SAXSdb — 1fo0

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fo0
沉积日期 deposition_date	2000-08-24
结构标题 title	MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULE COMPLEX
关键词 keywords	T CELL RECEPTOR, CLASS I MHC, H-2KB, TCR-PMHC COMPLEX, IMMUNE SYSTEM; IMMUNE SYSTEM
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	30.67 Å
回转半径 Rg (电子) rg_electron	30.76 Å
零角强度 I(0) i0	80383600.00
分子量 molecular_weight	70242.0 kDa
排除体积 excluded_volume	87587 Å³
包络体积 envelope_volume	111060 Å³
水化壳体积 shell_volume	32398 Å³
包络直径 envelope_diameter	115.4 Å
壳层 Rg shell_rg	35.31 Å
包络 Rg envelope_rg	31.04 Å
形状 Rg shape_rg	30.71 Å
总 Rg total_rg	31.33 Å
总原子数 total_atoms	4948
残基数 n_residues	610
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	108.1 Å
Rg (实空间) rg_real	30.97 Å
Rg 误差 (实空间) rg_real_error	1.05 Å
I(0) (实空间) i0_real	8.0380e+07
I(0) 误差 (实空间) i0_real_error	1.3720e+06
Rg (倒空间) rg_reciprocal	30.85 Å
I(0) (倒空间) i0_reciprocal	80380000.0000
解质量估计 total_estimate	0.8247
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	31.2 Å
偏度 Skewness skewness	0.622
峰度 Kurtosis kurtosis	-0.054
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11910000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.778; Smooth: 0.873

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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 (6)

Entity 1 polymer

描述 description	PROTEIN (ALLOGENEIC H-2KB MHC CLASS I MOLECULE)
分子量 formula_weight	31908.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H
原子数 atom_count	5139

MGPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGTFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWE

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	PROTEIN (BETA-2 MICROGLOBULIN)
分子量 formula_weight	11704.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

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	NATURALLY PROCESSED OCTAPEPTIDE PBM1
分子量 formula_weight	983.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P

INFDFNTI

Entity 4 polymer

描述 description	PROTEIN (BM3.3 T CELL RECEPTOR ALPHA-CHAIN)
分子量 formula_weight	12945.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A

QKVTQTQTSISVMEKTTVTMDCVYETQDSSYFLFWYKQTASGEIVFLIRQDSYKKENATVGHYSLNFQKPKSSIGLIITATQIEDSAVYFCAMRGDYGGSGNKLIFGTGTLLSVKP

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	Mus musculus

Entity 5 polymer

描述 description	PROTEIN (BM3.3 T CELL RECEPTOR BETA-CHAIN)
分子量 formula_weight	12965.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKSLPGADYLATRVTDTELRLQVANMSQGRTLYCTCSADRVGNTLYFGEGSRLIV

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	Mus musculus

Entity 6 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	191

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1fo0a_
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.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1fo0b_
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.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1fo0h1
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	d1fo0h2
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	d1fo0l_
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)

CATH v4.4 (5 domains)

结构域编号 domain_id	1fo0A00
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	1fo0B00
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	1fo0H01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

结构域编号 domain_id	1fo0H02
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	1fo0L00
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 (7)

Crystal structure of a T cell receptor bound to an allogeneic MHC molecule.

Nat.Immunol. (2000)

PMID: 11017099 · DOI: 10.1038/79728 PRIMARY

Structural Basis of Plasticity in T Cell Receptor Recognition of a Self Peptide-Mhc Antigen

Science (1998)

DOI: 10.1126/science.279.5354.1166

Two Human T Cell Receptors Bind in a Similar Mode To the Hla-A2/Tax Peptide Complex Using Different Tcr Amino-acids

Immunity (1998)

DOI: 10.1016/S1074-7613(00)80546-4

The Three-Dimensional Structure of a T Cell Receptor Valpha-Vbeta Heterodimer Reveals a Novel Arrangement of the Vbeta Domain

Embo J. (1997)

DOI: 10.1093/emboj/16.14.4205

Structure of the Complex between Human T Cell Receptor, Viral Peptide and Hla-A2

Nature (1996)

DOI: 10.1038/384134a0

;Crystal Structure of an H-2Kb-Ovalbumin Peptide Com Reveals the Interplay of Primary and Secondary Anchor Positions in the Major Histocompatibility Complex Binding Groove ;

Proc.Natl.Acad.Sci.USA (1995)

;Each of Two Productive T Cell Receptor Alpha-Gene Rearrangements Found in Both the A10 and Bm3.3 Cell Clones Give Rise to an Alpha Chain which Can Contribute to the Constitution of a Surface-Expressed Alpha-Beta Dimer ;

Int.Immunol. (1991)

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晶胞边长 a length_a	76.580 Å
晶胞边长 b length_b	120.420 Å
晶胞边长 c length_c	102.850 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	4

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	12.000 Å
R 因子 r_factor	0.2180
R_work r_work	0.2250
R_free r_free	0.2760

fit	/app/data/saxs_computation/fo/1fo0/1fo0.fit
pddf	/app/data/pr_computation/fo/1fo0/1fo0.pr.out
profile	/app/data/saxs_computation/fo/1fo0/1fo0.dat

MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULE COMPLEX

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 (6)

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

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)