4ezm

Crystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23

Method: X-RAY DIFFRACTION Dmax: 182.4 Å Quality: REASONABLE

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

Ig epsilon chain C region

Homo sapiens

UniProt P01854

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 × 4 其他聚合物 2 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 A; UniProt 209–428 链 B; UniProt 209–428 片段:Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Low affinity immunoglobulin epsilon Fc receptor × 2 (P06734) ;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 ; × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K 分辨率 3.10 Å R-free 0.283
2 其他组合 异源复合物 蛋白 × 4 其他聚合物 2 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 C; UniProt 209–428 链 D; UniProt 209–428 片段:Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Low affinity immunoglobulin epsilon Fc receptor × 2 (P06734) ;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 ; × 2 MAN alpha-D-mannopyranose × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K 分辨率 3.10 Å R-free 0.283
3 其他组合 异源复合物 蛋白 × 4 其他聚合物 2 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 E; UniProt 209–428 链 F; UniProt 209–428 片段:Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Low affinity immunoglobulin epsilon Fc receptor × 2 (P06734) ;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 ; × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K 分辨率 3.10 Å R-free 0.283

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 33 个其他 PDB 条目、49 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 IGHE_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 4–223; UniProt 209–428 作者链 B; PDB构建体 4–223; UniProt 209–428 作者链 C; PDB构建体 4–223; UniProt 209–428 作者链 D; PDB构建体 4–223; UniProt 209–428 作者链 E; PDB构建体 4–223; UniProt 209–428 作者链 F; PDB构建体 4–223; UniProt 209–428

Low affinity immunoglobulin epsilon Fc receptor

Homo sapiens

UniProt P06734

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 × 4 其他聚合物 2 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 G; UniProt 156–298 链 H; UniProt 156–298 片段:Human derCD23, UNP residues 156-298 Ig epsilon chain C region × 2 (P01854) ;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 ; × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K 分辨率 3.10 Å R-free 0.283
2 其他组合 异源复合物 蛋白 × 4 其他聚合物 2 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 I; UniProt 156–298 链 J; UniProt 156–298 片段:Human derCD23, UNP residues 156-298 Ig epsilon chain C region × 2 (P01854) ;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 ; × 2 MAN alpha-D-mannopyranose × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K 分辨率 3.10 Å R-free 0.283
3 其他组合 异源复合物 蛋白 × 4 其他聚合物 2 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 K; UniProt 156–298 链 L; UniProt 156–298 片段:Human derCD23, UNP residues 156-298 Ig epsilon chain C region × 2 (P01854) ;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 ; × 2 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 7.5;298 K;3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K 分辨率 3.10 Å R-free 0.283

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 22 个其他 PDB 条目、77 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 FCER2_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 G; PDB构建体 1–143; UniProt 156–298 作者链 H; PDB构建体 1–143; UniProt 156–298 作者链 I; PDB构建体 1–143; UniProt 156–298 作者链 J; PDB构建体 1–143; UniProt 156–298 作者链 K; PDB构建体 1–143; UniProt 156–298 作者链 L; PDB构建体 1–143; UniProt 156–298

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 4ezm

P(r) 距离分布 P(r) Distribution

P(r) distribution for 4ezm
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id4ezm
沉积日期 deposition_date2012-05-03
结构标题 titleCrystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23
关键词 keywordsImmunoglobulin fold Lectin, Antibody Receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
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_guinier54.06
回转半径 Rg (电子) rg_electron53.91
零角强度 I(0) i0854995000.00
分子量 molecular_weight234590.0 kDa
排除体积 excluded_volume290040 ų
包络体积 envelope_volume469390 ų
水化壳体积 shell_volume75212 ų
包络直径 envelope_diameter190.4
壳层 Rg shell_rg54.71
包络 Rg envelope_rg51.90
形状 Rg shape_rg53.90
总 Rg total_rg53.94
总原子数 total_atoms16492
残基数 n_residues2022
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 dmax182.4
Rg (实空间) rg_real54.02
Rg 误差 (实空间) rg_real_error1.98
I(0) (实空间) i0_real8.5500e+08
I(0) 误差 (实空间) i0_real_error2.0560e+07
Rg (倒空间) rg_reciprocal54.08
I(0) (倒空间) i0_reciprocal855100000.0000
解质量估计 total_estimate0.6474
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary69.2
偏度 Skewness skewness0.239
峰度 Kurtosis kurtosis-0.334
角度范围 angular_range— – 0.1450 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha26030000.0000
实空间数据点数 n_real_points30
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.997; Smooth: 0.774

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) 36 domains

SCOP 2.08 (18 domains)

结构域编号 domain_idd4ezma1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezma2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmb2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmc1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmc2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmd1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmd2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezme1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezme2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmf1
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmf2
类 Class classb — All beta proteins
折叠类型 Fold foldb.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamilyb.1.1 — Immunoglobulin
家族 Family familyb.1.1.0 — automated matches
结构域编号 domain_idd4ezmg_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.169 — C-type lectin-like
超家族 Superfamily superfamilyd.169.1 — C-type lectin-like
家族 Family familyd.169.1.1 — C-type lectin domain
结构域编号 domain_idd4ezmh_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.169 — C-type lectin-like
超家族 Superfamily superfamilyd.169.1 — C-type lectin-like
家族 Family familyd.169.1.1 — C-type lectin domain
结构域编号 domain_idd4ezmi_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.169 — C-type lectin-like
超家族 Superfamily superfamilyd.169.1 — C-type lectin-like
家族 Family familyd.169.1.1 — C-type lectin domain
结构域编号 domain_idd4ezmj_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.169 — C-type lectin-like
超家族 Superfamily superfamilyd.169.1 — C-type lectin-like
家族 Family familyd.169.1.1 — C-type lectin domain
结构域编号 domain_idd4ezmk_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.169 — C-type lectin-like
超家族 Superfamily superfamilyd.169.1 — C-type lectin-like
家族 Family familyd.169.1.1 — C-type lectin domain
结构域编号 domain_idd4ezml_
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.169 — C-type lectin-like
超家族 Superfamily superfamilyd.169.1 — C-type lectin-like
家族 Family familyd.169.1.1 — C-type lectin domain

CATH v4.4 (18 domains)

结构域编号 domain_id4ezmA01
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_id4ezmA02
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_id4ezmB01
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_id4ezmB02
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_id4ezmC01
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_id4ezmC02
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_id4ezmD01
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_id4ezmD02
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_id4ezmE01
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_id4ezmE02
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_id4ezmF01
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_id4ezmF02
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_id4ezmG01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4ezmH01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4ezmI01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4ezmJ01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4ezmK01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
结构域编号 domain_id4ezmL01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology100 — Mannose-Binding Protein A; Chain A
同源超家族 H-superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A

8. 引用文献 (1)

9. 文件与曲线 (10)