3fcs

Structure of complete ectodomain of integrin aIIBb3

Method: X-RAY DIFFRACTION Dmax: 217.8 Å Quality: REASONABLE

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

Integrin, alpha 2b

Homo sapiens

UniProt Q17R67

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 × 2 其他聚合物 5 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 32–989 片段:UNP residues 32-989, Ectodomain Integrin beta-3 × 1 (P05106) 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 IMD IMIDAZOLE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7;298 K;10% PEG 3350, 50 mM magnesium acetate, and 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, temperature 298.0K 分辨率 2.55 Å R-free 0.268
2 其他组合 异源复合物 蛋白 × 2 其他聚合物 5 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 C; UniProt 32–989 片段:UNP residues 32-989, Ectodomain Integrin beta-3 × 1 (P05106) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 IMD IMIDAZOLE × 5 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7;298 K;10% PEG 3350, 50 mM magnesium acetate, and 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, temperature 298.0K 分辨率 2.55 Å R-free 0.268

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 1 个其他 PDB 条目、3 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 Q17R67_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–958; UniProt 32–989 作者链 C; PDB构建体 1–958; UniProt 32–989

Integrin beta-3

Homo sapiens

UniProt P05106

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 × 2 其他聚合物 5 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 B; UniProt 27–716 片段:UNP residues 27-716, Extracellular domain 突变:P688C Integrin, alpha 2b × 1 (Q17R67) 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 IMD IMIDAZOLE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7;298 K;10% PEG 3350, 50 mM magnesium acetate, and 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, temperature 298.0K 分辨率 2.55 Å R-free 0.268
2 其他组合 异源复合物 蛋白 × 2 其他聚合物 5 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 D; UniProt 27–716 片段:UNP residues 27-716, Extracellular domain 突变:P688C Integrin, alpha 2b × 1 (Q17R67) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 IMD IMIDAZOLE × 5 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7;298 K;10% PEG 3350, 50 mM magnesium acetate, and 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, temperature 298.0K 分辨率 2.55 Å R-free 0.268

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 124 个其他 PDB 条目、175 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 ITB3_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–690; UniProt 27–716 作者链 D; PDB构建体 1–690; UniProt 27–716

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 3fcs

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id3fcs
沉积日期 deposition_date2008-11-22
结构标题 titleStructure of complete ectodomain of integrin aIIBb3
关键词 keywords;beta propeller, rossmann fold, egf domain, Cell adhesion, Disease mutation, Glycoprotein, Host-virus interaction, Integrin, Membrane, Phosphoprotein, Receptor, Transmembrane, Cell Adhesion-immune System COMPLEX, Cell Adhesion-BLOOD CLOTTING COMPLEX ;; Cell Adhesion/BLOOD CLOTTING
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_guinier75.13
回转半径 Rg (电子) rg_electron76.72
零角强度 I(0) i01786420000.00
分子量 molecular_weight345010.0 kDa
排除体积 excluded_volume426720 ų
包络体积 envelope_volume688340 ų
水化壳体积 shell_volume80390 ų
包络直径 envelope_diameter242.1
壳层 Rg shell_rg62.67
包络 Rg envelope_rg74.04
形状 Rg shape_rg76.82
总 Rg total_rg76.18
总原子数 total_atoms24113
残基数 n_residues3098
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 dmax217.8
Rg (实空间) rg_real75.70
Rg 误差 (实空间) rg_real_error1.61
I(0) (实空间) i0_real1.7850e+09
I(0) 误差 (实空间) i0_real_error3.8490e+07
Rg (倒空间) rg_reciprocal72.21
I(0) (倒空间) i0_reciprocal1773000000.0000
解质量估计 total_estimate0.7176
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks3
主峰位置 r_peak_primary51.9
偏度 Skewness skewness0.412
峰度 Kurtosis kurtosis-0.986
角度范围 angular_range— – 0.1050 −1
当前正则化参数 α current_alpha0.0014
最高正则化参数 α highest_alpha102200000.0000
实空间数据点数 n_real_points22
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.545; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.696; Smooth: 0.000

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

6. 实体与聚合物信息 Entities & Polymers (11)

7. 折叠分类 (SCOP + CATH) 19 domains

CATH v4.4 (19 domains)

结构域编号 domain_id3fcsA01
类 Class class2 — Mainly Beta
架构 Architecture architecture130 — 7 Propeller
拓扑 Topology topology10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily130 — Integrin alpha, N-terminal
结构域编号 domain_id3fcsA02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1460 — Integrin domains. Chain A, domain 2
结构域编号 domain_id3fcsA03
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1510 — ntegrin, alpha v. Chain A, domain 3
结构域编号 domain_id3fcsA04
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1530 — ntegrin, alpha v. Chain A, domain 4
结构域编号 domain_id3fcsB02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1510 — ntegrin, alpha v. Chain A, domain 3
结构域编号 domain_id3fcsB03
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily410 — von Willebrand factor, type A domain
结构域编号 domain_id3fcsB04
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology25 — Laminin
同源超家族 H-superfamily homologous superfamily10 — Laminin
结构域编号 domain_id3fcsB05
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology25 — Laminin
同源超家族 H-superfamily homologous superfamily10 — Laminin
结构域编号 domain_id3fcsB06
类 Class class4 — Few Secondary Structures
架构 Architecture architecture10 — Irregular
拓扑 Topology topology1240 — Hormone receptor fold
同源超家族 H-superfamily homologous superfamily30
结构域编号 domain_id3fcsC01
类 Class class2 — Mainly Beta
架构 Architecture architecture130 — 7 Propeller
拓扑 Topology topology10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily130 — Integrin alpha, N-terminal
结构域编号 domain_id3fcsC02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1460 — Integrin domains. Chain A, domain 2
结构域编号 domain_id3fcsC03
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1510 — ntegrin, alpha v. Chain A, domain 3
结构域编号 domain_id3fcsC04
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1530 — ntegrin, alpha v. Chain A, domain 4
结构域编号 domain_id3fcsD01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology1680 — ligand-binding face of the semaphorins, domain 2
同源超家族 H-superfamily homologous superfamily10 — ligand-binding face of the semaphorins, domain 2
结构域编号 domain_id3fcsD02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1510 — ntegrin, alpha v. Chain A, domain 3
结构域编号 domain_id3fcsD03
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily410 — von Willebrand factor, type A domain
结构域编号 domain_id3fcsD04
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology25 — Laminin
同源超家族 H-superfamily homologous superfamily10 — Laminin
结构域编号 domain_id3fcsD05
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology25 — Laminin
同源超家族 H-superfamily homologous superfamily10 — Laminin
结构域编号 domain_id3fcsD06
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology25 — Laminin
同源超家族 H-superfamily homologous superfamily10 — Laminin

8. 引用文献 (1)

9. 文件与曲线 (10)