1rd8

Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)

Method: X-RAY DIFFRACTION D_max: 139.7 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	1rd8
沉积日期 deposition_date	2003-11-05
结构标题 title	Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)
关键词 keywords	GLYCOPROTEIN, MEMBRANE-FUSION PRECURSOR, VIRUS/VIRAL PROTEIN, Viral protein; VIRAL 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	42.28 Å
回转半径 Rg (电子) rg_electron	42.02 Å
零角强度 I(0) i0	462029000.00
分子量 molecular_weight	171590.0 kDa
排除体积 excluded_volume	212530 Å³
包络体积 envelope_volume	274650 Å³
水化壳体积 shell_volume	56424 Å³
包络直径 envelope_diameter	142.1 Å
壳层 Rg shell_rg	45.21 Å
包络 Rg envelope_rg	41.72 Å
形状 Rg shape_rg	42.04 Å
总 Rg total_rg	42.10 Å
总原子数 total_atoms	12082
残基数 n_residues	1479
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	139.7 Å
Rg (实空间) rg_real	42.54 Å
Rg 误差 (实空间) rg_real_error	1.50 Å
I(0) (实空间) i0_real	4.6200e+08
I(0) 误差 (实空间) i0_real_error	8.4370e+06
Rg (倒空间) rg_reciprocal	42.28 Å
I(0) (倒空间) i0_reciprocal	461900000.0000
解质量估计 total_estimate	0.8233
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	41.5 Å
偏度 Skewness skewness	0.504
峰度 Kurtosis kurtosis	-0.447
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	54200000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.485

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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	hemagglutinin
分子量 formula_weight	36971.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E
原子数 atom_count	12082

ADPGYLLEDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPSIQSR

来源 Source

来源生物 organism	Influenza A virus
NCBI 分类编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	hemagglutinin
分子量 formula_weight	20804.0 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

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

GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVRSLVPR

来源 Source

来源生物 organism	Influenza A virus
NCBI 分类编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 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	man
拷贝数 entity_count	6

Entity 6 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1rd8a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.19 — Viral protein domain
超家族 Superfamily superfamily	b.19.1 — Viral protein domain
家族 Family family	b.19.1.2 — Influenza hemagglutinin headpiece

结构域编号 domain_id	d1rd8a2
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	d1rd8b_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.3 — Stalk segment of viral fusion proteins
超家族 Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
家族 Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

结构域编号 domain_id	d1rd8c1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.19 — Viral protein domain
超家族 Superfamily superfamily	b.19.1 — Viral protein domain
家族 Family family	b.19.1.2 — Influenza hemagglutinin headpiece

结构域编号 domain_id	d1rd8c2
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	d1rd8d_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.3 — Stalk segment of viral fusion proteins
超家族 Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
家族 Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

结构域编号 domain_id	d1rd8e1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.19 — Viral protein domain
超家族 Superfamily superfamily	b.19.1 — Viral protein domain
家族 Family family	b.19.1.2 — Influenza hemagglutinin headpiece

结构域编号 domain_id	d1rd8e2
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	d1rd8f_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.3 — Stalk segment of viral fusion proteins
超家族 Superfamily superfamily	h.3.1 — Influenza hemagglutinin (stalk)
家族 Family family	h.3.1.1 — Influenza hemagglutinin (stalk)

CATH v4.4 (9 domains)

结构域编号 domain_id	1rd8A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	77 — Hemagglutinin; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

结构域编号 domain_id	1rd8A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

结构域编号 domain_id	1rd8B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	20 — Hemagglutinin Ectodomain; Chain B
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rd8C01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	77 — Hemagglutinin; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

结构域编号 domain_id	1rd8C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

结构域编号 domain_id	1rd8D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	20 — Hemagglutinin Ectodomain; Chain B
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1rd8E01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	77 — Hemagglutinin; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Hemagglutinin Chain A, Domain 2

结构域编号 domain_id	1rd8E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
同源超家族 H-superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

结构域编号 domain_id	1rd8F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	20 — Hemagglutinin Ectodomain; Chain B
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	190.529 Å
晶胞边长 b length_b	109.953 Å
晶胞边长 c length_c	136.238 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	108.63 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	49.390 Å
R 因子 r_factor	0.2713
R_work r_work	0.2700
R_free r_free	0.2952

fit	/app/data/saxs_computation/rd/1rd8/1rd8.fit
pddf	/app/data/pr_computation/rd/1rd8/1rd8.pr.out
profile	/app/data/saxs_computation/rd/1rd8/1rd8.dat

Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)

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 branched

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

6. 折叠分类 (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)