1k5d

Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex

Method: X-RAY DIFFRACTION Dmax: 193.3 Å Quality: GOOD

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

GTP-binding nuclear protein RAN

Homo sapiens

UniProt P62826

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 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 A; UniProt 1–216 未记录 Ran-specific GTPase-activating protein × 1 (P43487) Ran GTPase activating protein 1 × 1 (P41391) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 D; UniProt 1–216 未记录 Ran-specific GTPase-activating protein × 1 (P43487) Ran GTPase activating protein 1 × 1 (P41391) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
3 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 G; UniProt 1–216 未记录 Ran-specific GTPase-activating protein × 1 (P43487) Ran GTPase activating protein 1 × 1 (P41391) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
4 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 J; UniProt 1–216 未记录 Ran-specific GTPase-activating protein × 1 (P43487) Ran GTPase activating protein 1 × 1 (P41391) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267

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 137 个其他 PDB 条目、200 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 RAN_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–216; UniProt 1–216 作者链 D; PDB构建体 1–216; UniProt 1–216 作者链 G; PDB构建体 1–216; UniProt 1–216 作者链 J; PDB构建体 1–216; UniProt 1–216

Ran-specific GTPase-activating protein

Homo sapiens

UniProt P43487

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 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 B; UniProt 1–201 突变:S2A GTP-binding nuclear protein RAN × 1 (P62826) Ran GTPase activating protein 1 × 1 (P41391) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 E; UniProt 1–201 突变:S2A GTP-binding nuclear protein RAN × 1 (P62826) Ran GTPase activating protein 1 × 1 (P41391) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
3 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 H; UniProt 1–201 突变:S2A GTP-binding nuclear protein RAN × 1 (P62826) Ran GTPase activating protein 1 × 1 (P41391) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
4 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 K; UniProt 1–201 突变:S2A GTP-binding nuclear protein RAN × 1 (P62826) Ran GTPase activating protein 1 × 1 (P41391) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267

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、6 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 RANG_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–201; UniProt 1–201 作者链 E; PDB构建体 1–201; UniProt 1–201 作者链 H; PDB构建体 1–201; UniProt 1–201 作者链 K; PDB构建体 1–201; UniProt 1–201

Ran GTPase activating protein 1

Schizosaccharomyces pombe

UniProt P41391

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 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 C; UniProt 1–386 未记录 GTP-binding nuclear protein RAN × 1 (P62826) Ran-specific GTPase-activating protein × 1 (P43487) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
2 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 F; UniProt 1–386 未记录 GTP-binding nuclear protein RAN × 1 (P62826) Ran-specific GTPase-activating protein × 1 (P43487) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
3 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 I; UniProt 1–386 未记录 GTP-binding nuclear protein RAN × 1 (P62826) Ran-specific GTPase-activating protein × 1 (P43487) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267
4 蛋白异源复合物 异源复合物 蛋白 × 3 PDB 声明:trimeric(3) 与蛋白拷贝数一致 链 L; UniProt 1–386 未记录 GTP-binding nuclear protein RAN × 1 (P62826) Ran-specific GTPase-activating protein × 1 (P43487) MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;PEG4000, POTASSIUM ACETATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 分辨率 2.70 Å R-free 0.267

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、8 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 RNA1_SCHPO
Isoform
PDB实体 3
链与序列区间 作者链 C; PDB构建体 1–386; UniProt 1–386 作者链 F; PDB构建体 1–386; UniProt 1–386 作者链 I; PDB构建体 1–386; UniProt 1–386 作者链 L; PDB构建体 1–386; UniProt 1–386

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 1k5d

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1k5d
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1k5d
沉积日期 deposition_date2001-10-10
结构标题 titleCrystal structure of Ran-GPPNHP-RanBP1-RanGAP complex
关键词 keywords;RAN, RANBP1, RANGAP, GAP, SIGNAL TRANSDUCTION, NUCLEAR TRANSPORT, GTP HYDROLYSIS, GROUND STATE, COMPLEX (GTP-BINDING-GTPASE ACTIVATION), SIGNALING PROTEIN-SIGNALING ACTIVATOR COMPLEX ;; SIGNALING PROTEIN/SIGNALING ACTIVATOR
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_guinier56.37
回转半径 Rg (电子) rg_electron56.47
零角强度 I(0) i01431680000.00
分子量 molecular_weight318250.0 kDa
排除体积 excluded_volume399300 ų
包络体积 envelope_volume579340 ų
水化壳体积 shell_volume87534 ų
包络直径 envelope_diameter204.1
壳层 Rg shell_rg56.82
包络 Rg envelope_rg55.09
形状 Rg shape_rg56.48
总 Rg total_rg56.45
总原子数 total_atoms22396
残基数 n_residues2784
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 dmax193.3
Rg (实空间) rg_real56.42
Rg 误差 (实空间) rg_real_error1.96
I(0) (实空间) i0_real1.4320e+09
I(0) 误差 (实空间) i0_real_error3.1810e+07
Rg (倒空间) rg_reciprocal56.32
I(0) (倒空间) i0_reciprocal1431000000.0000
解质量估计 total_estimate0.8502
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary75.9
偏度 Skewness skewness0.349
峰度 Kurtosis kurtosis-0.136
角度范围 angular_range— – 0.1400 −1
当前正则化参数 α current_alpha0.0001
最高正则化参数 α highest_alpha57680000.0000
实空间数据点数 n_real_points29
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.700

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

6. 实体与聚合物信息 Entities & Polymers (6)

7. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_idd1k5da_
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_idd1k5db_
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.55.1.3 — Ran-binding domain
结构域编号 domain_idd1k5dc_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
超家族 Superfamily superfamilyc.10.1 — RNI-like
家族 Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain
结构域编号 domain_idd1k5dd_
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_idd1k5de_
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.55.1.3 — Ran-binding domain
结构域编号 domain_idd1k5df_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
超家族 Superfamily superfamilyc.10.1 — RNI-like
家族 Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain
结构域编号 domain_idd1k5dg_
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_idd1k5dh_
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.55.1.3 — Ran-binding domain
结构域编号 domain_idd1k5di_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
超家族 Superfamily superfamilyc.10.1 — RNI-like
家族 Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain
结构域编号 domain_idd1k5dj_
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_idd1k5dk_
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.55.1.3 — Ran-binding domain
结构域编号 domain_idd1k5dl_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
超家族 Superfamily superfamilyc.10.1 — RNI-like
家族 Family familyc.10.1.2 — Rna1p (RanGAP1), N-terminal domain

CATH v4.4 (12 domains)

结构域编号 domain_id1k5dA00
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_id1k5dB00
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_id1k5dC00
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
同源超家族 H-superfamily homologous superfamily10 — Ribonuclease Inhibitor
结构域编号 domain_id1k5dD00
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_id1k5dE00
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_id1k5dF00
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
同源超家族 H-superfamily homologous superfamily10 — Ribonuclease Inhibitor
结构域编号 domain_id1k5dG00
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_id1k5dH00
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_id1k5dI00
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
同源超家族 H-superfamily homologous superfamily10 — Ribonuclease Inhibitor
结构域编号 domain_id1k5dJ00
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_id1k5dK00
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_id1k5dL00
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
同源超家族 H-superfamily homologous superfamily10 — Ribonuclease Inhibitor

8. 引用文献 (6)

9. 文件与曲线 (10)