6m8q

Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531

Method: X-RAY DIFFRACTION Dmax: 97.3 Å Quality: EXCELLENT

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

Cleavage and polyadenylation specificity factor subunit 3

Homo sapiens

UniProt Q9UKF6

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 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 A; UniProt 1–459 未记录 ZN ZINC ION × 2 JBG N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 7;294 K;Reservoir solution: 100 mM Tris HCl pH 7.0; 0.4 M NaH2PO4; 1.466 K2HPO; 0.2 M NaCl 10 mg/mL Protein solution: CPSF3 protein in; 20 mM Hepes pH 7.7; 150 mM NaCl; 5 % glycerol; 1 mM DTT; 0.5 mM NVP-LTM531 Co-crystallization Protocol: 50 nL of protein mixed with 50 nL of reservoir solution. Crystals grew within 1 day with tetragonal bipyramidal habitus and reached a maximum size of 50 micrometers after 3 days. Cryo-protection Protocol: supplemented reservoir solution with 10 and 20% glycerol, respectively, and subsequently added both solution within 5 min. Crystals incubate for another 5 min before harvesting. 分辨率 2.49 Å R-free 0.221
2 蛋白单体 单体 蛋白 × 1 PDB 声明:monomeric(1) 与蛋白拷贝数一致 链 B; UniProt 1–459 未记录 ZN ZINC ION × 2 JBG N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 7;294 K;Reservoir solution: 100 mM Tris HCl pH 7.0; 0.4 M NaH2PO4; 1.466 K2HPO; 0.2 M NaCl 10 mg/mL Protein solution: CPSF3 protein in; 20 mM Hepes pH 7.7; 150 mM NaCl; 5 % glycerol; 1 mM DTT; 0.5 mM NVP-LTM531 Co-crystallization Protocol: 50 nL of protein mixed with 50 nL of reservoir solution. Crystals grew within 1 day with tetragonal bipyramidal habitus and reached a maximum size of 50 micrometers after 3 days. Cryo-protection Protocol: supplemented reservoir solution with 10 and 20% glycerol, respectively, and subsequently added both solution within 5 min. Crystals incubate for another 5 min before harvesting. 分辨率 2.49 Å R-free 0.221

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 9 个其他 PDB 条目、9 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 CPSF3_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 20–478; UniProt 1–459 作者链 B; PDB构建体 20–478; UniProt 1–459

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 6m8q

P(r) 距离分布 P(r) Distribution

P(r) distribution for 6m8q
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id6m8q
沉积日期 deposition_date2018-08-22
结构标题 titleCleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531
关键词 keywords;POLYADENYLATION, METALLO-B-LACTAMASE, PRE-MRNA PROCESSING, ARTEMIS, V(D)J RECOMBINATION, DOUBLE-STRAND BREAK REPAIR, HYDROLASE, RNA BINDING PROTEIN, HYDROXYLASE ;; HYDROLASE
实验方法 methodX-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier30.90
回转半径 Rg (电子) rg_electron30.23
零角强度 I(0) i0174085000.00
分子量 molecular_weight104540.0 kDa
排除体积 excluded_volume130530 ų
包络体积 envelope_volume159100 ų
水化壳体积 shell_volume42510 ų
包络直径 envelope_diameter96.4
壳层 Rg shell_rg38.59
包络 Rg envelope_rg30.08
形状 Rg shape_rg30.24
总 Rg total_rg30.92
总原子数 total_atoms7323
残基数 n_residues904
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 dmax97.3
Rg (实空间) rg_real30.78
Rg 误差 (实空间) rg_real_error0.54
I(0) (实空间) i0_real1.7410e+08
I(0) 误差 (实空间) i0_real_error2.6190e+06
Rg (倒空间) rg_reciprocal30.83
I(0) (倒空间) i0_reciprocal174100000.0000
解质量估计 total_estimate0.9066
解质量评级 solution_quality EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary34.3
偏度 Skewness skewness0.190
峰度 Kurtosis kurtosis-0.605
角度范围 angular_range— – 0.2550 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha82130000.0000
实空间数据点数 n_real_points52
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.975

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

6. 实体与聚合物信息 Entities & Polymers (5)

7. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_idd6m8qa_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamilyd.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family familyd.157.1.10 — beta-CASP RNA-metabolising hydrolases
结构域编号 domain_idd6m8qb_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.157 — Metallo-hydrolase/oxidoreductase
超家族 Superfamily superfamilyd.157.1 — Metallo-hydrolase/oxidoreductase
家族 Family familyd.157.1.10 — beta-CASP RNA-metabolising hydrolases

CATH v4.4 (4 domains)

结构域编号 domain_id6m8qA01
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
结构域编号 domain_id6m8qA02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10890
结构域编号 domain_id6m8qB01
类 Class class3 — Alpha Beta
架构 Architecture architecture60 — 4-Layer Sandwich
拓扑 Topology topology15 — Metallo-beta-lactamase; Chain A
同源超家族 H-superfamily homologous superfamily10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
结构域编号 domain_id6m8qB02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily10890

8. 引用文献 (1)

9. 文件与曲线 (10)