1foe

CRYSTAL STRUCTURE OF RAC1 IN COMPLEX WITH THE GUANINE NUCLEOTIDE EXCHANGE REGION OF TIAM1

Method: X-RAY DIFFRACTION Dmax: 150.2 Å Quality: GOOD

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

T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1

Mus musculus

UniProt Q60610

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 1030–1406 片段:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN 突变:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS 非标准单体:是(mmCIF未提供具体位点) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 1 (P63000) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
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 1030–1406 片段:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN 突变:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS 非标准单体:是(mmCIF未提供具体位点) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 1 (P63000) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
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 1030–1406 片段:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN 突变:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS 非标准单体:是(mmCIF未提供具体位点) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 1 (P63000) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
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 1030–1406 片段:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN 突变:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS 非标准单体:是(mmCIF未提供具体位点) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 1 (P63000) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
5 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 A; UniProt 1030–1406 链 C; UniProt 1030–1406 链 E; UniProt 1030–1406 链 G; UniProt 1030–1406 片段:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN 突变:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS 非标准单体:是(mmCIF未提供具体位点) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 4 (P63000) SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
6 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 A; UniProt 1030–1406 链 G; UniProt 1030–1406 片段:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN 突变:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS 非标准单体:是(mmCIF未提供具体位点) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 2 (P63000) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
7 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 1030–1406 链 E; UniProt 1030–1406 片段:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN 突变:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS 非标准单体:是(mmCIF未提供具体位点) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 2 (P63000) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293

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、5 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 TIAM1_MOUSE
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–377; UniProt 1030–1406 作者链 C; PDB构建体 1–377; UniProt 1030–1406 作者链 E; PDB构建体 1–377; UniProt 1030–1406 作者链 G; PDB构建体 1–377; UniProt 1030–1406

RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE

Homo sapiens

UniProt P63000

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 1–177 片段:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 1 (Q60610) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
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 1–177 片段:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 1 (Q60610) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
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 1–177 片段:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 1 (Q60610) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
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 1–177 片段:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 1 (Q60610) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
5 蛋白异源复合物 异源复合物 蛋白 × 8 PDB 声明:octameric(8) 与蛋白拷贝数一致 链 B; UniProt 1–177 链 D; UniProt 1–177 链 F; UniProt 1–177 链 H; UniProt 1–177 片段:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 4 (Q60610) SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
6 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 1–177 链 H; UniProt 1–177 片段:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 2 (Q60610) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293
7 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 D; UniProt 1–177 链 F; UniProt 1–177 片段:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 2 (Q60610) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K 分辨率 2.80 Å R-free 0.293

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 74 个其他 PDB 条目、96 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 RAC1_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–177; UniProt 1–177 作者链 D; PDB构建体 1–177; UniProt 1–177 作者链 F; PDB构建体 1–177; UniProt 1–177 作者链 H; PDB构建体 1–177; UniProt 1–177

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 1foe

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1foe
下载 Download

2. 结构基本信息 2. Structure Basics

条目编号 entry_id1foe
沉积日期 deposition_date2000-08-27
结构标题 titleCRYSTAL STRUCTURE OF RAC1 IN COMPLEX WITH THE GUANINE NUCLEOTIDE EXCHANGE REGION OF TIAM1
关键词 keywords;DBL HOMOLOGY DOMAIN, PLECKSTRIN HOMOLOGY DOMAIN, GTPASE, GUANINE NUCLEOTIDE EXCHANGE FACTOR, signaling protein, immune system-signaling protein COMPLEX ;; signaling protein, immune system/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_guinier45.87
回转半径 Rg (电子) rg_electron45.74
零角强度 I(0) i0865703000.00
分子量 molecular_weight249440.0 kDa
排除体积 excluded_volume314730 ų
包络体积 envelope_volume442050 ų
水化壳体积 shell_volume80888 ų
包络直径 envelope_diameter158.5
壳层 Rg shell_rg50.16
包络 Rg envelope_rg44.32
形状 Rg shape_rg45.72
总 Rg total_rg45.99
总原子数 total_atoms17477
残基数 n_residues2152
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 dmax150.2
Rg (实空间) rg_real45.82
Rg 误差 (实空间) rg_real_error1.21
I(0) (实空间) i0_real8.6570e+08
I(0) 误差 (实空间) i0_real_error1.6210e+07
Rg (倒空间) rg_reciprocal45.87
I(0) (倒空间) i0_reciprocal865700000.0000
解质量估计 total_estimate0.8723
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary53.0
偏度 Skewness skewness0.308
峰度 Kurtosis kurtosis-0.393
角度范围 angular_range— – 0.1700 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha117000000.0000
实空间数据点数 n_real_points35
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.673

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

6. 实体与聚合物信息 Entities & Polymers (4)

7. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_idd1foea1
类 Class classa — All alpha proteins
折叠类型 Fold folda.87 — DBL homology domain (DH-domain)
超家族 Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
家族 Family familya.87.1.1 — DBL homology domain (DH-domain)
结构域编号 domain_idd1foea2
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.55.1.1 — Pleckstrin-homology domain (PH domain)
结构域编号 domain_idd1foeb_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.8 — G proteins
结构域编号 domain_idd1foec1
类 Class classa — All alpha proteins
折叠类型 Fold folda.87 — DBL homology domain (DH-domain)
超家族 Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
家族 Family familya.87.1.1 — DBL homology domain (DH-domain)
结构域编号 domain_idd1foec2
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.55.1.1 — Pleckstrin-homology domain (PH domain)
结构域编号 domain_idd1foed_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.8 — G proteins
结构域编号 domain_idd1foee1
类 Class classa — All alpha proteins
折叠类型 Fold folda.87 — DBL homology domain (DH-domain)
超家族 Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
家族 Family familya.87.1.1 — DBL homology domain (DH-domain)
结构域编号 domain_idd1foee2
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.55.1.1 — Pleckstrin-homology domain (PH domain)
结构域编号 domain_idd1foef_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.8 — G proteins
结构域编号 domain_idd1foeg1
类 Class classa — All alpha proteins
折叠类型 Fold folda.87 — DBL homology domain (DH-domain)
超家族 Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
家族 Family familya.87.1.1 — DBL homology domain (DH-domain)
结构域编号 domain_idd1foeg2
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.55.1.1 — Pleckstrin-homology domain (PH domain)
结构域编号 domain_idd1foeh_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family familyc.37.1.8 — G proteins

CATH v4.4 (12 domains)

结构域编号 domain_id1foeA01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology900 — Dbl Homology Domain; Chain A
同源超家族 H-superfamily homologous superfamily10 — Dbl homology (DH) domain
结构域编号 domain_id1foeA02
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_id1foeB00
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1foeC01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology900 — Dbl Homology Domain; Chain A
同源超家族 H-superfamily homologous superfamily10 — Dbl homology (DH) domain
结构域编号 domain_id1foeC02
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_id1foeD00
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1foeE01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology900 — Dbl Homology Domain; Chain A
同源超家族 H-superfamily homologous superfamily10 — Dbl homology (DH) domain
结构域编号 domain_id1foeE02
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_id1foeF00
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id1foeG01
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology900 — Dbl Homology Domain; Chain A
同源超家族 H-superfamily homologous superfamily10 — Dbl homology (DH) domain
结构域编号 domain_id1foeG02
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_id1foeH00
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. 引用文献 (1)

9. 文件与曲线 (10)