3j9f

Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C

Method: ELECTRON MICROSCOPY Dmax: 154.3 Å Quality: REASONABLE

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

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 × 420 其他聚合物 360 PDB 声明:420-meric(420) 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) Poliovirus receptor × 60 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 Å
2 其他组合 异源复合物 蛋白 × 7 其他聚合物 6 PDB 声明:heptameric(7) 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) Poliovirus receptor × 1 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 Å
3 其他组合 异源复合物 蛋白 × 35 其他聚合物 30 PDB 声明:35-meric(35) 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) Poliovirus receptor × 5 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 Å
4 其他组合 异源复合物 蛋白 × 42 其他聚合物 36 PDB 声明:42-meric(42) 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) Poliovirus receptor × 6 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 Å
5 其他组合 异源复合物 蛋白 × 7 其他聚合物 6 PDB 声明:heptameric(7) 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) Poliovirus receptor × 1 (P15151) 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 ;alpha-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 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 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

物种未注明

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 × 420 其他聚合物 360 PDB 声明:420-meric(420) 与蛋白拷贝数一致 链 7; UniProt 28–143 链 8; UniProt 142–243 链 9; UniProt 242–333 片段:SEE REMARK 999 Protein VP1 × 60 (P03300) Protein VP2 × 60 (P03300) Protein VP3 × 60 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 Å
2 其他组合 异源复合物 蛋白 × 7 其他聚合物 6 PDB 声明:heptameric(7) 与蛋白拷贝数一致 链 7; UniProt 28–143 链 8; UniProt 142–243 链 9; UniProt 242–333 片段:SEE REMARK 999 Protein VP1 × 1 (P03300) Protein VP2 × 1 (P03300) Protein VP3 × 1 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 Å
3 其他组合 异源复合物 蛋白 × 35 其他聚合物 30 PDB 声明:35-meric(35) 与蛋白拷贝数一致 链 7; UniProt 28–143 链 8; UniProt 142–243 链 9; UniProt 242–333 片段:SEE REMARK 999 Protein VP1 × 5 (P03300) Protein VP2 × 5 (P03300) Protein VP3 × 5 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 Å
4 其他组合 异源复合物 蛋白 × 42 其他聚合物 36 PDB 声明:42-meric(42) 与蛋白拷贝数一致 链 7; UniProt 28–143 链 8; UniProt 142–243 链 9; UniProt 242–333 片段:SEE REMARK 999 Protein VP1 × 6 (P03300) Protein VP2 × 6 (P03300) Protein VP3 × 6 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 Å
5 其他组合 异源复合物 蛋白 × 7 其他聚合物 6 PDB 声明:heptameric(7) 与蛋白拷贝数一致 链 7; UniProt 28–143 链 8; UniProt 142–243 链 9; UniProt 242–333 片段:SEE REMARK 999 Protein VP1 × 1 (P03300) Protein VP2 × 1 (P03300) Protein VP3 × 1 (P03300) 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 ;alpha-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 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM玻璃化条件:冷冻剂 ETHANE 分辨率 9.00 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, 6, 7
链与序列区间 作者链 7; PDB构建体 1–116; UniProt 28–143 作者链 8; PDB构建体 1–102; UniProt 142–243 作者链 9; PDB构建体 1–92; UniProt 242–333

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 3j9f

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3j9f
下载 Download

2. 结构基本信息 2. Structure Basics

条目编号 entry_id3j9f
沉积日期 deposition_date2015-01-15
结构标题 titlePoliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C
关键词 keywordsdeglycosylated receptor, picornavirus, PVR, CD155, enterovirus, cell entry, VIRUS-CELL ADHESION complex; VIRUS/CELL ADHESION
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_guinier40.59
回转半径 Rg (电子) rg_electron41.12
零角强度 I(0) i0267979000.00
分子量 molecular_weight131980.0 kDa
排除体积 excluded_volume165000 ų
包络体积 envelope_volume229830 ų
水化壳体积 shell_volume50332 ų
包络直径 envelope_diameter165.5
壳层 Rg shell_rg42.22
包络 Rg envelope_rg43.71
形状 Rg shape_rg41.09
总 Rg total_rg41.27
总原子数 total_atoms9281
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 dmax154.3
Rg (实空间) rg_real41.26
Rg 误差 (实空间) rg_real_error1.77
I(0) (实空间) i0_real2.6800e+08
I(0) 误差 (实空间) i0_real_error5.1500e+06
Rg (倒空间) rg_reciprocal40.60
I(0) (倒空间) i0_reciprocal267800000.0000
解质量估计 total_estimate0.7188
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary43.5
偏度 Skewness skewness0.928
峰度 Kurtosis kurtosis0.585
角度范围 angular_range— – 0.1950 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha25350000.0000
实空间数据点数 n_real_points40
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.344; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.538; Smooth: 0.770

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

6. 实体与聚合物信息 Entities & Polymers (13)

8. 引用文献 (1)

9. 文件与曲线 (10)