIC INITIATION FACTOR 5B; RIBOSOME
实验方法 methodELECTRON MICROSCOPY

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier96.36
回转半径 Rg (电子) rg_electron96.93
零角强度 I(0) i0312568000000.00
分子量 molecular_weight3305700.0 kDa
排除体积 excluded_volume3531100 ų
包络体积 envelope_volume6187700 ų
水化壳体积 shell_volume481880 ų
包络直径 envelope_diameter316.9
壳层 Rg shell_rg114.20
包络 Rg envelope_rg95.69
形状 Rg shape_rg96.97
总 Rg total_rg96.89
总原子数 total_atoms223911
残基数 n_residues17928
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −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

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax247.8
Rg (实空间) rg_real93.75
Rg 误差 (实空间) rg_real_error0.37
I(0) (实空间) i0_real2.9930e+11
I(0) 误差 (实空间) i0_real_error4.8590e+09
Rg (倒空间) rg_reciprocal98.39
I(0) (倒空间) i0_reciprocal314700000000.0000
解质量估计 total_estimate0.9106
解质量评级 solution_quality EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary108.4
偏度 Skewness skewness0.097
峰度 Kurtosis kurtosis-0.607
角度范围 angular_range— – 0.0800 −1
当前正则化参数 α current_alpha0.9805
最高正则化参数 α highest_alpha20660000000.0000
实空间数据点数 n_real_points17
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 1.000; Stabil: 0.949; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (85)

8. 引用文献 (1)

9. 文件与曲线 (10)