9ddb

Cryo-EM structure of gB-Ecto.516P.531E, a prefusion-stabilized HSV-1 glycoprotein B extracellular domain

Method: ELECTRON MICROSCOPY D_max: 120.7 Å Quality: EXCELLENT

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9ddb
沉积日期 deposition_date	2024-08-27
结构标题 title	Cryo-EM structure of gB-Ecto.516P.531E, a prefusion-stabilized HSV-1 glycoprotein B extracellular domain
关键词 keywords	gB trimer, fusogen, postfusion-destabilization, VIRAL PROTEIN; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

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

回转半径 Rg (Guinier) rg_guinier	38.92 Å
回转半径 Rg (电子) rg_electron	38.21 Å
零角强度 I(0) i0	606935000.00
分子量 molecular_weight	196190.0 kDa
排除体积 excluded_volume	243320 Å³
包络体积 envelope_volume	336990 Å³
水化壳体积 shell_volume	70775 Å³
包络直径 envelope_diameter	126.0 Å
壳层 Rg shell_rg	46.06 Å
包络 Rg envelope_rg	38.06 Å
形状 Rg shape_rg	38.23 Å
总 Rg total_rg	38.62 Å
总原子数 total_atoms	13821
残基数 n_residues	1680
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

▼

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

最大尺寸 Dmax dmax	120.7 Å
Rg (实空间) rg_real	38.64 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	6.0690e+08
I(0) 误差 (实空间) i0_real_error	8.6590e+06
Rg (倒空间) rg_reciprocal	38.82 Å
I(0) (倒空间) i0_reciprocal	607000000.0000
解质量估计 total_estimate	0.9020
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	47.1 Å
偏度 Skewness skewness	0.117
峰度 Kurtosis kurtosis	-0.551
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	87310000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.964

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Glycoprotein B
分子量 formula_weight	90320.1 kDa
突变 mutation	H516P,L531E
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	C,D,E
原子数 atom_count	13821

MHQGAPSWGRRWFVVWALLGLTLGVLVASAAPSSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDNATVAAGHATLREHLRDIKAENTDANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYLANGGFLIAYQPLLSNTLAELYVREHLREQSRKPPNPTPPPPGASANASVERIKTTSSIEFARLQFTYNHIQRPVNDMLGRVAIAWCEEQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIHADANGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK

来源 Source

来源生物 organism	Human alphaherpesvirus 1
通用名 common_name	Herpes simplex virus type 1
NCBI 分类编号 ncbi_taxonomy_id	10298
宿主生物 host_organism	Homo sapiens

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

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	3

Entity 4 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	6

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	—

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

分辨率 resolution	3.71 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	169306

fit	/app/data/saxs_computation/dd/9ddb/9ddb.fit
pddf	/app/data/pr_computation/dd/9ddb/9ddb.pr.out
profile	/app/data/saxs_computation/dd/9ddb/9ddb.dat