3o4x

Crystal structure of complex between amino and carboxy terminal fragments of mDia1

Method: X-RAY DIFFRACTION Dmax: 164.7 Å Quality: GOOD

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

Protein diaphanous homolog 1

Mus musculus

UniProt O08808

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 蛋白同源多聚体 同源多聚体 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 A; UniProt 131–458 链 D; UniProt 131–458 链 E; UniProt 736–1200 链 H; UniProt 736–1200 片段:mDia1 N-terminal regulatory domain (unp residues 131-458) 片段:mDia1 C-terminal FH2-DAD domain (unp residues 736-1200) 无其他共同聚合物 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7;313 K;Peg 4000, sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 313K 分辨率 3.20 Å R-free 0.298
2 蛋白同源多聚体 同源多聚体 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 B; UniProt 131–458 链 C; UniProt 131–458 链 F; UniProt 736–1200 链 G; UniProt 736–1200 片段:mDia1 N-terminal regulatory domain (unp residues 131-458) 片段:mDia1 C-terminal FH2-DAD domain (unp residues 736-1200) 无其他共同聚合物 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7;313 K;Peg 4000, sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 313K 分辨率 3.20 Å R-free 0.298

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 12 个其他 PDB 条目、17 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 DIAP1_MOUSE
Isoform
PDB实体 1, 2
链与序列区间 作者链 A; PDB构建体 3–330; UniProt 131–458 作者链 B; PDB构建体 3–330; UniProt 131–458 作者链 C; PDB构建体 3–330; UniProt 131–458 作者链 D; PDB构建体 3–330; UniProt 131–458 作者链 E; PDB构建体 3–467; UniProt 736–1200 作者链 F; PDB构建体 3–467; UniProt 736–1200 作者链 G; PDB构建体 3–467; UniProt 736–1200 作者链 H; PDB构建体 3–467; UniProt 736–1200

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 3o4x

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3o4x
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3o4x
沉积日期 deposition_date2010-07-27
结构标题 titleCrystal structure of complex between amino and carboxy terminal fragments of mDia1
关键词 keywordsautoinhibition, actin nucleator, actin binding, PROTEIN BINDING; PROTEIN BINDING
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_guinier52.30
回转半径 Rg (电子) rg_electron51.76
零角强度 I(0) i01728460000.00
分子量 molecular_weight346570.0 kDa
排除体积 excluded_volume434200 ų
包络体积 envelope_volume669920 ų
水化壳体积 shell_volume106450 ų
包络直径 envelope_diameter168.1
壳层 Rg shell_rg56.79
包络 Rg envelope_rg50.22
形状 Rg shape_rg51.71
总 Rg total_rg52.10
总原子数 total_atoms24287
残基数 n_residues2997
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 dmax164.7
Rg (实空间) rg_real52.06
Rg 误差 (实空间) rg_real_error0.97
I(0) (实空间) i0_real1.7280e+09
I(0) 误差 (实空间) i0_real_error3.1390e+07
Rg (倒空间) rg_reciprocal52.48
I(0) (倒空间) i0_reciprocal1729000000.0000
解质量估计 total_estimate0.8112
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary71.4
偏度 Skewness skewness0.110
峰度 Kurtosis kurtosis-0.379
角度范围 angular_range— – 0.1500 −1
当前正则化参数 α current_alpha0.0001
最高正则化参数 α highest_alpha236700000.0000
实空间数据点数 n_real_points31
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.000

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) 20 domains

CATH v4.4 (20 domains)

结构域编号 domain_id3o4xA01
类 Class class1 — Mainly Alpha
架构 Architecture architecture25 — Alpha Horseshoe
拓扑 Topology topology10 — Leucine-rich Repeat Variant
同源超家族 H-superfamily homologous superfamily10 — Leucine-rich Repeat Variant
结构域编号 domain_id3o4xA02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily150 — Formin, FH3 diaphanous domain
结构域编号 domain_id3o4xB01
类 Class class1 — Mainly Alpha
架构 Architecture architecture25 — Alpha Horseshoe
拓扑 Topology topology10 — Leucine-rich Repeat Variant
同源超家族 H-superfamily homologous superfamily10 — Leucine-rich Repeat Variant
结构域编号 domain_id3o4xB02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily150 — Formin, FH3 diaphanous domain
结构域编号 domain_id3o4xC01
类 Class class1 — Mainly Alpha
架构 Architecture architecture25 — Alpha Horseshoe
拓扑 Topology topology10 — Leucine-rich Repeat Variant
同源超家族 H-superfamily homologous superfamily10 — Leucine-rich Repeat Variant
结构域编号 domain_id3o4xC02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily150 — Formin, FH3 diaphanous domain
结构域编号 domain_id3o4xD01
类 Class class1 — Mainly Alpha
架构 Architecture architecture25 — Alpha Horseshoe
拓扑 Topology topology10 — Leucine-rich Repeat Variant
同源超家族 H-superfamily homologous superfamily10 — Leucine-rich Repeat Variant
结构域编号 domain_id3o4xD02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily150 — Formin, FH3 diaphanous domain
结构域编号 domain_id3o4xE01
类 Class class6 — Special
架构 Architecture architecture10 — Helix non-globular
拓扑 Topology topology30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily30
结构域编号 domain_id3o4xE02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily630
结构域编号 domain_id3o4xE03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily2220 — Formin, FH2 domain
结构域编号 domain_id3o4xF01
类 Class class6 — Special
架构 Architecture architecture10 — Helix non-globular
拓扑 Topology topology30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily30
结构域编号 domain_id3o4xF02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily630
结构域编号 domain_id3o4xF03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily2220 — Formin, FH2 domain
结构域编号 domain_id3o4xG01
类 Class class6 — Special
架构 Architecture architecture10 — Helix non-globular
拓扑 Topology topology30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily30
结构域编号 domain_id3o4xG02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily630
结构域编号 domain_id3o4xG03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily2220 — Formin, FH2 domain
结构域编号 domain_id3o4xH01
类 Class class6 — Special
架构 Architecture architecture10 — Helix non-globular
拓扑 Topology topology30 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily30
结构域编号 domain_id3o4xH02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily630
结构域编号 domain_id3o4xH03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily2220 — Formin, FH2 domain

8. 引用文献 (1)

9. 文件与曲线 (10)