7qne

Cryo-EM structure of human full-length synaptic alpha1beta3gamma2 GABA(A)R in complex with Ro15-4513 and megabody Mb38

Method: ELECTRON MICROSCOPY Dmax: 129.3 Å Quality: GOOD

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

GABA(A) receptor subunit alpha-1

Homo sapiens

UniProt A0A1B0GV38

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 其他组合 异源复合物 蛋白 × 6 其他聚合物 6 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 A; UniProt 16–471 链 D; UniProt 16–471 未记录 Gamma-aminobutyric acid receptor subunit beta-3 × 2 (P28472) GABA(A) receptor subunit gamma-2 × 1 (A0A286YFI6) Megabody Mb38 × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 OCT N-OCTANE × 1 D10 DECANE × 4 CL CHLORIDE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EIE ethyl 8-[(azanylidene-$l^{4}-azanylidene)amino]-5-methyl-6-oxidanylidene-4~{H}-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.6 cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 2.70 Å

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。

数据库中没有找到同一 UniProt 蛋白的其他 PDB 条目。

查看构建体与数据证据
UniProt名称 A0A1B0GV38_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–456; UniProt 16–471 作者链 D; PDB构建体 1–456; UniProt 16–471

Gamma-aminobutyric acid receptor subunit beta-3

Homo sapiens

UniProt P28472

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 其他组合 异源复合物 蛋白 × 6 其他聚合物 6 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 B; UniProt 1–473 链 E; UniProt 1–473 未记录 GABA(A) receptor subunit alpha-1 × 2 (A0A1B0GV38) GABA(A) receptor subunit gamma-2 × 1 (A0A286YFI6) Megabody Mb38 × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 OCT N-OCTANE × 1 D10 DECANE × 4 CL CHLORIDE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EIE ethyl 8-[(azanylidene-$l^{4}-azanylidene)amino]-5-methyl-6-oxidanylidene-4~{H}-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.6 cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 2.70 Å

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 94 个其他 PDB 条目、94 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 GBRB3_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–473; UniProt 1–473 作者链 E; PDB构建体 1–473; UniProt 1–473

GABA(A) receptor subunit gamma-2

Homo sapiens

UniProt A0A286YFI6

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 其他组合 异源复合物 蛋白 × 6 其他聚合物 6 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 C; UniProt 1–498 未记录 GABA(A) receptor subunit alpha-1 × 2 (A0A1B0GV38) Gamma-aminobutyric acid receptor subunit beta-3 × 2 (P28472) Megabody Mb38 × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 2 OCT N-OCTANE × 1 D10 DECANE × 4 CL CHLORIDE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EIE ethyl 8-[(azanylidene-$l^{4}-azanylidene)amino]-5-methyl-6-oxidanylidene-4~{H}-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate × 1 ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.6 cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 2.70 Å

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。

数据库中没有找到同一 UniProt 蛋白的其他 PDB 条目。

查看构建体与数据证据
UniProt名称 A0A286YFI6_HUMAN
Isoform
PDB实体 3
链与序列区间 作者链 C; PDB构建体 1–475; UniProt 1–498

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 7qne

P(r) 距离分布 P(r) Distribution

P(r) distribution for 7qne
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id7qne
沉积日期 deposition_date2021-12-20
结构标题 titleCryo-EM structure of human full-length synaptic alpha1beta3gamma2 GABA(A)R in complex with Ro15-4513 and megabody Mb38
关键词 keywordspentameric ligand-gated ion channel, neurotransmitter receptor, GABA receptor, MEMBRANE PROTEIN; MEMBRANE PROTEIN
实验方法 methodELECTRON MICROSCOPY

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

回转半径 Rg (Guinier) rg_guinier39.50
回转半径 Rg (电子) rg_electron38.98
零角强度 I(0) i0639270000.00
分子量 molecular_weight216730.0 kDa
排除体积 excluded_volume274900 ų
包络体积 envelope_volume344210 ų
水化壳体积 shell_volume71613 ų
包络直径 envelope_diameter130.1
壳层 Rg shell_rg46.36
包络 Rg envelope_rg38.76
形状 Rg shape_rg38.98
总 Rg total_rg39.36
总原子数 total_atoms15265
残基数 n_residues1808
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 dmax129.3
Rg (实空间) rg_real39.39
Rg 误差 (实空间) rg_real_error0.78
I(0) (实空间) i0_real6.3930e+08
I(0) 误差 (实空间) i0_real_error1.0570e+07
Rg (倒空间) rg_reciprocal39.47
I(0) (倒空间) i0_reciprocal639300000.0000
解质量估计 total_estimate0.8821
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary48.5
偏度 Skewness skewness0.302
峰度 Kurtosis kurtosis-0.351
角度范围 angular_range— – 0.2000 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha117300000.0000
实空间数据点数 n_real_points41
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.891

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

6. 实体与聚合物信息 Entities & Polymers (14)

7. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id7qneG01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily10 — Immunoglobulins

8. 引用文献 (1)

9. 文件与曲线 (10)