SAXSdb — 8xpo

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8xpo
沉积日期 deposition_date	2024-01-04
结构标题 title	Cryo-EM structure of Lassa virus RdRP elongation complex with the NTP form of compound HNC-1664 bound in the active site
关键词 keywords	Lassa virus, RNA-dependent RNA polymerase, elongation complex, nucleoside analog, REPLICATION; REPLICATION
实验方法 method	ELECTRON MICROSCOPY

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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	38.68 Å
回转半径 Rg (电子) rg_electron	38.40 Å
零角强度 I(0) i0	1229930000.00
分子量 molecular_weight	187770.0 kDa
排除体积 excluded_volume	179540 Å³
包络体积 envelope_volume	332620 Å³
水化壳体积 shell_volume	69654 Å³
包络直径 envelope_diameter	134.3 Å
壳层 Rg shell_rg	46.18 Å
包络 Rg envelope_rg	38.29 Å
形状 Rg shape_rg	38.47 Å
总 Rg total_rg	38.58 Å
总原子数 total_atoms	14133
残基数 n_residues	1761
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	124.8 Å
Rg (实空间) rg_real	38.52 Å
Rg 误差 (实空间) rg_real_error	0.78 Å
I(0) (实空间) i0_real	1.2300e+09
I(0) 误差 (实空间) i0_real_error	2.0000e+07
Rg (倒空间) rg_reciprocal	38.62 Å
I(0) (倒空间) i0_reciprocal	1230000000.0000
解质量估计 total_estimate	0.8859
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	48.7 Å
偏度 Skewness skewness	0.255
峰度 Kurtosis kurtosis	-0.316
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	175600000.0000
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: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.888

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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 (5)

Entity 1 polymer

描述 description	RNA-directed RNA polymerase L
分子量 formula_weight	255200.4 kDa
EC 编号 ec_number	2.7.7.48,3.1.-.-
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
原子数 atom_count	14140

MEEDIAYVKDLVSKYLVDNERLSRQKLAFLVQTEPRMLLMEGLKLLSLCIEVDSCNANGCEHNSEDKSVEKILHECGILTPSLCFVVPDGYKLTGNVLILLECFVRSSPANFEQKYIEDLKKLEQLREDLKSVDINLIPLIDGRTSFYNEQLPDWVNDKLRDTLFSLLRYAQESNSLFEESEYSRLCESLSMTSGRLSGIESLNTLLDNRSDHYEEIIALCHQGINNKLTAHEVKLQIEEEYQVFRNRLRGGEIKCQFMRVNKDHLLSEFNKLYIDDGVVVEENLEQLTHQFKRASPILRFLYSDIEGEEDRRNTQAIKEHQMQCWRSFLNKVKSLRILNTRRKLLLIFDTLILLASKYDHIKQGCLQGWLGSCFVSVNDRLVSLDSTKRDLKKWIERRQQVESSKSTAPSQCLSKNQILSSIIQKTIKRATAAMEDVGINMNHFGVDMSVIGLDCYDSIMNFDVTGVTPTISYQKSQEETFPYAMGVVELSETTDLGRLSSLSLALINSMKTSSTVKLRQNEFGAARYQVVRCKEAYCQEFLLDGVKFQLVYQKTGECSKCYAINNDKVGEVCSFYADPKRYFPAIFSAEVLQATVDTMITWIKDCNELEKELTHIKLLTKMILVLILAHPSKRSQKLLQNLRYFIMAYVSDYHHVDLMDKIKEKLITETEFLLYKLIRALISLILCNEVKSMMTNRFKFILNVSYMCHFITKETPDRLTDQIKCFEKFLEPKIEFGHVSVNPADIATEEELMDMAYHAKKFLSKEGCTAPRGPEYKKPGVSKKFLSLLTSSFNNGSLFKEKEVKKELRDPIITSGCATALDLASNKSVVVNKYTDGSRVLNYDFNKLTALAVTQLTEVFSRKGKHLLNRQDYEYKVQQAMSNLVLGSQQQGVNVDRSDLDEILLEGSASLYFDQLRETVQKIVDQYREPAGLGSMKGGNSEPSINDLDELIPNKFHIRLIKGELSNHMVEDFDCEILPDSFYKEFCDNVYSNHKMKEKYFYCGHMSQCPIGELSKAVTTRTYFEQEYFQCFKSVLLIMNANKLMGKYSHYRSRNLNFKFDTGKLSDDVRISERESNSEALSKALSLTNCTTAMLKNLCFYSQESPQSYNSVGPDTGRLKFSLSYKEQVGGNRELYIGDLRTKMFTRLIEDYFEALSLQLSGSCLNNEKEFENAILSMKLNVSLAHVSYSMDHSKWGPMMCPFLFLAVLQNLIFLSKDLQADIKGRDYLSTLLTWHMHKMVEIPFNVVSAMMKSFIKAQLGLRKSTSQSITEDFFYSNFQVGVVPSHVSSILDMGQGILHNTSDFYALISERFINYAISSVCGGSIDAYTSSDDQISLFNQDLTDLMQRDPEEFKTLLEFHYYMSNQLNKFISPKSVVGRFVAEFKSRFYVWGDEVPLLTKFVAAALHNIKCKEPHQLAETIDTIIDQSVANGVPVHLCNLIQLRTLSLLQYARYPIDPFLLNCETDVKDWVDGNRSYRIMRQIESLIPEACGKIRSMLRKLFNKLKTGQLHEEFTTNYLSGEHVSSLKNLCIILDVDPPSESDLEFSWLNLAAYHPLRMVLRQKVIYSGAVNLDDEKIPTIVKTIQNKLSSTFTRGAQKLLSEAINKSAFQSSIASGFVGLCRTLGSKCVRGPNKENLYIKSIQSLISNTQGIELLTNNHGIQYWRVPLNLKEEKISVAGYFRPLLWDYMCISLSTAIELGAWVLGEPKAAKPLEFFKHNPCDYFPLKPTASKLLEDRVGVNHIIHSLRRLYPSMFEKHILPFMSDLASTKMKWSPRIKFLDLCVALDVNCEALSLVSHIVKWKREEHYIVLSSELRLSHSRSHEPMVEERVVSTSDAVDNFMRQIYFESYVRSFVATTRTLGSFTWFPHKTSIPEGEGLQRLGPFSSFVEKVIYKGIERPMFKYDLMMGYAWIDFDVEPAKFNYNQLIASGLVSSKFDSLEDFFDAIESLPPGSVKLSQTIRFQIKSQDASFRESFAIHLNFVGSMNEQGKYLVQDVAVMYSGAVNSCVLTDCWRLVLSGPTFKGKSAWYVDTEAINEFMSDTNQLGEVTPVEIVIDIDRLQFVEHDFVLVGPCSEAIPLVVHRGGLWECNKRLASFSPVLQDQDLELFVREVGDTSPDLLIGALSAMMLDRLKLRMQWSGVDIVSVLKKVMPKDGLKVLNAAFEAVDDWIEFKGYALCFSKSKRRVMIQSSGGKLRLKGRTCEELLEKEEEVEDIESASNSLEVLFQ

来源 Source

来源生物 organism	Lassa virus Josiah
NCBI 分类编号 ncbi_taxonomy_id	11622
宿主生物 host_organism	Pichia

Entity 2 polymer

描述 description	RNA (14-MER)
分子量 formula_weight	4516.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	A

GCGCACCGGGGAUC

Entity 3 polymer

描述 description	RNA (32-MER)
分子量 formula_weight	10374.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	T

GGGAGAUGAAAGUCUCCAACUGAAGAGUCCAA

Entity 4 polymer

描述 description	RNA (9-MER)
分子量 formula_weight	2808.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	P

GGACUCUUC

Entity 5 non-polymer

描述 description	;[[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate ;
分子量 formula_weight	633.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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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	3.02 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	225955

fit	/app/data/saxs_computation/xp/8xpo/8xpo.fit
pddf	/app/data/pr_computation/xp/8xpo/8xpo.pr.out
profile	/app/data/saxs_computation/xp/8xpo/8xpo.dat

Cryo-EM structure of Lassa virus RdRP elongation complex with the NTP form of compound HNC-1664 bound in the active site

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)