1r5w

Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T-cell activation

Method: X-RAY DIFFRACTION D_max: 135.0 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r5w
沉积日期 deposition_date	2003-10-13
结构标题 title	Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T-cell activation
关键词 keywords	TCR, MHC class II, structural rearangement, SIGNALING PROTEIN; SIGNALING PROTEIN
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	35.06 Å
回转半径 Rg (电子) rg_electron	35.02 Å
零角强度 I(0) i0	116574000.00
分子量 molecular_weight	86599.0 kDa
排除体积 excluded_volume	108040 Å³
包络体积 envelope_volume	140090 Å³
水化壳体积 shell_volume	36303 Å³
包络直径 envelope_diameter	141.4 Å
壳层 Rg shell_rg	37.42 Å
包络 Rg envelope_rg	36.20 Å
形状 Rg shape_rg	34.99 Å
总 Rg total_rg	35.30 Å
总原子数 total_atoms	6136
残基数 n_residues	756
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	135.0 Å
Rg (实空间) rg_real	35.58 Å
Rg 误差 (实空间) rg_real_error	2.02 Å
I(0) (实空间) i0_real	1.1660e+08
I(0) 误差 (实空间) i0_real_error	2.2780e+06
Rg (倒空间) rg_reciprocal	35.26 Å
I(0) (倒空间) i0_reciprocal	116500000.0000
解质量估计 total_estimate	0.7495
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	36.0 Å
偏度 Skewness skewness	0.771
峰度 Kurtosis kurtosis	0.282
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12600000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.448; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.551; Smooth: 0.843

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	H-2 class II histocompatibility antigen, E-K alpha chain
分子量 formula_weight	20962.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C
原子数 atom_count	6136

EEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	MHC H2-IE-beta
分子量 formula_weight	21737.2 kDa
突变 mutation	S8C
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D

APWFLEYSKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	artificial peptide
分子量 formula_weight	1460.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,F

ADLIAYFKAATKF

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

结构域编号 domain_id	d1r5wa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1r5wa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1r5wb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1r5wb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1r5wb3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1r5wc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1r5wc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1r5wd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1r5wd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.19 — MHC antigen-recognition domain
超家族 Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
家族 Family family	d.19.1.1 — MHC antigen-recognition domain

结构域编号 domain_id	d1r5wd3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

结构域编号 domain_id	1r5wA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1r5wA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1r5wB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1r5wB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1r5wC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1r5wC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1r5wD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

结构域编号 domain_id	1r5wD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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晶胞边长 a length_a	116.132 Å
晶胞边长 b length_b	116.132 Å
晶胞边长 c length_c	85.935 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 41
空间群编号 int_tables_number	76
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2910
R_work r_work	0.2890
R_free r_free	0.3080

fit	/app/data/saxs_computation/r5/1r5w/1r5w.fit
pddf	/app/data/pr_computation/r5/1r5w/1r5w.pr.out
profile	/app/data/saxs_computation/r5/1r5w/1r5w.dat

Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T-cell activation

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (10 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)