6c98

Crystal structure of FcRn bound to UCB-84

Method: X-RAY DIFFRACTION Dmax: 101.2 Å Quality: GOOD

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

IgG receptor FcRn large subunit p51

Homo sapiens

UniProt P55899

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 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 24–297 未记录 Beta-2-microglobulin × 1 (P61769) CYS CYSTEINE × 1 ER7 1-[7-(3-fluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethan-1-one × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 3;289 K;APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0 AND 20% W/V PEG 6,000. CRYSTALS OF FCRN WERE SOAKED FOR THREE DAYS IN BUFFER CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0, 20% W/V PEG 6,000, AND 20% GLYCEROL AND 20MM UCB-84). 分辨率 1.85 Å R-free 0.213
2 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 C; UniProt 24–297 未记录 Beta-2-microglobulin × 1 (P61769) CYS CYSTEINE × 1 ER7 1-[7-(3-fluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethan-1-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 3;289 K;APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0 AND 20% W/V PEG 6,000. CRYSTALS OF FCRN WERE SOAKED FOR THREE DAYS IN BUFFER CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0, 20% W/V PEG 6,000, AND 20% GLYCEROL AND 20MM UCB-84). 分辨率 1.85 Å R-free 0.213

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 30 个其他 PDB 条目、69 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 FCGRN_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–274; UniProt 24–297 作者链 C; PDB构建体 1–274; UniProt 24–297

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 B; UniProt 21–119 未记录 IgG receptor FcRn large subunit p51 × 1 (P55899) CYS CYSTEINE × 1 ER7 1-[7-(3-fluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethan-1-one × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 3;289 K;APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0 AND 20% W/V PEG 6,000. CRYSTALS OF FCRN WERE SOAKED FOR THREE DAYS IN BUFFER CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0, 20% W/V PEG 6,000, AND 20% GLYCEROL AND 20MM UCB-84). 分辨率 1.85 Å R-free 0.213
2 蛋白异源复合物 异源复合物 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 D; UniProt 21–119 未记录 IgG receptor FcRn large subunit p51 × 1 (P55899) CYS CYSTEINE × 1 ER7 1-[7-(3-fluorophenyl)-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethan-1-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, SITTING DROP;pH 3;289 K;APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0 AND 20% W/V PEG 6,000. CRYSTALS OF FCRN WERE SOAKED FOR THREE DAYS IN BUFFER CONTAINING 0.1M CITRIC ACID/NAOH PH 3.0, 20% W/V PEG 6,000, AND 20% GLYCEROL AND 20MM UCB-84). 分辨率 1.85 Å R-free 0.213

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 1313 个其他 PDB 条目、1997 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 B2MG_HUMAN
Isoform
PDB实体 2
链与序列区间 作者链 B; PDB构建体 1–99; UniProt 21–119 作者链 D; PDB构建体 1–99; UniProt 21–119

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 6c98

P(r) 距离分布 P(r) Distribution

P(r) distribution for 6c98
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id6c98
沉积日期 deposition_date2018-01-25
结构标题 titleCrystal structure of FcRn bound to UCB-84
关键词 keywordsNeonatal Fc Receptor, FcRn, Inhibitor, beta 2 microglobulin, b2m, 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_guinier29.76
回转半径 Rg (电子) rg_electron29.20
零角强度 I(0) i0104991000.00
分子量 molecular_weight79856.0 kDa
排除体积 excluded_volume99180 ų
包络体积 envelope_volume123040 ų
水化壳体积 shell_volume35665 ų
包络直径 envelope_diameter105.5
壳层 Rg shell_rg35.75
包络 Rg envelope_rg29.22
形状 Rg shape_rg29.19
总 Rg total_rg29.83
总原子数 total_atoms5651
残基数 n_residues722
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 dmax101.2
Rg (实空间) rg_real29.77
Rg 误差 (实空间) rg_real_error0.97
I(0) (实空间) i0_real1.0500e+08
I(0) 误差 (实空间) i0_real_error1.6710e+06
Rg (倒空间) rg_reciprocal29.77
I(0) (倒空间) i0_reciprocal105000000.0000
解质量估计 total_estimate0.8703
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary36.3
偏度 Skewness skewness0.393
峰度 Kurtosis kurtosis-0.116
角度范围 angular_range— – 0.2650 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha20090000.0000
实空间数据点数 n_real_points54
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.811; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.899

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

6. 实体与聚合物信息 Entities & Polymers (7)

7. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_idd6c98a1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.19 — MHC antigen-recognition domain
超家族 Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
家族 Family familyd.19.1.0 — automated matches
结构域编号 domain_idd6c98a2
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_idd6c98b_
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_idd6c98c1
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.19 — MHC antigen-recognition domain
超家族 Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
家族 Family familyd.19.1.0 — automated matches
结构域编号 domain_idd6c98c2
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_idd6c98d_
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)

CATH v4.4 (6 domains)

结构域编号 domain_id6c98A01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
结构域编号 domain_id6c98A02
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_id6c98B00
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_id6c98C01
类 Class class3 — Alpha Beta
架构 Architecture architecture30 — 2-Layer Sandwich
拓扑 Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
结构域编号 domain_id6c98C02
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_id6c98D00
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)