5wb7

Crystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin

Method: X-RAY DIFFRACTION Dmax: 170.5 Å Quality: GOOD

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

Epidermal growth factor receptor

Homo sapiens

UniProt P00533

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 3 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 A; UniProt 25–525 链 D; UniProt 25–525 未记录 Proepiregulin × 2 (O14944) ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.6;294 K;0.03 M citric acid, 0.07 M Bis-Tris propane, 16% PEG3350 分辨率 2.94 Å R-free 0.268
2 其他组合 异源复合物 蛋白 × 4 其他聚合物 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 B; UniProt 25–525 链 C; UniProt 25–525 未记录 Proepiregulin × 2 (O14944) ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[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 ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.6;294 K;0.03 M citric acid, 0.07 M Bis-Tris propane, 16% PEG3350 分辨率 2.94 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 383 个其他 PDB 条目、564 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 EGFR_HUMAN
Isoform P00533-4
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–501; UniProt 25–525 作者链 B; PDB构建体 1–501; UniProt 25–525 作者链 C; PDB构建体 1–501; UniProt 25–525 作者链 D; PDB构建体 1–501; UniProt 25–525

Proepiregulin

Homo sapiens

UniProt O14944

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 3 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 E; UniProt 56–116 链 H; UniProt 56–116 未记录 Epidermal growth factor receptor × 2 (P00533) ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.6;294 K;0.03 M citric acid, 0.07 M Bis-Tris propane, 16% PEG3350 分辨率 2.94 Å R-free 0.268
2 其他组合 异源复合物 蛋白 × 4 其他聚合物 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 F; UniProt 56–116 链 G; UniProt 56–116 未记录 Epidermal growth factor receptor × 2 (P00533) ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[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 ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.6;294 K;0.03 M citric acid, 0.07 M Bis-Tris propane, 16% PEG3350 分辨率 2.94 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 7 个其他 PDB 条目、13 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 EREG_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 E; PDB构建体 2–62; UniProt 56–116 作者链 F; PDB构建体 2–62; UniProt 56–116 作者链 G; PDB构建体 2–62; UniProt 56–116 作者链 H; PDB构建体 2–62; UniProt 56–116

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 5wb7

P(r) 距离分布 P(r) Distribution

P(r) distribution for 5wb7
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id5wb7
沉积日期 deposition_date2017-06-28
结构标题 titleCrystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin
关键词 keywordsReceptor tyrosine kinase, growth factor, signaling, membrane protein, SIGNALING PROTEIN; SIGNALING PROTEIN
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_guinier48.60
回转半径 Rg (电子) rg_electron48.60
零角强度 I(0) i0976918000.00
分子量 molecular_weight244910.0 kDa
排除体积 excluded_volume300810 ų
包络体积 envelope_volume436600 ų
水化壳体积 shell_volume76924 ų
包络直径 envelope_diameter171.8
壳层 Rg shell_rg50.61
包络 Rg envelope_rg47.52
形状 Rg shape_rg48.61
总 Rg total_rg48.62
总原子数 total_atoms17062
残基数 n_residues2186
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 dmax170.5
Rg (实空间) rg_real48.73
Rg 误差 (实空间) rg_real_error1.83
I(0) (实空间) i0_real9.7690e+08
I(0) 误差 (实空间) i0_real_error2.0200e+07
Rg (倒空间) rg_reciprocal48.60
I(0) (倒空间) i0_reciprocal976700000.0000
解质量估计 total_estimate0.8585
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary58.6
偏度 Skewness skewness0.424
峰度 Kurtosis kurtosis-0.166
角度范围 angular_range— – 0.1600 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha61730000.0000
实空间数据点数 n_real_points33
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.791

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

6. 实体与聚合物信息 Entities & Polymers (8)

7. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (4 domains)

结构域编号 domain_idd5wb7e_
类 Class classg — Small proteins
折叠类型 Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamilyg.3.11 — EGF/Laminin
家族 Family familyg.3.11.1 — EGF-type module
结构域编号 domain_idd5wb7f_
类 Class classg — Small proteins
折叠类型 Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamilyg.3.11 — EGF/Laminin
家族 Family familyg.3.11.1 — EGF-type module
结构域编号 domain_idd5wb7g_
类 Class classg — Small proteins
折叠类型 Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamilyg.3.11 — EGF/Laminin
家族 Family familyg.3.11.1 — EGF-type module
结构域编号 domain_idd5wb7h_
类 Class classg — Small proteins
折叠类型 Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamilyg.3.11 — EGF/Laminin
家族 Family familyg.3.11.1 — EGF-type module

CATH v4.4 (11 domains)

结构域编号 domain_id5wb7A01
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
同源超家族 H-superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
结构域编号 domain_id5wb7A02
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
同源超家族 H-superfamily homologous superfamily20 — Receptor L-domain
结构域编号 domain_id5wb7B01
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
同源超家族 H-superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
结构域编号 domain_id5wb7B02
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
同源超家族 H-superfamily homologous superfamily20 — Receptor L-domain
结构域编号 domain_id5wb7C01
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
同源超家族 H-superfamily homologous superfamily20 — Receptor L-domain
结构域编号 domain_id5wb7D01
类 Class class2 — Mainly Beta
架构 Architecture architecture10 — Ribbon
拓扑 Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
同源超家族 H-superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
结构域编号 domain_id5wb7D02
类 Class class3 — Alpha Beta
架构 Architecture architecture80 — Alpha-Beta Horseshoe
拓扑 Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
同源超家族 H-superfamily homologous superfamily20 — Receptor L-domain
结构域编号 domain_id5wb7E00
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_id5wb7F00
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_id5wb7G00
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_id5wb7H00
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)