1d3i

CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 14 (HRV14) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY

Method: ELECTRON MICROSCOPY Dmax: 114.1 Å Quality: GOOD

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

PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)

物种未注明

UniProt P05362

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 × 300 PDB 声明:300-MERIC(300) 与蛋白拷贝数一致 链 I; UniProt 28–212 片段:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 60 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 60 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 60 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 60 (P03303) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 Å
2 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 I; UniProt 28–212 片段:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 1 (P03303) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 Å
3 蛋白异源复合物 异源复合物 蛋白 × 25 PDB 声明:25-meric(25) 与蛋白拷贝数一致 链 I; UniProt 28–212 片段:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 5 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 5 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 5 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 5 (P03303) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 Å
4 蛋白异源复合物 异源复合物 蛋白 × 30 PDB 声明:30-meric(30) 与蛋白拷贝数一致 链 I; UniProt 28–212 片段:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 6 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 6 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 6 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 6 (P03303) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 Å
5 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 I; UniProt 28–212 片段:FIRST TWO DOMAINS, RESIDUES 1-185 PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3) × 1 (P03303) PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4) × 1 (P03303) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 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、36 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 ICAM1_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 I; PDB构建体 1–185; UniProt 28–212

PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1)

物种未注明

UniProt P03303

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 × 300 PDB 声明:300-MERIC(300) 与蛋白拷贝数一致 链 1; UniProt 567–855 链 2; UniProt 69–330 链 3; UniProt 331–566 链 4; UniProt 1–68 未记录 PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 60 (P05362) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 Å
2 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 1; UniProt 567–855 链 2; UniProt 69–330 链 3; UniProt 331–566 链 4; UniProt 1–68 未记录 PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 1 (P05362) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 Å
3 蛋白异源复合物 异源复合物 蛋白 × 25 PDB 声明:25-meric(25) 与蛋白拷贝数一致 链 1; UniProt 567–855 链 2; UniProt 69–330 链 3; UniProt 331–566 链 4; UniProt 1–68 未记录 PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 5 (P05362) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 Å
4 蛋白异源复合物 异源复合物 蛋白 × 30 PDB 声明:30-meric(30) 与蛋白拷贝数一致 链 1; UniProt 567–855 链 2; UniProt 69–330 链 3; UniProt 331–566 链 4; UniProt 1–68 未记录 PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 6 (P05362) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 Å
5 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 1; UniProt 567–855 链 2; UniProt 69–330 链 3; UniProt 331–566 链 4; UniProt 1–68 未记录 PROTEIN (INTERCELLULAR ADHESION MOLECULE-1) × 1 (P05362) ELECTRON MICROSCOPY cryo-EM缓冲液:pH 7.5 cryo-EM玻璃化条件:HRV14 WAS INCUBATED WITH D1D2-ICAM-1 FOR 30 MINUTES AT 4 DEGREES CELSIUS (277 KELVIN) USING AN EIGHT-FOLD EXCESS OF D1D2-ICAM-1 FOR EACH OF THE SIXTY POSSIBLE BINDING SITES PER VIRION. AFTER INCUBATION, SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER. 分辨率 26.00 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 58 个其他 PDB 条目、236 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_HRV14
Isoform
PDB实体 2, 3, 4, 5
链与序列区间 作者链 1; PDB构建体 1–289; UniProt 567–855 作者链 2; PDB构建体 1–262; UniProt 69–330 作者链 3; PDB构建体 1–236; UniProt 331–566 作者链 4; PDB构建体 1–68; UniProt 1–68

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 1d3i

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1d3i
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1d3i
沉积日期 deposition_date1999-09-29
结构标题 titleCRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 14 (HRV14) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY
关键词 keywords;HUMAN RHINOVIRUS, HRV14, ICAM-1, FITTING OF X-RAY STRUCTURES INTO CRYO-EM RECONSTRUCTIONS, COMMON COLD, VIRUS UNCOATING, VIRUS/ VIRAL PROTEIN, RHINOVIRUS-RECEPTOR COMPLEX, Icosahedral virus, Virus-Receptor COMPLEX ;; Virus/Receptor
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_guinier33.90
回转半径 Rg (电子) rg_electron33.49
零角强度 I(0) i0182260000.00
分子量 molecular_weight109410.0 kDa
排除体积 excluded_volume133650 ų
包络体积 envelope_volume118210 ų
水化壳体积 shell_volume33103 ų
包络直径 envelope_diameter123.2
壳层 Rg shell_rg35.89
包络 Rg envelope_rg31.88
形状 Rg shape_rg33.47
总 Rg total_rg33.64
总原子数 total_atoms
残基数 n_residues
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 dmax114.1
Rg (实空间) rg_real33.94
Rg 误差 (实空间) rg_real_error0.87
I(0) (实空间) i0_real1.8230e+08
I(0) 误差 (实空间) i0_real_error2.9940e+06
Rg (倒空间) rg_reciprocal33.92
I(0) (倒空间) i0_reciprocal182300000.0000
解质量估计 total_estimate0.8823
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary36.4
偏度 Skewness skewness0.378
峰度 Kurtosis kurtosis-0.368
角度范围 angular_range— – 0.2350 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha19970000.0000
实空间数据点数 n_real_points48
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: 0.949; Smooth: 0.941

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

6. 实体与聚合物信息 Entities & Polymers (5)

7. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (5 domains)

结构域编号 domain_idd1d3i1_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
家族 Family familyi.6.1.1 — Viruses and virus-receptor complexes
结构域编号 domain_idd1d3i2_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
家族 Family familyi.6.1.1 — Viruses and virus-receptor complexes
结构域编号 domain_idd1d3i3_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
家族 Family familyi.6.1.1 — Viruses and virus-receptor complexes
结构域编号 domain_idd1d3i4_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
家族 Family familyi.6.1.1 — Viruses and virus-receptor complexes
结构域编号 domain_idd1d3ii_
类 Class classi — Low resolution protein structures
折叠类型 Fold foldi.6 — Viruses and virus-receptor complexes
超家族 Superfamily superfamilyi.6.1 — Viruses and virus-receptor complexes
家族 Family familyi.6.1.1 — Viruses and virus-receptor complexes

8. 引用文献 (6)

9. 文件与曲线 (10)