1y19

Structural basis for phosphatidylinositol phosphate kinase type I-gamma binding to talin at focal adhesions

Method: X-RAY DIFFRACTION Dmax: 153.0 Å Quality: GOOD

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

Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma

Mus musculus

UniProt O70161

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 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 638–651 片段:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
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 638–651 片段:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
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 638–651 片段:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
4 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 G; UniProt 638–651 片段:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
5 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 I; UniProt 638–651 片段:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
6 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 K; UniProt 638–651 片段:C-TERMINAL REGION Talin 1 × 1 (P26039) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286

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 2 个其他 PDB 条目、2 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 PI51C_MOUSE
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–14; UniProt 638–651 作者链 C; PDB构建体 1–14; UniProt 638–651 作者链 E; PDB构建体 1–14; UniProt 638–651 作者链 G; PDB构建体 1–14; UniProt 638–651 作者链 I; PDB构建体 1–14; UniProt 638–651 作者链 K; PDB构建体 1–14; UniProt 638–651

Talin 1

Mus musculus

UniProt P26039

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 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 B; UniProt 209–410 片段:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
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 D; UniProt 209–410 片段:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
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 209–410 片段:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
4 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 H; UniProt 209–410 片段:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
5 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 J; UniProt 209–410 片段:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286
6 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 L; UniProt 209–410 片段:F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma × 1 (O70161) X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.2;277 K;0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K 分辨率 2.60 Å R-free 0.286

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 50 个其他 PDB 条目、65 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 TLN1_MOUSE
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–202; UniProt 209–410 作者链 D; PDB构建体 1–202; UniProt 209–410 作者链 F; PDB构建体 1–202; UniProt 209–410 作者链 H; PDB构建体 1–202; UniProt 209–410 作者链 J; PDB构建体 1–202; UniProt 209–410 作者链 L; PDB构建体 1–202; UniProt 209–410

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 1y19

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1y19
下载 Download

2. 结构基本信息 2. Structure Basics

条目编号 entry_id1y19
沉积日期 deposition_date2004-11-17
结构标题 titleStructural basis for phosphatidylinositol phosphate kinase type I-gamma binding to talin at focal adhesions
关键词 keywordsFOCAL ADHESION; FERM DOMAIN; CYTOSKELETON; NPXY MOTIF; PTB DOMAIN, STRUCTURAL PROTEIN, SIGNALING PROTEIN; STRUCTURAL PROTEIN, SIGNALING PROTEIN
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_guinier47.42
回转半径 Rg (电子) rg_electron47.04
零角强度 I(0) i0270681000.00
分子量 molecular_weight140040.0 kDa
排除体积 excluded_volume177530 ų
包络体积 envelope_volume281490 ų
水化壳体积 shell_volume52784 ų
包络直径 envelope_diameter157.5
壳层 Rg shell_rg48.33
包络 Rg envelope_rg45.03
形状 Rg shape_rg47.02
总 Rg total_rg47.19
总原子数 total_atoms9882
残基数 n_residues1218
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 dmax153.0
Rg (实空间) rg_real47.37
Rg 误差 (实空间) rg_real_error1.61
I(0) (实空间) i0_real2.7070e+08
I(0) 误差 (实空间) i0_real_error5.5820e+06
Rg (倒空间) rg_reciprocal47.42
I(0) (倒空间) i0_reciprocal270700000.0000
解质量估计 total_estimate0.8927
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary55.6
偏度 Skewness skewness0.183
峰度 Kurtosis kurtosis-0.542
角度范围 angular_range— – 0.1650 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha10370000.0000
实空间数据点数 n_real_points34
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.749

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) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_idd1y19b1
类 Class classa — All alpha proteins
折叠类型 Fold folda.11 — Acyl-CoA binding protein-like
超家族 Superfamily superfamilya.11.2 — Second domain of FERM
家族 Family familya.11.2.1 — Second domain of FERM
结构域编号 domain_idd1y19b2
类 Class classb — All beta proteins
折叠类型 Fold foldb.55 — PH domain-like barrel
超家族 Superfamily superfamilyb.55.1 — PH domain-like
家族 Family familyb.55.1.5 — Third domain of FERM
结构域编号 domain_idd1y19d1
类 Class classa — All alpha proteins
折叠类型 Fold folda.11 — Acyl-CoA binding protein-like
超家族 Superfamily superfamilya.11.2 — Second domain of FERM
家族 Family familya.11.2.1 — Second domain of FERM
结构域编号 domain_idd1y19d2
类 Class classb — All beta proteins
折叠类型 Fold foldb.55 — PH domain-like barrel
超家族 Superfamily superfamilyb.55.1 — PH domain-like
家族 Family familyb.55.1.5 — Third domain of FERM
结构域编号 domain_idd1y19f1
类 Class classa — All alpha proteins
折叠类型 Fold folda.11 — Acyl-CoA binding protein-like
超家族 Superfamily superfamilya.11.2 — Second domain of FERM
家族 Family familya.11.2.1 — Second domain of FERM
结构域编号 domain_idd1y19f2
类 Class classb — All beta proteins
折叠类型 Fold foldb.55 — PH domain-like barrel
超家族 Superfamily superfamilyb.55.1 — PH domain-like
家族 Family familyb.55.1.5 — Third domain of FERM
结构域编号 domain_idd1y19h1
类 Class classa — All alpha proteins
折叠类型 Fold folda.11 — Acyl-CoA binding protein-like
超家族 Superfamily superfamilya.11.2 — Second domain of FERM
家族 Family familya.11.2.1 — Second domain of FERM
结构域编号 domain_idd1y19h2
类 Class classb — All beta proteins
折叠类型 Fold foldb.55 — PH domain-like barrel
超家族 Superfamily superfamilyb.55.1 — PH domain-like
家族 Family familyb.55.1.5 — Third domain of FERM
结构域编号 domain_idd1y19j1
类 Class classa — All alpha proteins
折叠类型 Fold folda.11 — Acyl-CoA binding protein-like
超家族 Superfamily superfamilya.11.2 — Second domain of FERM
家族 Family familya.11.2.1 — Second domain of FERM
结构域编号 domain_idd1y19j2
类 Class classb — All beta proteins
折叠类型 Fold foldb.55 — PH domain-like barrel
超家族 Superfamily superfamilyb.55.1 — PH domain-like
家族 Family familyb.55.1.5 — Third domain of FERM
结构域编号 domain_idd1y19l1
类 Class classa — All alpha proteins
折叠类型 Fold folda.11 — Acyl-CoA binding protein-like
超家族 Superfamily superfamilya.11.2 — Second domain of FERM
家族 Family familya.11.2.1 — Second domain of FERM
结构域编号 domain_idd1y19l2
类 Class classb — All beta proteins
折叠类型 Fold foldb.55 — PH domain-like barrel
超家族 Superfamily superfamilyb.55.1 — PH domain-like
家族 Family familyb.55.1.5 — Third domain of FERM

CATH v4.4 (12 domains)

结构域编号 domain_id1y19B01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology80 — Acyl-CoA Binding Protein
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1y19B02
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology29 — PH-domain like
同源超家族 H-superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
结构域编号 domain_id1y19D01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology80 — Acyl-CoA Binding Protein
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1y19D02
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology29 — PH-domain like
同源超家族 H-superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
结构域编号 domain_id1y19F01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology80 — Acyl-CoA Binding Protein
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1y19F02
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology29 — PH-domain like
同源超家族 H-superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
结构域编号 domain_id1y19H01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology80 — Acyl-CoA Binding Protein
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1y19H02
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology29 — PH-domain like
同源超家族 H-superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
结构域编号 domain_id1y19J01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology80 — Acyl-CoA Binding Protein
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1y19J02
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology29 — PH-domain like
同源超家族 H-superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
结构域编号 domain_id1y19L01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology80 — Acyl-CoA Binding Protein
同源超家族 H-superfamily homologous superfamily10
结构域编号 domain_id1y19L02
类 Class class2 — Mainly Beta
架构 Architecture architecture30 — Roll
拓扑 Topology topology29 — PH-domain like
同源超家族 H-superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

8. 引用文献 (1)

9. 文件与曲线 (10)