3tnp

Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme

Method: X-RAY DIFFRACTION Dmax: 122.0 Å Quality: GOOD

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

cAMP-dependent protein kinase catalytic subunit alpha

Mus musculus

UniProt P05132

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 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 C; UniProt 2–351 链 F; UniProt 2–351 非标准单体:是(mmCIF未提供具体位点) cAMP-dependent protein kinase type II-beta regulatory subunit × 2 (P31324) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K 分辨率 2.30 Å R-free 0.235
2 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 C; UniProt 2–351 非标准单体:是(mmCIF未提供具体位点) cAMP-dependent protein kinase type II-beta regulatory subunit × 1 (P31324) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K 分辨率 2.30 Å R-free 0.235
3 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 F; UniProt 2–351 非标准单体:是(mmCIF未提供具体位点) cAMP-dependent protein kinase type II-beta regulatory subunit × 1 (P31324) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K 分辨率 2.30 Å R-free 0.235

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 84 个其他 PDB 条目、97 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 KAPCA_MOUSE
Isoform
PDB实体 1
链与序列区间 作者链 C; PDB构建体 1–350; UniProt 2–351 作者链 F; PDB构建体 1–350; UniProt 2–351

cAMP-dependent protein kinase type II-beta regulatory subunit

Mus musculus

UniProt P31324

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 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 B; UniProt 1–416 链 E; UniProt 1–416 突变:R230K cAMP-dependent protein kinase catalytic subunit alpha × 2 (P05132) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K 分辨率 2.30 Å R-free 0.235
2 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 B; UniProt 1–416 突变:R230K cAMP-dependent protein kinase catalytic subunit alpha × 1 (P05132) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K 分辨率 2.30 Å R-free 0.235
3 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 E; UniProt 1–416 突变:R230K cAMP-dependent protein kinase catalytic subunit alpha × 1 (P05132) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K 分辨率 2.30 Å R-free 0.235

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 3 个其他 PDB 条目、3 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 KAP3_MOUSE
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–416; UniProt 1–416 作者链 E; PDB构建体 1–416; UniProt 1–416

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 3tnp

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3tnp
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3tnp
沉积日期 deposition_date2011-09-01
结构标题 titleStructure and Allostery of the PKA RIIb Tetrameric Holoenzyme
关键词 keywordsPKA RIIb tetrameric holoenzyme, TRANSFERASE; TRANSFERASE
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_guinier38.75
回转半径 Rg (电子) rg_electron38.23
零角强度 I(0) i0285756000.00
分子量 molecular_weight139900.0 kDa
排除体积 excluded_volume176230 ų
包络体积 envelope_volume240180 ų
水化壳体积 shell_volume51974 ų
包络直径 envelope_diameter122.5
壳层 Rg shell_rg44.66
包络 Rg envelope_rg37.64
形状 Rg shape_rg38.20
总 Rg total_rg38.72
总原子数 total_atoms9836
残基数 n_residues1206
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 dmax122.0
Rg (实空间) rg_real38.69
Rg 误差 (实空间) rg_real_error0.72
I(0) (实空间) i0_real2.8580e+08
I(0) 误差 (实空间) i0_real_error4.5460e+06
Rg (倒空间) rg_reciprocal38.73
I(0) (倒空间) i0_reciprocal285800000.0000
解质量估计 total_estimate0.8964
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary44.6
偏度 Skewness skewness0.238
峰度 Kurtosis kurtosis-0.589
角度范围 angular_range— – 0.2050 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha41070000.0000
实空间数据点数 n_real_points42
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.764

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

6. 实体与聚合物信息 Entities & Polymers (3)

7. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

结构域编号 domain_idd3tnpc_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
家族 Family familyd.144.1.7 — Protein kinases, catalytic subunit
结构域编号 domain_idd3tnpf_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.144 — Protein kinase-like (PK-like)
超家族 Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
家族 Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (8 domains)

结构域编号 domain_id3tnpB01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily10 — Jelly Rolls
结构域编号 domain_id3tnpB02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily10 — Jelly Rolls
结构域编号 domain_id3tnpC01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id3tnpC02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
结构域编号 domain_id3tnpE01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily10 — Jelly Rolls
结构域编号 domain_id3tnpE02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily10 — Jelly Rolls
结构域编号 domain_id3tnpF01
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology510 — Transferase(Phosphotransferase); domain 1
同源超家族 H-superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
结构域编号 domain_id3tnpF02
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology200 — Phosphorylase Kinase; domain 1
同源超家族 H-superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1

8. 引用文献 (1)

9. 文件与曲线 (10)