3kxf

Crystal Structure of SB27 TCR in complex with the 'restriction triad' mutant HLA-B*3508-13mer

Method: X-RAY DIFFRACTION Dmax: 213.0 Å Quality: GOOD

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

HLA class I histocompatibility antigen, B-35 alpha chain

Homo sapiens

UniProt P30685

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 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 A; UniProt 25–300 片段:residues in UNP 25-300 突变:Q65A, T69A, Q155A Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
2 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 C; UniProt 25–300 片段:residues in UNP 25-300 突变:Q65A, T69A, Q155A Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
3 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 K; UniProt 25–300 片段:residues in UNP 25-300 突变:Q65A, T69A, Q155A Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
4 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 I; UniProt 25–300 片段:residues in UNP 25-300 突变:Q65A, T69A, Q155A Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291

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、34 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 1B35_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–276; UniProt 25–300 作者链 C; PDB构建体 1–276; UniProt 25–300 作者链 I; PDB构建体 1–276; UniProt 25–300 作者链 K; PDB构建体 1–276; UniProt 25–300

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 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 B; UniProt 21–119 未记录 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
2 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 F; UniProt 21–119 未记录 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
3 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 L; UniProt 21–119 未记录 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
4 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 J; UniProt 21–119 未记录 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 peptide from Trans-activator protein BZLF1 × 1 (P03206) IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291

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、1995 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 F; PDB构建体 1–99; UniProt 21–119 作者链 J; PDB构建体 1–99; UniProt 21–119 作者链 L; PDB构建体 1–99; UniProt 21–119

peptide from Trans-activator protein BZLF1

物种未注明

UniProt P03206

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 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 Q; UniProt 52–64 未记录 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
2 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 R; UniProt 52–64 未记录 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 IOD IODIDE ION × 7 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
3 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 T; UniProt 52–64 未记录 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291
4 蛋白异源复合物 异源复合物 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 S; UniProt 52–64 未记录 HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) SB27 T cell receptor alpha chain × 1 SB27 T cell receptor beta chain × 1 IOD IODIDE ION × 5 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION;pH 6.7;298 K;0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K 分辨率 3.10 Å R-free 0.291

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 9 个其他 PDB 条目、10 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 BZLF1_EBVB9
Isoform
PDB实体 5
链与序列区间 作者链 Q; PDB构建体 1–13; UniProt 52–64 作者链 R; PDB构建体 1–13; UniProt 52–64 作者链 S; PDB构建体 1–13; UniProt 52–64 作者链 T; PDB构建体 1–13; UniProt 52–64

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 3kxf

P(r) 距离分布 P(r) Distribution

P(r) distribution for 3kxf
下载 Download

2. 结构基本信息 2. Structure Basics

条目编号 entry_id3kxf
沉积日期 deposition_date2009-12-03
结构标题 titleCrystal Structure of SB27 TCR in complex with the 'restriction triad' mutant HLA-B*3508-13mer
关键词 keywords;MHC, HLA, TCR, Disulfide bond, Host-virus interaction, Immune response, Membrane, MHC I, Transmembrane, Immunoglobulin domain, 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_guinier59.63
回转半径 Rg (电子) rg_electron60.27
零角强度 I(0) i02299950000.00
分子量 molecular_weight384180.0 kDa
排除体积 excluded_volume471890 ų
包络体积 envelope_volume717750 ų
水化壳体积 shell_volume104380 ų
包络直径 envelope_diameter238.8
壳层 Rg shell_rg57.46
包络 Rg envelope_rg59.69
形状 Rg shape_rg60.30
总 Rg total_rg60.09
总原子数 total_atoms26934
残基数 n_residues3332
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 dmax213.0
Rg (实空间) rg_real60.07
Rg 误差 (实空间) rg_real_error1.98
I(0) (实空间) i0_real2.2990e+09
I(0) 误差 (实空间) i0_real_error4.7920e+07
Rg (倒空间) rg_reciprocal59.22
I(0) (倒空间) i0_reciprocal2297000000.0000
解质量估计 total_estimate0.8370
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary65.5
偏度 Skewness skewness0.639
峰度 Kurtosis kurtosis0.271
角度范围 angular_range— – 0.1300 −1
当前正则化参数 α current_alpha0.0062
最高正则化参数 α highest_alpha96600000.0000
实空间数据点数 n_real_points27
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.680; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.838

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) 28 domains

CATH v4.4 (28 domains)

结构域编号 domain_id3kxfA01
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_id3kxfA02
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_id3kxfB00
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_id3kxfC01
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_id3kxfC02
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_id3kxfD01
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_id3kxfD02
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_id3kxfE01
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_id3kxfE02
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_id3kxfF00
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_id3kxfG01
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_id3kxfG02
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_id3kxfH01
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_id3kxfH02
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_id3kxfI01
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_id3kxfI02
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_id3kxfJ00
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_id3kxfK01
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_id3kxfK02
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_id3kxfL00
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_id3kxfM01
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_id3kxfM02
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_id3kxfN01
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_id3kxfN02
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_id3kxfO01
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_id3kxfO02
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_id3kxfP01
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_id3kxfP02
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)