3j8f

Cryo-EM reconstruction of poliovirus-receptor complex

Method: ELECTRON MICROSCOPY Dmax: 156.0 Å Quality: REASONABLE

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

Capsid protein VP1

物种未注明

UniProt P03300

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 × 300 其他聚合物 360 PDB 声明:300-meric(300) 与蛋白拷贝数一致 链 1; UniProt 580–881 链 2; UniProt 70–341 链 3; UniProt 342–579 链 4; UniProt 2–69 片段:UNP residues 580-881 片段:UNP residues 70-341 片段:UNP residues 342-579 片段:UNP residues 2-69 非标准单体:是(mmCIF未提供具体位点) Poliovirus receptor × 60 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 60 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 Å
2 其他组合 异源复合物 蛋白 × 5 其他聚合物 6 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 1; UniProt 580–881 链 2; UniProt 70–341 链 3; UniProt 342–579 链 4; UniProt 2–69 片段:UNP residues 580-881 片段:UNP residues 70-341 片段:UNP residues 342-579 片段:UNP residues 2-69 非标准单体:是(mmCIF未提供具体位点) Poliovirus receptor × 1 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]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 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 Å
3 其他组合 异源复合物 蛋白 × 25 其他聚合物 30 PDB 声明:25-meric(25) 与蛋白拷贝数一致 链 1; UniProt 580–881 链 2; UniProt 70–341 链 3; UniProt 342–579 链 4; UniProt 2–69 片段:UNP residues 580-881 片段:UNP residues 70-341 片段:UNP residues 342-579 片段:UNP residues 2-69 非标准单体:是(mmCIF未提供具体位点) Poliovirus receptor × 5 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 Å
4 其他组合 异源复合物 蛋白 × 30 其他聚合物 36 PDB 声明:30-meric(30) 与蛋白拷贝数一致 链 1; UniProt 580–881 链 2; UniProt 70–341 链 3; UniProt 342–579 链 4; UniProt 2–69 片段:UNP residues 580-881 片段:UNP residues 70-341 片段:UNP residues 342-579 片段:UNP residues 2-69 非标准单体:是(mmCIF未提供具体位点) Poliovirus receptor × 6 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 Å
5 其他组合 异源复合物 蛋白 × 5 其他聚合物 6 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 1; UniProt 580–881 链 2; UniProt 70–341 链 3; UniProt 342–579 链 4; UniProt 2–69 片段:UNP residues 580-881 片段:UNP residues 70-341 片段:UNP residues 342-579 片段:UNP residues 2-69 非标准单体:是(mmCIF未提供具体位点) Poliovirus receptor × 1 (P15151) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]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 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 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 80 个其他 PDB 条目、246 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 POLG_POL1M
Isoform
PDB实体 1, 2, 3, 4
链与序列区间 作者链 1; PDB构建体 1–302; UniProt 580–881 作者链 2; PDB构建体 1–272; UniProt 70–341 作者链 3; PDB构建体 1–238; UniProt 342–579 作者链 4; PDB构建体 2–69; UniProt 2–69

Poliovirus receptor

Homo sapiens

UniProt P15151

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 × 300 其他聚合物 360 PDB 声明:300-meric(300) 与蛋白拷贝数一致 链 7; UniProt 1–417 未记录 Capsid protein VP1 × 60 (P03300) Capsid protein VP2 × 60 (P03300) Capsid protein VP3 × 60 (P03300) Capsid protein VP4 × 60 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 60 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 120 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 Å
2 其他组合 异源复合物 蛋白 × 5 其他聚合物 6 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 7; UniProt 1–417 未记录 Capsid protein VP1 × 1 (P03300) Capsid protein VP2 × 1 (P03300) Capsid protein VP3 × 1 (P03300) Capsid protein VP4 × 1 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]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 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 Å
3 其他组合 异源复合物 蛋白 × 25 其他聚合物 30 PDB 声明:25-meric(25) 与蛋白拷贝数一致 链 7; UniProt 1–417 未记录 Capsid protein VP1 × 5 (P03300) Capsid protein VP2 × 5 (P03300) Capsid protein VP3 × 5 (P03300) Capsid protein VP4 × 5 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 Å
4 其他组合 异源复合物 蛋白 × 30 其他聚合物 36 PDB 声明:30-meric(30) 与蛋白拷贝数一致 链 7; UniProt 1–417 未记录 Capsid protein VP1 × 6 (P03300) Capsid protein VP2 × 6 (P03300) Capsid protein VP3 × 6 (P03300) Capsid protein VP4 × 6 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 Å
5 其他组合 异源复合物 蛋白 × 5 其他聚合物 6 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 7; UniProt 1–417 未记录 Capsid protein VP1 × 1 (P03300) Capsid protein VP2 × 1 (P03300) Capsid protein VP3 × 1 (P03300) Capsid protein VP4 × 1 (P03300) beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]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 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM缓冲液:PBS;pH 7;PBS cryo-EM玻璃化条件:Sample mixed and frozen within 2 minutes.;120 K;冷冻剂 ETHANE;Sample mixed and frozen within 2 minutes before plunging into liquid ethane. 分辨率 3.70 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 12 个其他 PDB 条目、37 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 PVR_HUMAN
Isoform
PDB实体 5
链与序列区间 作者链 7; PDB构建体 1–417; UniProt 1–417

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 3j8f

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3j8f
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3j8f
沉积日期 deposition_date2014-10-20
结构标题 titleCryo-EM reconstruction of poliovirus-receptor complex
关键词 keywordspoliovirus, receptor, PVR, CD155, VIRUS-SIGNALING PROTEIN complex; VIRUS/SIGNALING 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_guinier41.33
回转半径 Rg (电子) rg_electron41.99
零角强度 I(0) i0267914000.00
分子量 molecular_weight131720.0 kDa
排除体积 excluded_volume164550 ų
包络体积 envelope_volume235820 ų
水化壳体积 shell_volume50826 ų
包络直径 envelope_diameter166.6
壳层 Rg shell_rg42.61
包络 Rg envelope_rg44.83
形状 Rg shape_rg41.96
总 Rg total_rg42.11
总原子数 total_atoms9263
残基数 n_residues1159
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 dmax156.0
Rg (实空间) rg_real42.08
Rg 误差 (实空间) rg_real_error1.98
I(0) (实空间) i0_real2.6790e+08
I(0) 误差 (实空间) i0_real_error5.1560e+06
Rg (倒空间) rg_reciprocal41.34
I(0) (倒空间) i0_reciprocal267700000.0000
解质量估计 total_estimate0.7286
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary41.0
偏度 Skewness skewness0.936
峰度 Kurtosis kurtosis0.558
角度范围 angular_range— – 0.1900 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha25210000.0000
实空间数据点数 n_real_points39
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.347; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.774; Smooth: 0.653

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

6. 实体与聚合物信息 Entities & Polymers (10)

7. 折叠分类 (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

结构域编号 domain_id3j8f100
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id3j8f200
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id3j8f300
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id3j8f400
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology80 — Rhinovirus 14, subunit 4
同源超家族 H-superfamily homologous superfamily10 — Picornavirus coat protein VP4
结构域编号 domain_id3j8f701
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
结构域编号 domain_id3j8f702
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
结构域编号 domain_id3j8f703
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)