6whe

Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state

Method: X-RAY DIFFRACTION D_max: 74.8 Å Quality: GOOD

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

Ras-related protein Rab-8A

Homo sapiens

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 1–181	突变：Q67L/T72E	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION；pH 7；289 K；20% PEG3350, 0.1M Hepes pH 7	分辨率 1.73 Å R-free 0.230
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 1–181	突变：Q67L/T72E	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION；pH 7；289 K；20% PEG3350, 0.1M Hepes pH 7	分辨率 1.73 Å R-free 0.230

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。

其他 PDB	相对当前条目 6WHE	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp 提交 2011-01-14	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	分辨率 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp 提交 2011-01-14	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 C 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	分辨率 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp 提交 2011-01-14	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 E 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	分辨率 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp 提交 2011-01-14	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 G 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	分辨率 2.00 Å R-free 0.241
3TNF LidA from Legionella in complex with active Rab8a 提交 2011-09-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；50% (v/v) MPD , 0.1 M sodium cacodylate pH 5.6, 10 mM spermidine, vapor diffusion, hanging drop, temperature 293K	分辨率 2.50 Å R-free 0.275
4LHV Crystal structure of Rab8 in its inactive GDP-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 6–176（171 aa）片段：unp residues 6-176	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.95 Å R-free 0.244
4LHV Crystal structure of Rab8 in its inactive GDP-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 6–176（171 aa）片段：unp residues 6-176	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.95 Å R-free 0.244
4LHV Crystal structure of Rab8 in its inactive GDP-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 6–176（171 aa）片段：unp residues 6-176	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.95 Å R-free 0.244
4LHV Crystal structure of Rab8 in its inactive GDP-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 D 6–176（171 aa）片段：unp residues 6-176	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.95 Å R-free 0.244
4LHV Crystal structure of Rab8 in its inactive GDP-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 E 6–176（171 aa）片段：unp residues 6-176	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.95 Å R-free 0.244
4LHW Crystal structure of Rab8 in its active GppNHp-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.55 Å R-free 0.183
4LHW Crystal structure of Rab8 in its active GppNHp-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.55 Å R-free 0.183
4LHW Crystal structure of Rab8 in its active GppNHp-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.55 Å R-free 0.183
4LHW Crystal structure of Rab8 in its active GppNHp-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 D 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.55 Å R-free 0.183
4LHW Crystal structure of Rab8 in its active GppNHp-bound form 提交 2013-07-01	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 E 6–176（171 aa）片段：unp residues 6-176	未记录	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.55 Å R-free 0.183
4LHX Crystal structure of nucleotide-free Rab8:Rabin8 提交 2013-07-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 1–184（184 aa）片段：unp residues 1-184	未记录	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES. cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES), pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.05 Å R-free 0.300
4LHX Crystal structure of nucleotide-free Rab8:Rabin8 提交 2013-07-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 B 1–184（184 aa）片段：unp residues 1-184	未记录	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES. cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES), pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.05 Å R-free 0.300
4LHY Crystal structure of GDP-bound Rab8:Rabin8 提交 2013-07-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 1–184（184 aa）片段：unp residues 1-184	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hour at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.10 Å R-free 0.310
4LHY Crystal structure of GDP-bound Rab8:Rabin8 提交 2013-07-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 B 1–184（184 aa）片段：unp residues 1-184	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hour at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.10 Å R-free 0.310
4LHZ Crystal structure of GTP-bound Rab8:Rabin8 提交 2013-07-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 1–184（184 aa）片段：unp residues 1-184	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hours at 278 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.20 Å R-free 0.309
4LHZ Crystal structure of GTP-bound Rab8:Rabin8 提交 2013-07-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 B 1–184（184 aa）片段：unp residues 1-184	未记录	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hours at 278 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.20 Å R-free 0.309
4LI0 Crystal structure of GDP-bound Rab8:GRAB 提交 2013-07-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 1–184（184 aa）片段：unp residues 1-184	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1.6 M ammonium sulphate and sodium acetate. cryo solution containing 20% glycerol in the reservoir solution, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.30 Å R-free 0.290
4LI0 Crystal structure of GDP-bound Rab8:GRAB 提交 2013-07-01	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 B 1–184（184 aa）片段：unp residues 1-184	未记录	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1.6 M ammonium sulphate and sodium acetate. cryo solution containing 20% glycerol in the reservoir solution, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 3.30 Å R-free 0.290
5SZI Structure of human Rab8a in complex with the bMERB domain of Mical-cL 提交 2016-08-14	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 1–207（207 aa）	未记录	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；293 K；0.1M bis tris propane 0.2M tri sodium citrate 20% PEG 3350	分辨率 2.85 Å R-free 0.288
6RIR Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2 提交 2019-04-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–181（181 aa）链 B 1–181（181 aa）	突变：Q67L 非标准单体：是（mmCIF未提供具体位点）突变：Q67L 非标准单体：是（mmCIF未提供具体位点）	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；8% PEG 8K 100mM Na HEPES	分辨率 1.77 Å R-free 0.210
6SQ2 Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab binding domain of RILPL2 提交 2019-09-03	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–181（181 aa）链 B 1–181（181 aa）	突变：Q67L, T72E 突变：Q67L, T72E	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；100mM HEPES 10% PEG 4,000 10% 2-propanol	分辨率 1.68 Å R-free 0.202
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP 提交 2019-09-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 6–176（171 aa）	非标准单体：是（mmCIF未提供具体位点）	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	分辨率 2.40 Å R-free 0.262
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP 提交 2019-09-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 6–176（171 aa）	非标准单体：是（mmCIF未提供具体位点）	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	分辨率 2.40 Å R-free 0.262
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP 提交 2019-09-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 C 6–176（171 aa）	非标准单体：是（mmCIF未提供具体位点）	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	分辨率 2.40 Å R-free 0.262
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP 提交 2019-09-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 D 6–176（171 aa）	非标准单体：是（mmCIF未提供具体位点）	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	分辨率 2.40 Å R-free 0.262
6STF Human Rab8a phosphorylated at Ser111 in complex with GDP 提交 2019-09-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 5 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 E 6–176（171 aa）	非标准单体：是（mmCIF未提供具体位点）	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000	分辨率 2.40 Å R-free 0.262
6STG Human Rab8a phosphorylated at Ser111 in complex with GPPNP 提交 2019-09-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 6–176（171 aa）	非标准单体：是（mmCIF未提供具体位点）	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 30% PEG300	分辨率 2.50 Å R-free 0.278
6STG Human Rab8a phosphorylated at Ser111 in complex with GPPNP 提交 2019-09-10	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 B 6–176（171 aa）	非标准单体：是（mmCIF未提供具体位点）	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 30% PEG300	分辨率 2.50 Å R-free 0.278
6ZSI The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. 提交 2020-07-15	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 1–176（176 aa）	未记录	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Mes pH 6.0 5% w/v PEG 3000 30% v/v PEG 200	分辨率 1.91 Å R-free 0.267
6ZSI The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. 提交 2020-07-15	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 B 1–176（176 aa）	未记录	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Mes pH 6.0 5% w/v PEG 3000 30% v/v PEG 200	分辨率 1.91 Å R-free 0.267
6ZSJ The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. 提交 2020-07-15	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 1–176（176 aa）	未记录	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Mes pH 6.5 10 % (w/v) Peg-MME5000 12% (v/v) 1-propanol	分辨率 2.00 Å R-free 0.291
6ZSJ The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. 提交 2020-07-15	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 B 1–176（176 aa）	未记录	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Mes pH 6.5 10 % (w/v) Peg-MME5000 12% (v/v) 1-propanol	分辨率 2.00 Å R-free 0.291
7BWT SopD-Rab8 complex structure 提交 2020-04-16	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 B 2–183（182 aa）	未记录	PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 9 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；291 K；0.05M Sodium cacodylate trihydrate pH 6.5, 0.2 M MgCl2, 11.5% PEG4000	分辨率 2.30 Å R-free 0.215
7LWB Crystal Structure of phospho-Rab8a with the RH2 domain (117-165) of RILPL2 提交 2021-02-28	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–181（181 aa）	突变：Q67L 非标准单体：是（mmCIF未提供具体位点）	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；pH 7.5；288 K；150mM DL-Malic acid, 20% PEG3350	分辨率 1.90 Å R-free 0.267
9IKQ Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L) 提交 2024-06-28	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 A 1–181（181 aa）链 B 1–181（181 aa）	突变：Q67L 突变：Q67L	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 6 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M BIS-TRIS pH 6.5, 16% (w/v) PEG 10000	分辨率 1.93 Å R-free 0.218
9M0O Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L) 提交 2025-02-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 4 PDB 声明：tetrameric	链 D 1–176（176 aa）	突变：Q67L	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GOL GLYCEROL × 6 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05 M Imidazole pH 6.5, 0.5 M Sodium acetate trihydrate	分辨率 1.83 Å R-free 0.222

共 19 个其他 PDB 条目、41 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	RAB8A_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 4–184； UniProt 1–181 作者链 B； PDB构建体 4–184； UniProt 1–181

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

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	6whe
沉积日期 deposition_date	2020-04-08
结构标题 title	Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state
关键词 keywords	;Rab GTPase, membrane trafficking, Leucine-rich repeat kinase 2 (LRRK2), switch 2 phosphorylation, effector recruitment, Golgi membranes, ciliogenesis, Parkinson's disease, Rab-interacting lysosomal protein-like 2 (RILPL2), SIGNALING PROTEIN, HYDROLASE ;; SIGNALING PROTEIN, HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier	22.66 Å
回转半径 Rg (电子) rg_electron	21.98 Å
零角强度 I(0) i0	29423500.00
分子量 molecular_weight	41137.0 kDa
排除体积 excluded_volume	51355 Å³
包络体积 envelope_volume	60981 Å³
水化壳体积 shell_volume	23173 Å³
包络直径 envelope_diameter	77.8 Å
壳层 Rg shell_rg	28.75 Å
包络 Rg envelope_rg	22.28 Å
形状 Rg shape_rg	21.99 Å
总 Rg total_rg	22.79 Å
总原子数 total_atoms	2882
残基数 n_residues	347
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	74.8 Å
Rg (实空间) rg_real	22.64 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	2.9420e+07
I(0) 误差 (实空间) i0_real_error	3.8870e+05
Rg (倒空间) rg_reciprocal	22.64 Å
I(0) (倒空间) i0_reciprocal	29420000.0000
解质量估计 total_estimate	0.8906
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.1 Å
偏度 Skewness skewness	0.319
峰度 Kurtosis kurtosis	-0.411
角度范围 angular_range	— – 0.3500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5641000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.996

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

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6. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	Ras-related protein Rab-8A
分子量 formula_weight	21077.2 kDa
EC 编号 ec_number	3.6.5.2
突变 mutation	Q67L/T72E
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	3209

GSHMAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGLERFREITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKKLEGNS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 non-polymer

描述 description	GUANOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 3 Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 4 Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

实体 5 Entity 5 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	316

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7. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d6whea_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d6wheb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

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8. 引用文献 (1)

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晶胞边长 a length_a	36.092 Å
晶胞边长 b length_b	118.377 Å
晶胞边长 c length_c	39.603 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	101.96 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.730 Å
最低分辨率 resolution_low	29.290 Å
R 因子 r_factor	0.1888
R_work r_work	0.1866
R_free r_free	0.2304

fit	/app/data/saxs_computation/wh/6whe/6whe.fit
pddf	/app/data/pr_computation/wh/6whe/6whe.pr.out
profile	/app/data/saxs_computation/wh/6whe/6whe.dat