3g6j

C3b in complex with a C3b specific Fab

Method: X-RAY DIFFRACTION Dmax: 217.1 Å Quality: GOOD

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

Complement C3 beta chain

物种未注明

UniProt P01024

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 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 A; UniProt 23–666 链 B; UniProt 749–1663 未记录 Fab light chain × 1 Fab heavy chain × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.8;Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C from 4 ml hanging drops, consisting of a 1:1 ratio of protein solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH 7.8) to mother liquor (10% PEG 4000, 0.2 M MgCl2, 100 mM Na-HEPES, pH 7.0), suspended over mother liquor, VAPOR DIFFUSION, HANGING DROP 分辨率 3.10 Å R-free 0.282
2 蛋白异源复合物 异源复合物 蛋白 × 4 PDB 声明:tetrameric(4) 与蛋白拷贝数一致 链 C; UniProt 23–666 链 D; UniProt 749–1663 未记录 Fab light chain × 1 Fab heavy chain × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.8;Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C from 4 ml hanging drops, consisting of a 1:1 ratio of protein solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH 7.8) to mother liquor (10% PEG 4000, 0.2 M MgCl2, 100 mM Na-HEPES, pH 7.0), suspended over mother liquor, VAPOR DIFFUSION, HANGING DROP 分辨率 3.10 Å R-free 0.282
5 蛋白同源多聚体 同源多聚体 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 23–666 链 B; UniProt 749–1663 未记录 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.8;Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C from 4 ml hanging drops, consisting of a 1:1 ratio of protein solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH 7.8) to mother liquor (10% PEG 4000, 0.2 M MgCl2, 100 mM Na-HEPES, pH 7.0), suspended over mother liquor, VAPOR DIFFUSION, HANGING DROP 分辨率 3.10 Å R-free 0.282
6 蛋白同源多聚体 同源多聚体 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 C; UniProt 23–666 链 D; UniProt 749–1663 未记录 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7.8;Crystals of the C3b:S77 complex were obtained within a week at 19\xB0 C from 4 ml hanging drops, consisting of a 1:1 ratio of protein solution (10 mg/ml protein in 50 mM NaCl, 25 mM TRIS pH 7.8) to mother liquor (10% PEG 4000, 0.2 M MgCl2, 100 mM Na-HEPES, pH 7.0), suspended over mother liquor, VAPOR DIFFUSION, HANGING DROP 分辨率 3.10 Å R-free 0.282

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 74 个其他 PDB 条目、114 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 CO3_HUMAN
Isoform
PDB实体 1, 2
链与序列区间 作者链 A; PDB构建体 1–644; UniProt 23–666 作者链 C; PDB构建体 1–644; UniProt 23–666 作者链 B; PDB构建体 1–915; UniProt 749–1663 作者链 D; PDB构建体 1–915; UniProt 749–1663

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 3g6j

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3g6j
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3g6j
沉积日期 deposition_date2009-02-06
结构标题 titleC3b in complex with a C3b specific Fab
关键词 keywords;Complement, C3b, Fab, Antibody:Antigen, Age-related macular degeneration, Cleavage on pair of basic residues, Complement alternate pathway, Complement pathway, Disease mutation, Glycoprotein, Immune response, Inflammatory response, Innate immunity, Phosphoprotein, Secreted, Thioester bond, 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_guinier63.87
回转半径 Rg (电子) rg_electron63.63
零角强度 I(0) i02696850000.00
分子量 molecular_weight440610.0 kDa
排除体积 excluded_volume552980 ų
包络体积 envelope_volume863650 ų
水化壳体积 shell_volume115970 ų
包络直径 envelope_diameter220.9
壳层 Rg shell_rg62.46
包络 Rg envelope_rg61.99
形状 Rg shape_rg63.61
总 Rg total_rg63.69
总原子数 total_atoms31008
残基数 n_residues3940
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 dmax217.1
Rg (实空间) rg_real63.85
Rg 误差 (实空间) rg_real_error2.07
I(0) (实空间) i0_real2.6970e+09
I(0) 误差 (实空间) i0_real_error5.5300e+07
Rg (倒空间) rg_reciprocal63.85
I(0) (倒空间) i0_reciprocal2697000000.0000
解质量估计 total_estimate0.8766
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary78.2
偏度 Skewness skewness0.292
峰度 Kurtosis kurtosis-0.372
角度范围 angular_range— – 0.1250 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha113900000.0000
实空间数据点数 n_real_points26
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.780

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) 38 domains

SCOP 2.08 (6 domains)

结构域编号 domain_idd3g6je1
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_idd3g6je2
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.1.1.2 — C1 set domains (antibody constant domain-like)
结构域编号 domain_idd3g6jf_
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_idd3g6jg1
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_idd3g6jg2
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.1.1.2 — C1 set domains (antibody constant domain-like)
结构域编号 domain_idd3g6jh_
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

CATH v4.4 (32 domains)

结构域编号 domain_id3g6jA01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1930 — Macroglobulin (MG2) domain
结构域编号 domain_id3g6jA02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1930 — Macroglobulin (MG2) domain
结构域编号 domain_id3g6jA03
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1940
结构域编号 domain_id3g6jA04
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_id3g6jA05
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1930 — Macroglobulin (MG2) domain
结构域编号 domain_id3g6jA06
类 Class class6 — Special
架构 Architecture architecture20 — Other non-globular
拓扑 Topology topology50 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily160
结构域编号 domain_id3g6jB01
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology130 — S-adenosyl-L-methionine-dependent methyltransferases
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id3g6jB02
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_id3g6jB03
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily1540
结构域编号 domain_id3g6jB04
类 Class class1 — Mainly Alpha
架构 Architecture architecture50 — Alpha/alpha barrel
拓扑 Topology topology10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id3g6jB05
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily690 — Alpha-macroglobulin, receptor-binding domain
结构域编号 domain_id3g6jB06
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily120
结构域编号 domain_id3g6jC01
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1930 — Macroglobulin (MG2) domain
结构域编号 domain_id3g6jC02
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1930 — Macroglobulin (MG2) domain
结构域编号 domain_id3g6jC03
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1940
结构域编号 domain_id3g6jC04
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_id3g6jC05
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1930 — Macroglobulin (MG2) domain
结构域编号 domain_id3g6jC06
类 Class class6 — Special
架构 Architecture architecture20 — Other non-globular
拓扑 Topology topology50 — N-terminal domain of TfIIb
同源超家族 H-superfamily homologous superfamily160
结构域编号 domain_id3g6jD01
类 Class class2 — Mainly Beta
架构 Architecture architecture20 — Single Sheet
拓扑 Topology topology130 — S-adenosyl-L-methionine-dependent methyltransferases
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id3g6jD02
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_id3g6jD03
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily1540
结构域编号 domain_id3g6jD04
类 Class class1 — Mainly Alpha
架构 Architecture architecture50 — Alpha/alpha barrel
拓扑 Topology topology10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily20
结构域编号 domain_id3g6jD05
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily690 — Alpha-macroglobulin, receptor-binding domain
结构域编号 domain_id3g6jD06
类 Class class2 — Mainly Beta
架构 Architecture architecture40 — Beta Barrel
拓扑 Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily120
结构域编号 domain_id3g6jE01
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_id3g6jE02
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_id3g6jF01
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_id3g6jF02
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_id3g6jG01
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_id3g6jG02
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_id3g6jH01
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_id3g6jH02
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

8. 引用文献 (1)

9. 文件与曲线 (10)