6hjz

Xray structure of GLIC in complex with succinate

Method: X-RAY DIFFRACTION Dmax: 209.6 Å Quality: REASONABLE

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

Proton-gated ion channel

Gloeobacter violaceus (strain PCC 7421)

UniProt Q7NDN8

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 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 A; UniProt 43–359 链 B; UniProt 43–359 链 C; UniProt 43–359 链 D; UniProt 43–359 链 E; UniProt 43–359 未记录 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 15 CL CHLORIDE ION × 7 NA SODIUM ION × 6 LMT DODECYL-BETA-D-MALTOSIDE × 6 SIN SUCCINIC ACID × 10 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;293 K;100 mM NaSuccinate pH4 400 mM NaIsothiocynate 12-15% PEG4000 2% DMSO 15% glycerol 分辨率 2.50 Å R-free 0.227
2 蛋白同源多聚体 同源多聚体 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 F; UniProt 43–359 链 G; UniProt 43–359 链 H; UniProt 43–359 链 I; UniProt 43–359 链 J; UniProt 43–359 未记录 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 15 CL CHLORIDE ION × 7 NA SODIUM ION × 6 LMT DODECYL-BETA-D-MALTOSIDE × 6 SIN SUCCINIC ACID × 10 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;293 K;100 mM NaSuccinate pH4 400 mM NaIsothiocynate 12-15% PEG4000 2% DMSO 15% glycerol 分辨率 2.50 Å R-free 0.227

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 129 个其他 PDB 条目、134 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 GLIC_GLOVI
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–317; UniProt 43–359 作者链 B; PDB构建体 1–317; UniProt 43–359 作者链 C; PDB构建体 1–317; UniProt 43–359 作者链 D; PDB构建体 1–317; UniProt 43–359 作者链 E; PDB构建体 1–317; UniProt 43–359 作者链 F; PDB构建体 1–317; UniProt 43–359 作者链 G; PDB构建体 1–317; UniProt 43–359 作者链 H; PDB构建体 1–317; UniProt 43–359 作者链 I; PDB构建体 1–317; UniProt 43–359 作者链 J; PDB构建体 1–317; UniProt 43–359

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 6hjz

P(r) 距离分布 P(r) Distribution

P(r) distribution for 6hjz
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id6hjz
沉积日期 deposition_date2018-09-04
结构标题 titleXray structure of GLIC in complex with succinate
关键词 keywordsPentameric Ligand-Gated Ion channel, MEMBRANE PROTEIN; MEMBRANE 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_guinier69.87
回转半径 Rg (电子) rg_electron68.74
零角强度 I(0) i01521400000.00
分子量 molecular_weight371150.0 kDa
排除体积 excluded_volume481520 ų
包络体积 envelope_volume639770 ų
水化壳体积 shell_volume85694 ų
包络直径 envelope_diameter237.1
壳层 Rg shell_rg55.67
包络 Rg envelope_rg68.86
形状 Rg shape_rg68.71
总 Rg total_rg68.54
总原子数 total_atoms26280
残基数 n_residues3110
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 dmax209.6
Rg (实空间) rg_real70.37
Rg 误差 (实空间) rg_real_error1.61
I(0) (实空间) i0_real1.5200e+09
I(0) 误差 (实空间) i0_real_error3.1340e+07
Rg (倒空间) rg_reciprocal67.29
I(0) (倒空间) i0_reciprocal1512000000.0000
解质量估计 total_estimate0.6979
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks3
主峰位置 r_peak_primary47.6
偏度 Skewness skewness0.513
峰度 Kurtosis kurtosis-0.829
角度范围 angular_range— – 0.1100 −1
当前正则化参数 α current_alpha0.0032
最高正则化参数 α highest_alpha380000000.0000
实空间数据点数 n_real_points23
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.434; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.004

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

6. 实体与聚合物信息 Entities & Polymers (7)

7. 折叠分类 (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

结构域编号 domain_id6hjzA01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzA02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzB01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzB02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzC01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzC02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzD01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzD02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzE01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzE02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzF01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzF02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzG01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzG02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzH01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzH02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzI01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzI02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjzJ01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjzJ02
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 superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain

8. 引用文献 (1)

9. 文件与曲线 (10)