3rsj

Structure of HCRF in complex with Ganglioside GD1a

Method: X-RAY DIFFRACTION D_max: 133.8 Å Quality: GOOD

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

BoNT/F

Clostridium botulinum

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	其他组合单体蛋白 × 1 其他聚合物 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 A； UniProt 866–1278	片段：Receptor Binding Domain (UNP Residues 866-1276)	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K	分辨率 2.00 Å R-free 0.263
2	其他组合单体蛋白 × 1 其他聚合物 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 B； UniProt 866–1278	片段：Receptor Binding Domain (UNP Residues 866-1276)	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose ; × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K	分辨率 2.00 Å R-free 0.263
3	其他组合单体蛋白 × 1 其他聚合物 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 C； UniProt 866–1278	片段：Receptor Binding Domain (UNP Residues 866-1276)	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ; × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K	分辨率 2.00 Å R-free 0.263
4	其他组合单体蛋白 × 1 其他聚合物 1 PDB 声明：monomeric（1）与蛋白拷贝数一致	链 D； UniProt 866–1278	片段：Receptor Binding Domain (UNP Residues 866-1276)	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K	分辨率 2.00 Å R-free 0.263

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。

其他 PDB	相对当前条目 3RSJ	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
3FIE Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1) 提交 2008-12-11	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 1–419（419 aa）片段：residues 1-419, catalytic domain	未记录	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 2.10 Å R-free 0.279
3FIE Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1) 提交 2008-12-11	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 B 1–419（419 aa）片段：residues 1-419, catalytic domain	未记录	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 2.10 Å R-free 0.279
3FII Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh2) 提交 2008-12-11	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 2 PDB 声明：dimeric	链 A 1–419（419 aa）片段：residues 1-419, catalytic domain	未记录	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	分辨率 2.17 Å R-free 0.290
3FUQ Glycosylated SV2 and Gangliosides as Dual Receptors for Botulinum Neurotoxin Serotype F 提交 2009-01-14	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 862–1278（417 aa）片段：sequence database residues 862-1278	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；0.1 M Tris-HCL, 18% ethanol and 150 mM NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	分辨率 2.10 Å R-free 0.243

共 3 个其他 PDB 条目、4 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	Q57236_CLOBO
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–413； UniProt 866–1278 作者链 B； PDB构建体 1–413； UniProt 866–1278 作者链 C； PDB构建体 1–413； UniProt 866–1278 作者链 D； PDB构建体 1–413； UniProt 866–1278

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

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3rsj
沉积日期 deposition_date	2011-05-02
结构标题 title	Structure of HCRF in complex with Ganglioside GD1a
关键词 keywords	clostridium botulinum type F, ganglioside binding site, GD1a, TOXIN; TOXIN
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	40.50 Å
回转半径 Rg (电子) rg_electron	39.80 Å
零角强度 I(0) i0	550407000.00
分子量 molecular_weight	191080.0 kDa
排除体积 excluded_volume	238680 Å³
包络体积 envelope_volume	304210 Å³
水化壳体积 shell_volume	63659 Å³
包络直径 envelope_diameter	145.4 Å
壳层 Rg shell_rg	45.26 Å
包络 Rg envelope_rg	39.33 Å
形状 Rg shape_rg	39.78 Å
总 Rg total_rg	40.15 Å
总原子数 total_atoms	13498
残基数 n_residues	1614
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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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	133.8 Å
Rg (实空间) rg_real	40.51 Å
Rg 误差 (实空间) rg_real_error	0.93 Å
I(0) (实空间) i0_real	5.5040e+08
I(0) 误差 (实空间) i0_real_error	9.7500e+06
Rg (倒空间) rg_reciprocal	40.50 Å
I(0) (倒空间) i0_reciprocal	550400000.0000
解质量估计 total_estimate	0.8648
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	48.0 Å
偏度 Skewness skewness	0.403
峰度 Kurtosis kurtosis	-0.150
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	89680000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.683

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

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6. 实体与聚合物信息 Entities & Polymers (5)

实体 1 Entity 1 polymer

描述 description	BoNT/F
分子量 formula_weight	47912.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	13922

IKDNSILDMRYENNKFIDISGYGSNISINGDVYIYSTNRNQFGIYSSKPSEVNIAQNNDIIYNGRYQNFSISFWVRIPKYFNKVNLNNEYTIIDCIRNNNSGWKISLNYNKIIWTLQDTAGNNQKLVFNYTQMISISDYINKWIFVTITNNRLGNSRIYINGNLIDEKSISNLGDIHVSDNILFKIVGCNDTRYVGIRYFKVFDTELGKTEIETLYSDEPDPSILKDFWGNYLLYNKRYYLLNLLRTDKSITQNSNFLNINQQRGVYQKPNIFSNTRLYTGVEVIIRKNGSTDISNTDNFVRKNDLAYINVVDRDVEYRLYADISIAKPEKIIKLIRTSNSNNSLGQIIVMDSIGNNCTMNFQNNNGGNIGLLGFHSNNLVASSWYYNNIRKNTSSNGCFWSFISKEHGWQEN

来源 Source

来源生物 organism	Clostridium botulinum
NCBI 分类编号 ncbi_taxonomy_id	1491
宿主生物 host_organism	Escherichia coli

实体 2 Entity 2 branched

描述 description	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose
分子量 formula_weight	674.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 3 Entity 3 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose ;
分子量 formula_weight	1128.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 4 Entity 4 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ;
分子量 formula_weight	836.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 5 Entity 5 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	424

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7. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d3rsja1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.0 — automated matches

结构域编号 domain_id	d3rsja2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.4 — STI-like
家族 Family family	b.42.4.0 — automated matches

结构域编号 domain_id	d3rsjb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.0 — automated matches

结构域编号 domain_id	d3rsjb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.4 — STI-like
家族 Family family	b.42.4.0 — automated matches

结构域编号 domain_id	d3rsjc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.0 — automated matches

结构域编号 domain_id	d3rsjc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.4 — STI-like
家族 Family family	b.42.4.0 — automated matches

结构域编号 domain_id	d3rsjd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.0 — automated matches

结构域编号 domain_id	d3rsjd2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.4 — STI-like
家族 Family family	b.42.4.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	3rsjA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	3rsjA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	3rsjB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	3rsjB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	3rsjC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	3rsjC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	3rsjD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	3rsjD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

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8. 引用文献 (1)

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晶胞边长 a length_a	65.468 Å
晶胞边长 b length_b	84.266 Å
晶胞边长 c length_c	117.600 Å
晶胞夹角 α angle_alpha	72.55 °
晶胞夹角 β angle_beta	87.01 °
晶胞夹角 γ angle_gamma	67.13 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	29.860 Å
R 因子 r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2630

fit	/app/data/saxs_computation/rs/3rsj/3rsj.fit
pddf	/app/data/pr_computation/rs/3rsj/3rsj.pr.out
profile	/app/data/saxs_computation/rs/3rsj/3rsj.dat