2b4c

;Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody ;

Method: X-RAY DIFFRACTION D_max: 131.0 Å Quality: GOOD

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	2b4c
沉积日期 deposition_date	2005-09-23
结构标题 title	;Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody ;
关键词 keywords	HIV-1, gp120, JRFL, V3, X5, CD4 induced antibody, Viral protein-Immune system COMPLEX; Viral protein/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	38.02 Å
回转半径 Rg (电子) rg_electron	38.02 Å
零角强度 I(0) i0	186877000.00
分子量 molecular_weight	107190.0 kDa
排除体积 excluded_volume	132890 Å³
包络体积 envelope_volume	190700 Å³
水化壳体积 shell_volume	43460 Å³
包络直径 envelope_diameter	140.3 Å
壳层 Rg shell_rg	42.27 Å
包络 Rg envelope_rg	37.63 Å
形状 Rg shape_rg	37.98 Å
总 Rg total_rg	38.40 Å
总原子数 total_atoms	7517
残基数 n_residues	944
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	131.0 Å
Rg (实空间) rg_real	38.22 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	1.8690e+08
I(0) 误差 (实空间) i0_real_error	3.5790e+06
Rg (倒空间) rg_reciprocal	38.10 Å
I(0) (倒空间) i0_reciprocal	186900000.0000
解质量估计 total_estimate	0.8693
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	37.4 Å
偏度 Skewness skewness	0.420
峰度 Kurtosis kurtosis	-0.387
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21480000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.866

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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 (8)

Entity 1 polymer

描述 description	envelope glycoprotein
分子量 formula_weight	38452.7 kDa
突变 mutation	N301Q, T389A
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	G
原子数 atom_count	7543

GARSEVVLENVTEHFNMWKNDMVEQMQEDIISLWDQSLKPCVKLTPLCVGAGSCDTSVITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNQNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSAQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIE

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI 分类编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Drosophila melanogaster

Entity 2 polymer

描述 description	T-cell surface glycoprotein CD4
分子量 formula_weight	20129.9 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	C

KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 polymer

描述 description	anti-HIV-1 gp120 immunoglobulin X5 light chain
分子量 formula_weight	23267.8 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	L

ELVLTQSPGTLSLSAGERATLSCRASQSVSSGSLAWYQQKPGQAPRLLIYGASTRATGIPDRFSGSGSGTDFTLTIGRLEPEDLAVYYCQQYGTSPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSRDSTYSLGSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	anti-HIV-1 gp120 immunoglobulin X5 heavy chain
分子量 formula_weight	24990.7 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

EVQLLEQSGAEVKKPGSSVQVSCKASGGTFSMYGFNWVRQAPGHGLEWMGGIIPIFGTSNYAQKFRGRVTFTADQATSTAYMELTNLRSDDTAVYYCARDFGPDWEDGDSYDGSGRGFFDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 5 branched

描述 description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	367.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 7 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 8 non-polymer

描述 description	Xylitol
分子量 formula_weight	152.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d2b4cc1
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	d2b4cc2
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.1.1.3 — C2 set domains

结构域编号 domain_id	d2b4cg1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.172 — gp120 core
超家族 Superfamily superfamily	d.172.1 — gp120 core
家族 Family family	d.172.1.1 — gp120 core

结构域编号 domain_id	d2b4ch1
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	d2b4ch2
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	d2b4cl1
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	d2b4cl2
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 (7 domains)

结构域编号 domain_id	2b4cC01
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	2b4cC02
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	2b4cG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	40 — HIV Envelope Protein Gp120; Chain G
同源超家族 H-superfamily homologous superfamily	20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein

结构域编号 domain_id	2b4cH01
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	2b4cH02
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	2b4cL01
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	2b4cL02
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	225.993 Å
晶胞边长 b length_b	225.993 Å
晶胞边长 c length_c	97.968 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 6 2 2
空间群编号 int_tables_number	177
晶系 crystal_system	—

分辨率 resolution	3.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.3190
R_work r_work	0.3190
R_free r_free	0.3490

fit	/app/data/saxs_computation/b4/2b4c/2b4c.fit
pddf	/app/data/pr_computation/b4/2b4c/2b4c.pr.out
profile	/app/data/saxs_computation/b4/2b4c/2b4c.dat

;Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody ;

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 (8)

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

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)